CA2658813A1 - Synthetic cornea from retinal stem cells - Google Patents

Abstract

Methods of producing synthetic corneas are disclosed which are differentiated from retinal stem cells (rSC) derived from parthenogenetically activated human oocytes, including that such synthetic corneas are produced in the absence of a 3-D scaffold. Isolated synthetic corneas, produced by the disclosed methods, are also described.

Description

SYNTHETIC CORNEA FROM RETINAL STEM CELLS
FIELD OF THE INVENTION
[0001] The invention relates generally to embryonic stems cells (ES), and more specifically to a process for obtaining synthetic comeas.

BACKGROUND INFORMATION

[0002] Human embryonic stem cells (hES) cells are pluripotent cells that can differentiate into an array of cell types. When injected into immune-deficient mice, embryonic stem cells form differentiated tumors (teratomas). However, embryonic stem cells that are induced in vitro to form embryoid bodies (EBs) provide a source of embryonic stem cell lines that are amenable to differentiation into nlultiple cell types characteristic of several tissues under certain growth conditions. For example, hES have been differentiated into endoderm, ectoderm, and mesoderm derivatives.

[0003] Human ES cells and their differentiated progeny are important sources of human cells for therapeutic transplantation and for drug testing and development.
Required by both of these goals is the provision of sufficient cells that are differentiated into tissue types suitable for a patient's needs or the appropriate pharmacological test.
Associated with this is a need for an efficient and reliable method of producing differentiated cells from embryonic stem cells.

[0004] hES and hEG cells offer remarkable scientific and therapeutic possibilities, involving potential for generating more specialized cells or tissues. Ethical concerns about the sources of hES and hEG cells, however, and fears that use of nuclear transfer (NT) for research could lead to use of NT to produce a human being, have fostered a great deal of public discussion and debate.

[0005] Parthenogenic activation of mammalian oocytes may be used as an alterative to fertilization by sperm/NT to prepare oocytes for embryonic stem cell generation.
Parthenogenic activation is the production of embryonic cells, with or without eventual development into an adult, from a female gamete in the absence of any contribution from a male gamete.

[0006] Currently, a focus of stem cell research is the development of artificial organs, rehabilitation devices, or prosthesis to replace natural body tissues. This development generally envisages the use of biocompatible materials for engineering stem cells to control expansion/differentiation; i.e., the use of 3-D scaffolds (e.g., PLG
scaffolds, chitosan scaffolds, PCL/PEG scaffolds) to create devices which mimic tissue-like function by providing mechanical support for proliferation.

[0007] Alternatively," transplantation of cultured stem cells or differentiated stem cells is envisioned as a therapeutic modality. These methods are generally known as in vivo tissue engineering or in situ generation. While much of the work in this area purports the direct transplantation of cultured cells, as a practical matter, such modalities often require seeding differentiated stem cells within porous scaffold biomaterials (e.g., cardiomyocytes derived from stem cells and gels or porous alginate).

SUMMARY OF THE INVENTION

[0008] The present invention relates to the seminal discovery of a method of producing a 3-dimensional sensory system organ obtained from stem cells derived from parthenogenically activated human oocytes. The method of the invention does not require the use of external scaffolding. As disclosed in one embodiment, the sensory organ is a synthetic cornea.

[0010] In one embodiment, an isolated retinal-stem cell derived synthetic cornea is disclosed. In a related aspect, the retinal stem cell is obtained from a parthenogenetically activated human oocyte. In another related aspect, the cornea is terminally differentiated. In another aspect, the cornea is histocompatible with the oocyte donor, including that the cornea coinprises homoplasmic mitochondrial DNA, and is transplantable in humans.

[0011] In another embodiment, a method of producing a synthetic cornea is disclosed, including parthenogenetically activating a human oocyte, where activation includes contacting the oocyte with an ionophore at high 02 tension and contacting the oocyte with a serine-threonine kinase inliibitor under low 02 tension, cultivating the activated oocyte at low 02 tension until blastocyst formation, transferring the blastocyst to a layer of feeder cells, and culturing the transferred blastocyst under high 02 tension, mechanically isolating an inner cell mass (1CM) from trophectoderm of the blastocyst and culturing the cells of the ICM on a layer of feeder cells under high 02 tension, wllere retinal stem cells can be identified in the culture by human embryonic stem cell markers (hES) and neuron specific markers, and where the identified retinal stem cells are optionally isolated, culturing the isolated stem cells in media comprising serum replacement (M/SR), plasmonate, and at least one mitogen that activates the gp130/STAT pathway and/or the MAP kinase pathway on a fibroblast feeder layer treated with a DNA synthesis inhibitor, culturing the mitogen treated cells in MISR
comprising plasmonate (M/SRP), without added mitogen, to near confluence, where about about 1/2 volume of the M/SRP is replaced with M/SR periodically until the near confluent cells develop pigmentation and a domedappearance, and transferring the pigmented cells in M/SR to a gelatin coated substrate, where about 1/2 volume of the M/SR is replaced with M/SR periodically until a synthetic cornea develops. Optionally, the retinal cells can be cultured as an enriched rather than isolated population of cells.

[0012] In one aspect, the mitogen is selected from leukemia inhibitory factor (LIF), bFGF, and a combination thereof. In another aspect, the DNA synthesis inhibitor is an alkylating agent, including, but not limited to, mitomycin C. In a related aspect, the feeder cells are human.

[0013] In one embodiment, a method of treating a subject in need thereof is disclosed, including replacing a cornea of the subject with a synthetic cornea. In one aspect, the subject has a disease which effects the cornea such as keratitis, corneal ulcer, corneal abrasion, snow blindness, arc eye, Thygeson's superficial puncate keratopathy, Fuchs' dystrophy, keratoconus, keratpconjunctivitis sicca, corneal infections, or corneal dystrophy. In another aspect, the subject has an injured cornea.

[0014] In another embodiment, a method of identifying an agent that affects the cornea of an eye is disclosed including contacting a retinal-stem cell derived synthetic cornea with an agent and observing a change to the cornea in the presence and absence of the agent, where a change to the cornea is indicative of an agent that affects the cornea.

[0015] In one aspect, the agent has a therapeutic effect on the cornea. In another aspect, the agent has an adverse effect on the cornea. In a related aspect, the change to the cornea includes modulation of gene expression, modulation of protein expression, change in opacity, change in plasticity, change in hardness, change in light phase velocity, and change in shape.
[0016] In one embodiment, a method for replacement of a cornea of an eye with the synthetic cornea is disclosed including surgically excising the cornea from the eye, inserting the synthetic cornea into the area of the removed cornea, and allowing the synthetic cornea to interface with tissue underlying the excision to anchor the synthetic cornea to the eye.

[0017] In a related aspect, the method further includes separating a portion of the outer surface of a cornea thereby forming a corneal flap and a corneal bed, the corneal flap having an anterior surface and a posterior surface, the coxneal bed having a shaped anterior surface, iinplanting the synthetic cornea on the corneal bed, the cornea having an anterior surface and a posterior surface, and replacing the portion of the coxnea that was separated.

[0018] In another embodiment, a method of delivering an effective amount of an agent to the eye of a subject is disclosed including transfoiming at least a portion of the cells comprising the synthetic cornea with a nucleic acid vehicle, where the vehicle encodes the agent, identifying a population of cells comprising the synthetic cornea which express the agent encoded by the nucleic acid, and replacing cornea cells of the subject with transformed cells of the synthetic cornea, where the replaced cells deliver the agent to the eye of the subject.

[0019] In a related aspect, the replacing step includes replacing the cornea of the subject with the synthetic cornea.

[0020] Exemplary methods and compositions according to this invention are described in greater detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

[0021] Figure IA shows a micrograph of the surface marker expression of alkaline phosphatase for the parthenogenically derived hES cells.

[0022] Figure IB shows a micrograph of the expression for the surface marker Oct4.
[0023] Figure 1 C shows a micrograph of the expression for the surface marker SSEA-1.
[0024] Figure 1D shows a micrograph of the expression for the surface marker SSEA-3.
[0025] Figure 1E shows a micrograph of the expression for the stirface marker SSEA-4.
[0026] Figure 1F shows a micrograph of the expression for the surface marker TRA-1-60.
[0027] Figure 1 G shows a micrograph of the expression for the surface marker TRA-1-81.

[0028] Figure 2A shows the analysis of telomerase activity for the parthenogenically derived hES cells. 500, 1000, and 10000 (units) of extract was used to perform the analysis.
AH-heat treated test extract (negative control); positive control-telomerase positive cells;
CHAPS-lysis buffer; TSRB-control template.

[0029] Figure 2B shows a micrograph of embryoid body formation from parthenogenically derived hES cells, 9 day culture.

[0030] Figure 2C shows a micrograph of embryoid body formation from parthenogenically derived hES cells, 10 day culture.

[0031] Figure 2D illustrates the karyotype of parthenogenically derived hES
cells.
[0032] Figure 2E shows the results from DNA finger printing analysis of parthenogenically derived hES cells. 1- DNA from the blood of the oocyte donor; 2- DNA
from the parthenogenic hES cells derived from the same donor; 3 - DNA from human feeder fibroblasts.

[0033] Figure 3 shows Northern blot for characterizing the expression of genes associated with genomic imprinting. DNA probes: SNRPN, Pegl_2, Pegl_A, H19, and GAPDH (as an internal control). NSF, neonatal skin fibroblasts; hES, human embryonic sterri cell line derived from fertilized oocytes; 1, phESC-1; 2, phESC-3, 3, phESC-4, 4, phESC-5; 5, phESC-6; 6 phESC-7. NSF RT-, hES RT-, 1 RT- are negative controls.

[0034] Figure 4 shows the differentiation of phESC into derivatives of all three germ layers. Ectoderm differentiation is presented by positive immunocytochemical staining for neuron specific markers 68 (A), NCAM (B), beta III-tubulin (C) and glial cell marker GFAP
(D, M). Differentiated cells were positive for mesodermal markers: muscle specific alpha actinin (G) and desmin (J), endothelial markers PECAM-1 (E) and VE-Cadherin (F).
Endoderm differentiation is presented by positive staining for alpha-fetoprotein (H, L). The phESC produce pigmented epithelial-like cells (I, K). Magnification (I) x 100;
(A-H, J-M), x400.

[0035] Figure 5 shows the characterization of phESC lines for specific markers.
Undifferentiated colonies of phESC on human feeder layer cells (A-F), negative staining for SSEA-1 (G-L), expression of cell surface markers SSEA-3 (M-R), SSEA-4 (S-X).
Magnification (A) to (E) x 100; (F) x 200; (G) to (X) x 400. Alkaline phosphatase positive staining of phESC colonies on feeder cells (A-F), OCT-4 (GL), TR.A-1-60 (K-R) and TRA-1-81 (S-X). Magnification (A, B, 0, R) x 100; (C-F, M, S, X) x 200; (G-L, N, P, Q, T-W) x 400.

[0036] Figure 6 demonstrates that phESC cells possess high levels of telomerase activity by comparison with positive control cells: "+"-extract from 500 cells; "-"-heat treated cell extract with inactivated teloinerase; "Control +"-telomerase positive cell extract (applied with TRAPEZE Kit); "B"-CHAPS lysis buffer, primer-dimer/PCR contamination control;

telomerase quantitative control template (0.1 and 0.2 amole/ l); "M"-marker, DNA ladder.
[0037] Figure 7 shows the G-banded karyoptyping of phESC lines. The phESC-1 (A), phESC-3 (B); phESC-4 (C), phESC-5 (D) and phESC-6 (E) lines have normal 46, XX
karyotype. The phESC-7 line has 47, XXX karyotype (F).

[0038] Figure 8 shows a synthetic cornea obtained from stems cells derived from parthenogenetically activated human oocytes.

DETAILED DESCRIPTION OF THE INVENTION

[0039] Before the present composition, methods, and culturing methodologies are described, it is to be understood that this invention is not limited to particular compositions, methods, and experimental conditions described, as such compositions, methods, and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.

[0040] As used in this specification and the appended claims, the singular fonns "a", "an", and "the" include plural references unless the context clearly dictates otherwise. Thus, for example, references to "the method" includes one or more methods, and/or steps of the type described herein wliich will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

[0041] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, as it will be understood that modifications and variations are encompassed within the spirit and scope of the instant disclosure. All publications mentioned herein are incorporated herein by reference in their entirety.

[0042] "Differentiation" refers to a change that occurs in cells to cause those cells to assume certain specialized functions and to lose the ability to change into certain other specialized fitnctional units. Cells capable of differentiation may be any of totipotent, pluripotent or multipotent cells. Differentiation may be partial or complete with respect to mature adult cells.

[0043] Gynogenesis refers to the production of an embryo containing a discernible trophectoderm and inner cell mass that results upon activation of a cell, such as an oocyte, or other enibryonic cell type, containing mammalian DNA of all female origin, preferably human female origin, e.g., human or non-human primate oocyte DNA. Such female mammalian DNA may be genetically modified, e.g., by insertion, deletion or substitution of at least one DNA sequence, or may be unmodified. For example, the DNA may be modified by the insertion or deletion of desired coding sequences, or sequences that promote or inhibit enibryogenesis. Typically, such an embryo will be obtained by in vitro activation of an oocyte that contains DNA of all female origin. Gynogeinesis is inclusive of parthenogenesis which is defined below. It also includes activation methods where the spermatozoal DNA
does not contribute to the DNA in the activated oocyte.

[0044] In a related aspect, oocytes are obtained from superovulating subjects prepared for IVF. "Superovulation" techniques, such as treatment of a female subject with hormones, used in IVF are designed to stimulate the ovaries to produce several eggs (oocytes) rather than the usual single egg as in a natural cycle.

[0045] The medications required to boost egg production may include, but are not limited to the following: Lupron (gonadotropin releasing horinone-agonist), Orgalutran, Antagon or Cetrotide (gonadotropin releasing hormone-antagonist), Follistim, Bravelle or Gonal-F (FSH, follicle stimulating hormone), Repronex (combination of FSH and LH, luteinizing hormone), and Pregnyl or Novarel (hCG, human chorionic gonadotropin).

[0046] In a related aspect, collection of eggs can be perfonned under transvaginal ultrasound guidance. To accomplish this, a needle is inserted (e.g., under IV
sedation) through the vaginal wall into the ovaries using ultrasound to locate each follicle. The follicular fluid is drawn up into a test tube to obtain the eggs.

[0047] "Parthenogenesis" ("parthenogenically activated" and "parthenogenetically activated" is used interchangeably) the process by which activation of the oocyte occurs in the absence of sperm penetration, and refers to the development of an early stage embryo comprising trophectoderrn and inner, cell mass that is obtained by activation of an oocyte or embryonic cell, e.g., blastomere, comprising DNA of all female origin. In a related aspect, a "parthenote" refers to the resulting cell obtained by such activation. In another related aspect, "blastocyst: refers to a cleavage stage of a fertilized of activated oocyte comprising a hollow ball of cells made of outer trophoblast cells and an inner cell mass (ICM). In a further related aspect, "blastocyst formation" refers to the process, after oocyte fertilization or activation, where the oocyte is subsequently cultured in media for a time to enable it to develop into a hollow ball of cells made of outer trophoblast cells and ICM (e.g., 5 to 6 days).

[0048] "Pluripotent cell" refers to a cell derived fiom an embryo produced by activation of a cell containing DNA of all female or male origin that can be maintained in vitro for prolonged, theoretically indefinite period of time in an undifferentiated state, that can give rise to different differentiated tissue types, i.e., ectoderm, mesoderm, and endoderm. The pluripotent state of the cells is preferably maintained by culturing inner cell mass or cells derived from the inner cell mass of an embryo produced by androgenetic or gynogenetic methods under appropriate conditions, for example, by culturing on a fibroblast feeder layer or another feeder layer or culture that includes leukemia inhibitory factor (LIF). The pluripotent state of such cultured cells can be confirmed by various methods, e.g., (i) confirming the expression of markers characteristic of pluripotent cells; (ii) production of chimeric animals that contain cells that express the genotype of the pluripotent cells; (iii) injection of cells into animals, e.g., SCID mice, with the production of different differentiated cell types in vivo; and (iv) observation of the differentiation of the cells (e.g., when culttired in the absence of feeder layer or LIF) into,embryoid bodies and other differentiated cell types in vitro.

[0049] "Diploid cell" refers to a cell, e.g., an oocyte or blastomere, having a diploid DNA
content of all male or female origin.

[0050] "Haploid cell" refers to a cell, e.g., an oocyte or blastomere, having a haploid DNA
content, where the haploid DNA is of all male or female origin.

[0051] "Activation" refers to a process where a fertilized or unfertilized oocyte, for example, but not limited to, in metaphase II of meiosis, undergoes a process typically including separation of the chromatid pairs, extrusion of the second polar body, resulting in an oocyte having a haploid number of chromosomes, each with one chromatid.
Activation includes methods whereby a cell containing DNA of all male or female origin is induced to develop into an embryo that has a discernible inner cell mass and trophectodenn, which is useful for producing pluripotent cells but which is itself is likely to be incapable of developing into a viable offspring. Activation may be carried out, for example, under one of the following conditions: (1) conditions that do not cause second polar body extrusion; (ii) conditions that cause polar body extrusion but where the polar body extrusion is inhibited; or (iii) conditions that inhibit first cell division of the haploid oocyte.

[0052] "Metaphase II" refers to a stage of cell development where the DNA
content of a cell consists of a haploid number of chromosomes with each chromosome represented by two chromatids.

[0053] In one embodiment, metaphase II oocytes are activated/cultured by incubating oocytes under various 02 tension gas enviromnents. In a related aspect, the low 02 tension gas environment is created by a gas mixture comprising an 02 concentration of about 2%, 3%, 4%, or 5%. In a further related aspect, the gas mixture comprises about 5%
CO2.
Further, the gas mixture comprises about 90% N2, 91% N2, or 93% N2. This gas mixture is to be distinguished from 5% CO2 air, which is approximately about 5% CO2, 20% 02, and 75%
N2.

[0054] "02 tension" refers to the partial pressure (pressure exerted by a single component of a gas mixture) of oxygen in a fluid (i.e., liquid or gas). Low tension is when the partial pressure of oxygen (pO2) is low and high tension is when the p02 is high.

[0055] "Defined-medium conditions" refer to environments for culturing cells where the concentration of components therein required for optimal growth are detailed.
For example, depending on the use of the cells (e.g., therapeutic applications), removing cells from conditions that contain xenogenic proteins is important; i.e., the culture conditions are animal-free conditions or free of non-human animal proteins. In a related aspect, "in vitro fertilization (IVF) media" refers to a nutrient system which contains chemically defined substances on or in which fertilized oocytes can be grown.

[0056] "Extracellular matrix (ECM) substrates" refer to a surface beneath cells which supports optinium growth. For example, such ECM substrates include, but are not limited to, Matrigel, laminin, gelatin, and fibronectin substrates. In a related aspect, such substrates may comprise collagen IV, entactin, heparin sulfate proteoglycan, to include various growth factors (e.g., bFGF, epidermal growth factor, insulin-like growth factor-l, platelet derived growth factor, nerve growth factor, and TGF-(3-1).

[0057] "Embryo" refers to an embryo that results upon activation of a cell, e.g., oocyte or other einbryonic cells containing DNA of all male or female origin, which optionally may be modified, that comprises a discernible trophectoderm and inner cell mass, which cannot give rise to a viable offspring and where the DNA is of all male or female origin.
The inner cell mass or cells contained therein are useful for the production of pluripotent cells as defined previously.

[0058] "Inner cell mass (ICM)" refers to the inner portion of an embryo which gives rise to fetal tissues. Herein, these cells are used to provide a continuous source of pluripotent cells in vitro. Further, the ICM includes the inner portion of the embryo that results from androgenesis or gynogenesis, i.e., embryos that result upon activation of cells containing DNA of all male or female origin. Such DNA, for example, will be human DNA, e.g., human oocyte or spermatozoal DNA, which may or may not have been genetically modified.

[0059] "Trophectoderm" refers to another portion of early stage embryo whicli gives rise to placental tissues, including that tissue of an embryo that results from androgenesis or gynogenesis, i.e., embryos that result from activation of cells that contain DNA of all male or female origin, e.g., human ovarian or spermatozoan.

[0060] "Differentiated cell" refers to a non-embryonic cell that possesses a particular differentiated, i.e., non-embryonic, state. The three earliest differentiated cell types are endoderm, mesoderm, and ectoderm.

[0061] "Substantially identical" refers to a quality of sameness regarding a particular characteristic that is so close as to be essentially the same within the ability to measure difference (e.g., by HLA typing, SNP analysis, and the like).

[0062] "Histocompatible" refers to the extent to which an organism will tolerate a graft of a foreign tissue.

[0063] "Genomic inlprinting" refers to the meclianism by which a number of genes throughout the genome are monoallelically expressed according to their parental origin.
[0064] "Synthetic" refers to the characteristic of an object whose production is by defined artificial manipulation.

[0065] "Homoplasmy," including grammatical variations thereof, refers to the presence of the same type of the mitochondrial DNA (mtDNA) within a cell or individual.

[0066] "Heteroplasmy," including gramniatical variations thereof, refers to the presence of a mixture of more than one type of mitochondrial DNA (mtDNA) within a cell or individual.
[0067] "Uniparental" refers to one or more cells or individuals from which another arises and to which it remains subsidiary.

[0068] "Mechanically isolating" refers to the process of separating cell aggregates by physical forces. For example, such a process would exclude the use of enzymes (or other cell cleavage products) which might contain non-lluman materials.

[0069] In one embodiment, stem cells can be generated by methods known in the art, for example, but not limited to, the methods as described by Thomson (see, e.g., U.S. Pat. No.
7,029, 913; U.S. Pat. No. 6,200,806; U.S. Pat. No. 6,887,706; U.S. Pat. No.
5,843,780), Uchida (see, e.g., U.S. Pat. No. 7,083,977; U.S. Pat. No. 7,049,141), Carpenter (see, e.g., U.S. Pat. No. 6,777,233), Anderson et al. (see, e.g., U.S. Pat. No.
5,589,376), Hogan (see, e.g., U.S. Pat. No. 5,453,357), Naktsuji et al. (see, e.g., U.S. Pat. No.
7,083,977), and Khilian (see, e.g., U.S. Pat. No. 5,449,620), which are incorporated herein by reference. In one aspect, retinal stem cells are obtained by methods known in the art (see, e.g., U.S. Pat. No.
6,117,675).

[0070] In another embodiment, stem cells are generated from a parthogenetically activated human oocyte. In one aspect, a synthetic cornea is obtained from a retinal stem cell differentiated from stem cells derived from a parthenogenetically activated 1luinan oocyte.
[0071] In another aspect, the synthetic cornea of the present invention can be used as a replacement for subjects having refractive error, such as those subjects which are nearsighted, farsighted, or have astigmatism. Refractive errors occur when the curve of the cornea is irregularly shaped (too steep or too flat).

[0072] The cornea is a unique, transparent structure that covers the iris, pupil, and anterior chamber, providing most of the eye's optical power. Together with the lens, the coniea refracts light and, as a result, aids in focusing. The coinea contributes more to the total refraction than the lens does, but, whereas the curvature of the lens can be adjusted to "tune"
focus, the curvature of the cornea is fixed. The coxnea has no blood vessels, its nourishment is obtained via diffusion from the tear fluid, the aqueous humor, and neurotrophins supplied by nerve fibers that innervate it. Thus, for example, disturbances in circulation of these fluids or inflammatory processes play a large role in the pathogenesis of corneal abnormalities.
[0073] The cornea is composed mostly of dense connective tissue. However, the collagen fibers are arranged in a parallel pattern, allowing light waves to constructively interfere, thus letting light pass through relatively uninhibited.

[0074] The changes associated with aging of the cornea include increased opacity, increased anterior surface curvatures, and possibly changes in refractive index distribution.
Various refractive eye surgery techniques change the shape of the cornea in order to reduce the need for corrective lenses or otherwise improve the refractive state of the eye. In many techniques, reshaping of the cornea is performed by photoablation using an eximer laser.
[0075] If the corneal stroma develops visually significant opacity, irregularity, or edema, a cadaveric donor cornea can be transplanted. Because there are no blood vessels in the cornea, it is relatively shielded-off from immuno-response, thus the incidence of rejection of donated corneas is relatively low (approximately 20%).

[0076] . There are also synthetic comeas (keratoprotheses), however, these are typically plastic inserts or may be composed of biocompatible synthetic materials that encourage tissue in-growth into the synthetic cornea, thereby promoting biointegration.
Alternatively, orthokeratology offers the use of specialized hard or rigid gas-permeable contact lenses to transiently reshape the cornea in order to improve the refractive state of the eye or reduce the need for eyeglasses and contact lenses.

[0077] The cornea has unmyelinated nerve endings sensitive to touch, texnperature, and chemicals; a touch of the cornea causes an involuntary reflex to close the eyelid. Because transparency is of prime importance, the cornea does not have blood vessels;
it receives nutrients via diffusion from the tear fluid at the outside and the aqueous humour at the inside and also fiom neurotrophins supplied by nerve fibers that innervate it. In humans, the cornea has a diameter of about 11.5 mm and a thiclcness of 0.5 mm - 0.6 mm in the center and 0.6 mm - 0.8 mm at the periphery. In humans, the refractive power of the cornea is approximately 43 dioptres, roughly three-fourths of the eye's total refractive power.
Transparency, avascularity, and immunologic privilege make the cornea a special tissue.
[0078] The corneal tissue is arranged in five basic layers: epithelium, Bowman's layer, stroma, Descemet's membrane and endothelium, each having a separate function.
The epithelium is the outermost layer of the cornea, comprising about 10% of the tissue's thickness. The epithelium functions primarily to: (1) block passage of foreign materials, such as dust, water, and bacteria, into the eye and other layers of the cornea; and (2) provide a smooth surface that absorbs oxygen and cell nutrients from tears, then distributes these nutrients to the rest of the cornea. The epithelium is filled with thousands of tiny nerve endings that make the cornea extremely sensitive to pain when rubbed or scratched. The part of the epithelium that serves as the foundation one which the epithelial cells anchor and organize themselves is called the basement membrane.

[0079] Lying directly below the basement membrane of the epithelium is a transparent sheet known as Bowman's layer. It is composed of strong layered protein (collagen) fibers.
Once injured, Bowman's layer can form a scar as it heals. If these scars are large and centrally located, some vision loss can occur.

[0080] Beneath the Bowman's layer is the stroma, which comprises 90% of the cornea's thickness. It consists primarily of water (78%) and collagen (16%), and does not contain any blood vessels. Collagen give'the cornea it strength, elasticity, and form. The collagen's unique shape, arrangement, and spacing are essential in producing the cornea's light conducting transparency.

[0081] Under the stroma is Descemet's membrane, a thin but strong sheet of tissue that serves as a protective barrier against infection and injury. Descemet's membrane is composed of collagen fibers (different from those of stroma) and is made by the endothelial cells that lie below it. Descemet's membrane is regenerated readily after injury.

[0082] The endothelium is the extremely thin, innermost layer of the cornea.
Endothelial cells are essential in keeping the cornea clear. Normally, fluid leaks slowly from inside the eye into the middle corneal layer (stroma). The endotheliuin's primary task is to pump this excel fluid out of the stroma. Without this pumping action, the stroma would swell with water, become hazy, and ultimately opaque. Once endothelium cells are destroyed by disease or trauma, they are lost forever. If too many endothelial cells are destroyed, corneal edema and blindness ensue, with comeal transplantation the only available therapy.

[0083] The human cornea proteome has been characterized. About 52% (28 of 54) of the corneal extracellular proteins are common plasma proteins when the identified iinmunoglobulin chains and complement C3 are included. This group of corneal proteins also contain different serpins (a-l-antichyniotrypsin, a-l-antitiypsin, and antithrombin III), a-1-microglobulin, different apolipoproteins, fibrinogen, haptoglobin, hemopexin, albumin, amyloid P-component, tetranectin, transferrin, transthyretin, and vitamin D-binding protein.
Thus, these proteins are either synthesized by the corneal cells or originate from blood and enter the cornea with the bulk flow from the ciliary arteries located in the corneoscleral limbus area.

[0084] When the cornea is curved too much, faraway objects will appear blurry because they are focused in front of the retina: i.e., myopia or nearsightedness.
Myopia affects over 25% of all adults. Hyperopia, or farsightedness, is the opposite of myopia.
Distant objects are clear, and objects appear blurry close-up (i.e., images focus on a point beyond the retina).
Astigmatism is a condition in which the uneven curvature of the cornea blurs and distorts both distant and near objects. In astigmatism, the cornea is shaped like the back of a spoon, curved more in one direction than in another. This causes light rays to have more than one foal point and focus on two separate areas of the retina, distorting the visual image. Two thirds of adults who have myopia also have astigmatism.

[0085] Refractive errors are usually corrected by eyeglasses or contact lenses. Although refractive surgery is becoming an increasing popular option.

[0086] Additional disorders affecting the cornea include, but are not limited to, allergies, conjunctivitis, corneal infections, dry eye, Fuchs' dystrophy, herpes zoster, iridocomeal endothelial syndrome, keratoconus, lattice dystrophy, map-dot-fingerprint dystrophy, ocular herpes, Stevens-Johnson syndroine, pterygium, keratitis, corneal ulcer, corneal abrasion, snow blindness, arc eye, Thygeson's superficial puncate keratopathy, and keratpconjunctivitis sicca.

[0087] As used herein, "corneal transplant," "corneal graft," or "penetrating keratoplasty,"
refers to a surgical procedure where a damaged or diseased cornea is replaced by cornea tissue. In corneal transplant surgery, the surgeon removes the central portion of the diseased or injured cornea and replaces it with a clear cornea. The new cornea is placed in the opening and is sutured to the eye (see, e.g., Rapuano et al. Anterior Segment, The Requisites (Requisites in Ophthalmology), 1999, Mosby, Inc., Philadelphia, PA).
Approximately 20%
of corneal transplant patients reject their donor corneas. In one aspect of the present invention, the recipient of the synthetic cornea is the donor of the oocytes from which the cornea is derived. As such, the possibility of tissue rejection is minimized.

[0088] In one embodiment, a method for replacement of a cornea of an eye using the synthetic cornea includes surgically excising the cornea from the eye, inserting the synthetic cornea into the area of the removed cornea, and allowing the synthetic cornea to interface with tissue underlying the excision to anchor the synthetic cornea to the eye.

[0089] In a related aspect, the method includes separating a portion of the outer surface of a cornea thereby forming a comeal flap and a corneal bed, the corneal flap having an anterior surface and a posterior surface, the comeal bed having a shaped anterior surface, implanting the synthetic cornea on the comeal bed, the cornea having an anterior surface and a posterior surface, and replacing the portion of the cornea that was separated.

[0090] In another embodiment, a method delivering an effective amount of an agent to the eye of a subject using the synthetic cornea of the present invention includes transforming a portion of the cells comprising the synthetic cornea with a nucleic acid vehicle, where the vehicle encodes the agent, identifying a population of cells comprising the synthetic cornea which express the agent encoded by the nucleic acid, and replacing cornea cells of the subject with transfoimed cells of the synthetic cornea, where the replaced cells deliver the agent to the eye of the subject.

[0091] In a related aspect, the replacing step comprises replacing the corn.ea of the subject with the synthetic cornea. In a further related aspect, the subject can be a domesticated animal, including cats and dogs. Further, the subject may be human.

[0092] In the native environment, immature oocytes (eggs) from the ovary undergo a process of maturation which results in the progression through meiosis to metaphase II of meiosis. The oocytes then arrest at metaphase II. In metaphase II, the DNA
content of the cell consists of a haploid number of chroinosomes, each represented by two cliromatids.

[0093] Such oocytes may be maintained indefinitely by cryopreserving by, for example, but not limited to, microinjection with a sugar.

[0094] In one embodiment, a method for producing human stem cells from a cryopreseived oocyte is provided, including microinjecting into the cytoplasm of the oocyte cell a cryopreservation agent, freezing the oocyte to a cryogenic temperature to cause it to enter a dormant state, storing the oocyte in the dormant state, thawing the oocyte, parthenogenically activating the oocyte at high 02 tension, isolating an inner cell mass (ICM) from the activated oocyte, and culturing the cells of the ICM on a layer of human feeder cells, where culturing is carried out under low 02 tension.

[0095] In one aspect, oocytes obtained as described are transferred to modified, isotonic IVF covered with embryo-tested mineral oil (Sigina), or any other suitable medium. If desired, the oocytes may be incubated witli an extracellular sugar at the same concentration as the amount planned for microinjection. For example, to inject 0.1 M sugar, oocytes may be equilibrated in DMEM/F-12 with 0.1 M sugar. In one aspect, the cryopreservation agent comprises a lower Na+ concentration than standard DMEM (i.e., Na low media).
In a related aspect, the cryopreservation agent comprises a higher K+ concentration than standard DMEM
(i.e., K+ high). In a further related aspect, the cryopreservation agent comprises both a lower Na+ and higher K+ concentration than standard DMEM (i.e., Na+ low/ K+ high media). In one aspect, the cryopreservation agent comprises an organic buffer, including but not limited to, HEPES. In another aspect, the cryopreservation agent comprises moieties that inhibit apoptotic protein (e.g., capases).

[0096] Alternatively, the oocytes may be optionally equilibrated with any other substantially non-permeable solute, such a NaCl, to decrease their cell volume prior to microinjection. This initial decrease in cell volume may result in a smaller final volume of the microinjected oocytes compared to oocytes not incubated in a hypertonic media prior to microinjection. This smaller final volume may minimize any potential adverse effect from the swelling of the oocytes. This general procedure for the preparation of cells for microinjection may also be used for other cell types (e.g., activated oocytes, hES cells, and the like).

[0097] The oocytes are then microinjected with a cryopreservation agent.
Microinjection equipment and procedures are well characterized in the art and microinjection equipment known for use in injecting small molecules into cells may be used with the invention. In an exemplary microinjection step, oocytes can be microinj ected at a pressure of 10 psi for 30 milliseconds. Another example of a standard microinjection technique is the method described by Nakayama and Yanagimachi (Nature Biotech. 16:639-642, 1998).

[0098] A cryopreservation agent useful in this process includes any chemical that has cryo-protective properties and is ordinarily non-permeable. In particular, the cryopreservation agent can include sugars either alone or mixed together with other traditional cryopreservation agents. Carbohydrate sugars such as trehalose, sucrose, fructose, and raffinose, may be microinjected to concentrations less than or equal to about 1.0 M, and more preferably, less than or equal to about 0.4 M. In one aspect, the concentration is between 0.05 and 0.20 M, inclusive. Additionally, an extracellular sugar or traditional cryopreservation agent may be added prior to storage. If the cells were incubated in a hypertonic solution prior to microinjection, the substantially non-permeable solute may be allowed to remain in the media after microinjection or may be removed from the media by washing the cells with media containing a lower concentration, or none, of this solute.

[0099] Certain sugars or polysaccharides which ordinarily do not permeate cell membranes because they are too large to pass through the membrane have superior physiochemical and biological properties for cryopreservation purposes. While these sugars ordinarily do not permeate cell membranes on their own, using the method as described, these ordinarily non-permeating sugars may be microinjected intracellularly to result in a beneficial effect.

[0100] Non-permeating sugars having a stabilizing or preserving effect on cells that are especially useful as the cryopreservation agent in the present method include sucrose, trehalose, fructose, dextran, and raffinose. Among these sugars, trehalose, a non-reducing disaccharide of glucose, has been shown to be exceptionally effective in stabilizing cell structures at low concentrations. The addition of extracellular glycolipids or glycoproteins may also stabilize the cell membrane. -[0101] Following the microinjection of the cryopreservation agent, the cells are prepared for storage. A variety of methods for freezing and/or drying may be employed to prepare the cells for storage. In particular, three approaches are described herein:
vacuum or air drying, freeze drying, and freeze-thaw protocols. Drying processes have the advantage that the stabilized biological material may be transported and stored at ambient temperatures.

[0102] Typically, oocytes loaded with 1 to 2M DMSO are cooled at a very slow cooling rate (0.3 to 0.5 C/min) to an intermediate temperature (-60 C. to -80 C.) before plunging in liquid nitrogen for storage. The sample can then be stored at this temperature.

[0103] The suspended material can then be stored at cryopreservation temperatures, for example, by leaving the vials in liquid nitrogen (LN2), for the desired amount of time.
[0104] Protocols for vacuum or air drying and for freeze drying proteins are well characterized in the art (Franks et al., "Materials Science and the Production of Shelf-Stable Biologicals," BioPharm, October 1991, p. 39; Shalaev et al., "Changes in the Physical State of Model Mixtures during Freezing and Drying: Impact on Product Quality,"
Ciyobiol. 33, 14-26 (1996)) and such protocols may be used to prepare cell suspensions for storage with the method as described. In addition to air drying, other convective drying methods that may be used to remove water from cell suspensions include the convective flow of nitrogen or other gases.

[0105] An exemplary evaporative vacuum drying protocol useful with the method of the invention may include placing 20 1 each into wells on 12 well plates and vacuum drying for 2 hours at anibient temperature. Of course, other drying methods could be used, including drying the cells in vials. Cells prepared in this manner may be stored dry, and rehydrated by diluting in DMEM or any other suitable media.

[0106] A method of the invention using freeze drying to prepare the cells for storage begins with freezing the cell suspension. While prior art freezing methods may be employed, the simple plunge freezing method described herein for the freeze-thaw method may also be used for the freezing step in the freeze drying protocol.

[0107] After freezing, a two stage drying process may be employed. In the first stage, energy of sublimation is added to vaporize frozen water. Secondary drying is performed after the pure crystalline ice in the sample has been sublimated. Freeze dried cells can be stored and hydrated in the same manner as described above for vacuum drying. Viable cells may then be recovered. 1 [0108] After the recovery of cells from a frozen or dried state, any external cryopreservation agent may be optionally removed from the culture media. For example, the media may be diluted by the addition of the corresponding media with a lower concentration of cryopreservation agent. For example, the recovered cells may be incubated for approximately five minutes in media containing a lower concentration of sugar than that used for cell storage. For this incubation, the media may contain the same sugar that was used as the cryopreservation agent; a different cryopreservation agent, such as galactose; or any other substantially non-permeable solute. To minimize any osmotic shock induced by the decrease in the osmolarity of the media, the concentration of the extracellular cryopreservation agent may be slowly decreased by performing this dilution step multiple times, each time with a lower concentration of cryopreservation agent. These dilution steps may be repeated until there is no extracellular cryopreservation agent present or until the concentration of cryopreservation agent or the osmolarity of the media is reduced to a desired level.

[0109] The parthenogenetically activated oocytes, blastoeysts, ICM, and autologous stem cells can be stored or "banked" in a manner that allows the cells to be revived as needed in the future. An aliquot of the parthenogenetically activated oocytes and autologous stem cells can be removed at any time, to be grown into cultures of many undifferentiated cells and then differentiated into a particular cell type or tissue type, and may then be used to treat a disease or to replace nlalfunctioning tissues in a subject. Since the cells are parthenogenetically derived from the donor, the cells can be stored so that an individual or close relative can have access to cells for an extended period of time.

[0110] In one embodiment, a cell bank is provided for storing parthenogenetically activated oocytes, blastocysts, ICM, and/or autologous stem cell samples. In another embodiment, methods for administering such a cell bank are provided. U.S.
Published Patent Application No. 20030215942, which is incorporated by reference herein in its entirety, provides an example of a stem cell bank system.

[0111] Using methods such as those described above, the isolation and in vitro propagation of parthenogenetically activated oocytes, blastocysts, ICM, and autologous stem cell samples and their cryopreservation facilitates the establishment of a "bank" of transplantable human stem cells. Because it is possible to store smaller aliquots of cells, the banking procedure could take up a relatively small space. Therefore, the cells of many individuals could be stored or "banked" on a short term or long term basis, with relatively little expense.

[0112) In one einbodiment, a portion of the sample is made available for testing, either before or after processing and storage.

[0113] This invention also provides methods of recording the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell samples so that when a sample needs to be located, it can be easily retrieved. Any indexing and retrieval system can be used to fulfill this purpose. Any suitable type of storage system can be used so that the parthenogenetically activated oocytes, blastocysts, ICM, and/or autologous stem cells can be stored. The samples can be designed to store individual sainples, or can be designed to store hundreds, thousands, and even millions of different cell samples.

[0114] The stored parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell samples can be indexed for reliable and accurate retrieval. For example, each sample can be marked with alphanumeric codes, bar codes, or any other method or combinations thereof. There may also be an accessible and readable listing of information enabling identification of each parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample and its location in the bank and enabling identification of the source and/or type the cell sample, which is outside of the bank. This indexing system can be managed in any way known in the art, e.g., manually or non-manually, e.g. a computer and conventional software can be used.

[0115] In one embodiment, the cell samples are organized using an indexing system so that the sample will be available for the donor's use whenever needed. In other embodiments, the cell samples can be utilized by individuals related to the original donor.
Once recorded into the indexing system, the cell sample can be made available for matching purposes, e.g., a matching program will identify an individual with matching type information and the individual will have the option of being provided the matching sample.

[0116] The storage banking system can comprise a system for storing a plurality of records associated with a plurality of individuals and a plurality of cell saniples. Each record may contain type information, genotypic information or phenotypic information associated with the cell samples or specific individuals. In one embodiment, the system will include a cross-match table that matches types of the samples with types of individuals who wish to receive a sample.

[0117] In one embodiment, the database system stores information for each parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample in the bank. Certain information is stored in association with each sample. The infonnation may be associated with a particular donor, for example, an identif'ication of the donor and the donor's medical history. For example, each sample may be HLA typed and the HLA
type infoimation may be stored in association with each sample. The information stored may also be availability information. The information stored with each sample is searchable and identifies the sample in such a way that it can be located and supplied to the client immediately.

[0118] Accordingly, enibodiments of the invention utilize computer-based systems that contain information such as the donor, date of submission, type of cells submitted, types of cell surface markers present, genetic information relating to the donor, or other pertinent information, and storage details such as maintenance records and the location of the stored samples, and other useful information.

[0119] The term "a computer-based system" refers to the hardware, software, and any database used to store, search, and retrieve information about the stored cells. The computer-based system preferably includes the storage media described above, and a processor for accessing and manipulating the data. The hardware of the computer-based systems of this embodiment comprises a central processing unit (CPU) and a database. A skilled artisan can readily appreciate that any one of the currently available computer-based systems are suitable.

[0120] In one embodiment, the computer system includes a processor connected to a bus that is connected to a maui memory (preferably implemented as RAM) and a variety of secondary storage devices, such as a hard drive and removable medium storage device. The removable medium storage device can represent, for example, a floppy disk drive, a DVD
drive, an optical disk drive, a compact disk drive, a magnetic tape drive, etc. A removable storage medium, such as a floppy disk, a compact disk, a magnetic tape, etc.
containing control logic and/or data recorded therein can be inserted into the removable storage device.
The computer system includes appropriate software for reading the control logic and/or the data from the removable medium storage device once inserted in the removable medium storage device. Information relating to the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell can be stored in a well known manner in the main memory, any of the secondary storage devices, and/or a removable storage medium.
Software for accessing and processing these data (such as search tools, compare tools, etc.) reside in main memory during execution.

[0121] As used herein, "a database" refers to meinory that can store any useful information relating to the parthenogenetically activated oocyte and/or autologous stem cell collections and the donors.

[0122] The data relating to the stored parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell can be stored and manipulated in a variety of data processor programs in a variety of formats. For example, the data can be stored as text in a word processing file, such as Microsoft WORD or WORDPERFECT, an ASCII file, an html file, or a pdf file in a variety of database programs familiar to those of skill in the art, such as DB2, SYBASE, or ORACLE.

[0123] A "search program" refers to one or more programs that are implemented on the computer-based system to search for details or compare information relating to the cryopreserved samples within a database. A "retrieval program" refers to one or more programs that can be implemented on the computer-based system to identify parameters of interest in the database. For example, a retrieval program can be used to find samples that fit a particular profile, samples having specific markers or DNA sequences, or to find the location of samples corresponding to particular individuals.

[0124] There is no upper limit on the number of cell samples that can be stored in one cell bank. In one embodiment, hundreds of products from different individuals will be stored at one bank or storage facility. In another embodiment, up to millions of products may be stored in one storage facility. A single storage facility may be used to store parthenogenetically activated oocyte and/or autologous stem cell samples, or multiple storage facilities may be used.

[0125] In some embodiments of the present invention, the storage facility may have a means for any method of organizing and indexing the stored cell samples, such as, for example, automated robotic retrieval mechanisms and cell sample manipulation mechanisms.
The facility may include micromanipulation devices for processing cell samples. Kliown conventional technologies can be used for efficient storage and retrieval of the cell samples.
Exemplary technologies include but are not limited to Machine Vision, Robotics, Automated Guided Vehicle System, Automated Storage and Retrieval Systems, Computer Integrated Manufacturing, Computer Aided Process Plamiing, Statistical Process Control, and the like.

[0126] The type information or other information associated with the individual in need of a sample may be recorded into a system that can be used to identify an appropriate matching product, such as, for example, a database system, an indexing system, and the like. Once recorded in the system, a match can be made between the type of the individual and a donor cell sample. In preferred embodiments, the donor sample is from the same individual as the individual in iieed of the sample. However, similar but not identical donor/recipient matches can also be used. The matching sample is available for the individual possessing the matching type identifier. In one embodiment of this invention, the individual's identification information is stored in connection with the cell sample. In some embodiments, the matching process occurs around the time of harvesting the sample, or can occur at any time during processing, storage, or when a need arises. Accordingly, in some embodiments of the invention, the matcliing process occurs before the individual is in actual need of the cell sample.

[0127] When the parthenogenetically activated oocyte, blastocyst, ICM, and/or autologous stem cell sample is needed by an individual, it may be retrieved and made available for research, transplantation or other purposes within minutes, if desired. The sample may also be further processed to prepare it for transplantation or other needs.

[0128] Normally, the oocyte is ovulated at this stage and fertilized by the sperm. The sperm initiates the completion of ineiosis in a process called activation.
During activation, the pairs of chromatids separate, the second polar body is extruded, and the oocyte retains a haploid number of chromosomes, each with one chromatid. The spemi contributes the other haploid complement of chromosomes to make a full diploid cell with single chromatids. The chromosomes then progress through DNA synthesis during the first cell cycle.
These cells then develop into embryos.

[0129] By contrast, embryos described herein are developed by artificial activation of cells, typically mammalian oocytes or blastomeres containing DNA of all male or female origin. As discussed in the background of the invention, many methods have been reported in the literature for artificial activation of unfertilized oocytes. Such methods include physical methods, e.g., meclianical methods such as pricking, manipulation or oocytes in culture, thermal methods such as cooling and heating, repeated electric pulses, enzymatic treatments, such as trypsin, pronase, hyaluronidase, osmotic treatments, ionic treatments such as witli divalent cations and calcium ionophores, such as ionomycin and A23187, the use of anesthetics such as ether, ethanol, tetracaine, lignocaine, procaine, phenothiazine, tranquilizers such as thioridazine, trifluoperazine, fluphenazine, chlorpromazine, the use of protein synthesis inliibitors such as cycloheximide, puromycin, the use of phosphorylation inhibitors, e.g., protein kinase inhibitors such as staurosporine, 2-aminopurine, shingosine, and DMAP, coinbinations thereof, as well as other methods.

[0130] Such activation methods are well known in the art and are discussed U.S. Pat. No.
5,945,577, incorporated herein by reference.

[0131] In one embodiment,, a human cell in inetaphase II, typically an oocyte or blastomere comprising DNA of all male or female origin; is artificially activated for effecting artificial activation of oocytes.

(0132] In a related aspect, the activated cell, e.g., oocyte, which is diploid, is allowed to develop into an embryo that comprises a trophectoderm and an inner cell mass.
This can be effected using known methods and culture media that facilitate blastocyst development.
[0133] After the gynogenetic embryos have been cultured to produce a discernable trophectoderm and inner cell mass, the cells of the inner cell mass are then used to produce the desired pluripotent cell lines. This can be accomplished by transferring cells derived from the inner cell mass or the entire inner cell mass onto a culture that inhibits differentiation. This can be effected by transferring the inner cell mass cells onto a feeder layer that inhibits differentiation, e.g., fibroblasts or epithelial cells, such as fibroblasts derived from postnatal human tissues, etc., or other cells that produce LIF.
Other factors/components may be employed to provide appropriate culture conditions for maintaining cells in the undifferentiated state including, but not limited to, addition of conditioned media (Amit et al., Developmental Biol (2000) 227:271-278), bFGF
and TGF-(31 (with or without LIF) (Amit et al., Biol Reprod (2004) 70:837-845), factors which activate the gpl30/STAT3 pathway (Hoffinan and Carpenter, Nature Biotech (2005) 23(6):699-708), factors which activate the PI3K/Akt, PKB pathway (Kim et al., FEBS Lett (2005) 579:534-540), factors that are members of the bone morphogenetic protein (BMP) super-family (Hoffinan and Carpenter (2005), supra), and factors which activate the canonical/p-catenin Wnt signaling pathway (e.g., GSK-3-specific inhibitor; Sato et al., Nat Med (2004) 10:55-63). In a related aspect, such factors may comprise culture conditions that include feeder cells and/or ECM substrates (Hoffinan and Carpenter (2005), supra).

[0134] In one aspect, the inner cell mass cells are cultured on human postnatal foreskin or dermal fibroblast cells or other cells which produce leukemia inhibitory factor, or in the presence of leukemia inhibitory factor. In a related aspect, feeder cells are inactivated prior to seeding with the ICM. For example, the feeder cells can be mitotically inactivated using an antibiotic. In a related aspect, the antibiotic can be, but is not limited to, mytomycin C.
[0135] Culturing will be effected under conditions that maintain the cells in an undifferentiated, pluripotent state, for prolonged periods, theoretically indefinitely. In one embodiment, oocytes are parthenogenically activated with calcium ionophores under high 02 tension followed by contacting the oocytes with a serine-threonine kinase inhibitor under low 02 tension. The resulting ICM from the parthenogenically activated oocytes are cultured under high 02 tension, where the cells, for example, are maintained using a gas mixture comprising 20% 02. In one aspect, culturable refers to being capable of, or fit for, being cultivated. In a related aspect, ICM isolation is carried out mechanically after four days of blastocyst cultivation, where the cultivation is carried out on feeder cells.
Such cultivation, for example, eliminates the need to use materials derived from animal sources, as would be the case for immunosurgery.

[0136] In a related aspect, culture media for the ICM is supplemented with non-animal sera, including but not limited to, human umbilical cord serum, where the serum is present in defined media (e.g., IVF, available from MediCult A/S, Denmark; Vitrolife, Sweden; or Zander IVF, Inc., Vero Beach, FL). In another aspect, the media and processes as provided are free of animal products. In a related aspect, animal products are those products, including serum, interferons, chemokines, cytokines, hormones, and growth factors, that are from non-human sources.

[0137] The pluripotent state of the cells produced by the present invention can be confirmed by various methods. For example, the cells can be tested for the presence or absence of characteristic ES cell markers. In the case of human ES cells, examples of such markers are identified supra, and include SSEA-4, SSEA-3, TRA-1-60 and TRA-1-81 and are known in the art.

[0138] Also, pluripotency can be confirmed by injecting the cells into a suitable animal, e.g., a SCID mouse, and observing the production of differentiated cells and tissues. Still another method of confirming pluripotency is using the subject pluripotent cells to generate chimeric animals and observing the contribution of the introduced cells to different cell types.

Methods for producing chimeric animals are well known in the art and are described in U.S.
Pat. No. 6,642,433, incorporated by reference herein.

[0139] Yet another method of confirming pluripotency is to observe ES cell differentiation into embryoid bodies and other differentiated cell types when cultured under conditions that favor differentiation (e.g., removal of fibroblast feeder layers). This method has been utilized and it has been confirmed that the subject pluripotent cells give rise to embryoid bodies and different differentiated cell types in tissue culture.

[0140] The resultant pluripotent cells and cell lines, preferably human pluripotent cells and cell lines, which are derived from DNA of entirely female original, have numerous therapeutic and diagnostic applications. Such pluripotent cells may be used for cell transplantation therapies or gene therapy (if genetically modified) in the treatment of numerous disease conditions.

[0141] In this regard, it is known that mouse embryonic stem (ES) cells are capable of differentiating into almost any cell type, e.g., hematopoietic stem cells.
Therefore, human pluripotent (ES) cells produced according to the invention should possess similar differentiation capacity. The pluripotent cells according to the invention will be induced to differentiate to obtain the desired cell types according to known methods. For example, human ES cells produced according to the invention may be induced to differentiate into hematopoietic stem cells, muscle cells, cardiac muscle cells, liver cells, islet cells, retinal cells, cartilage cells, epithelial cells, urinary tract cells, etc., by culturing such cells in differentiation medium and under conditions which provide for cell differentiation. Medium and methods which result in the differentiation of ES cells are known in the art as are suitable culturing conditions.

[0142] For example, Palacios et al, Proc. Natl Acad. Sci., USA, 92:7530-7537 (1995) teach the production of hematopoietic stem cells from an embryonic cell line by subjecting stem cells to an induction procedure comprising initially culturing aggregates of such cells in a suspension culture medium lacking retinoic acid followed by culturing in the same medium containing retinoic acid, followed by transferal of cell aggregates to a substrate which provides for cell attachment.

[0143] Moreover, Pedersen, J. Reprod. Fertil. Dev., 6:543-552 (1994) is a review article which references numerous articles disclosing methods for in vitro differentiation of embryonic stem cells to produce various differentiated cell types including hematopoietic cells, muscle, cardiac muscle, nerve cells, among others.

[0144] Further, Bain et al, Dev. Biol., 168:342-357 (1995) teach in vitro differentiation of embryonic stem cells to produce neural cells which possess neuronal properties. These references are exemplary of reported methods for obtaining differentiated cells from embryonic or stein cells. These references and in particular the disclosures therein relating to methods for differentiating embryonic stem cells are incoiporated by reference in their entirety herein. Thus, using known methods and culture medium, one skilled in the art may culture the subject ES cells, including genetically engineered or transgenic ES cells, to obtain desired differentiated cell types, e.g., neural cells, muscle cells, hematopoietic cells, etc.
Pluripotent cells produced by the methods described herein may be used to obtain any desired differentiated cell type. Therapeutic usages of differentiated human cells are unparalleled.
For example, human hematopoietic stem cells may be used in medical treatments requiring bone marrow transplantation. Such procedures are used to treat many diseases, e.g., late stage cancers such as ovarian cancer and leukemia, as well as diseases that compromise the immune system, such as AIDS. Hematopoietic stem cells can be obtained, e.g., by incorporating male or female DNA derived from a male or female cancer or AIDS
patient with an enucleated oocyte, obtaining pluripotent cells as described above, and culturing such cells under conditions which favor differentiation, until hematopoietic stem cells are obtained. Such hematopoietic cells may be used in the treatment of diseases including cancer and AIDS.

[0145] Alternatively, the subject pluripotent cells may be used to treat a patient with a neurological disorder by culturing such cells under differentiation conditions that produce neural cell lines. Specific diseases treatable by transplantation of such human neural cells include, by way of example, Parkinson's disease, Alzlieimer's disease, ALS and cerebral palsy, among others. In the specific case of Parkinson's disease, it has been demonstrated that transplanted fetal brain neural cells make the proper connections with surrounding cells and produce dopainine. This can result in long-term reversal of Parkinson's disease symptoms.
[0146] One object of the subject invention is that it provides an essentially limitless supply of pluripotent, human cells that can be used to produce differentiated cells suitable for autologous transplantation for the oocyte donor. Human embryonic stem cells and their differentiated progeny derived from blastocysts remaining after infertility treatments, or created using NT, will likely be rejected by a recipient's immune system when used in allogenic cell transplantation therapy. Parthenogenically derived stem cells should result in differentiated cells that could alleviate the significant problem associated with current transplantation methods, i.e., rejection of the transplanted tissue which may occur because of host-vs-graft or graft-vs-host rejection relative to the oocyte donor.
Conventionally, rejection is prevented or reduced by the administration of anti-Tejection drugs such as cyclosporin.
However, such drugs have significant adverse side-effects, e.g., immunosuppression, carcinogenic properties, as well as being very expensive. Cells produced by the methods as disclosed should eliminate, or at least greatly reduce, the need for anti-rejection drugs relative to the oocyte donor.

[0147] Another object of the subject invention is that it provides an essentially limitless supply of pluripotent, human cells that can be used to produce differentiated cells suitable for allogenic transplantation to members of the oocyte donor's family. The cells will be immunologically and genetically similar to those of the oocytes donor's direct family members and thus less likely to be rejected by the donor's family members.

[0148] Another object of this method is that parthenogenic activation of mammalian oocytes is a relatively simple procedure when compared to SCNT and results in the creation of stem cells with less cell manipulation.

[0149] Parthenogenic activation of mammalian oocytes has shown to be more efficient in the creation of stem cells than methods requiring manipulation of the oocyte of blastocyst.
[0150] One drawback of SCNT is that subjects with deficient mitochondrial respiratory chain activity present phenotypes with striking similarities to abnormalities commonly encountered in SCNT fetuses and offspring (Hiendleder et al, Repro Fertil Dev (2005) 17(1-2):69-83). Cells normally contain only one type of mitochondrial DNA (mtDNA), termed homoplasmy, however, heteroplasmy does exist, usually as a combination of mutant and wild-type mt DNA molecules or form a combination of wild-type variants (Spikings et al., Hum Repro Update (2006) 12(4):401-415). As heteroplasmy can result in mitochondrial disease, various mechanisms exist to ensure maternal-only transmission.
However, with the increasing use of protocols which bypass normal mechanisms for homoplasmy maintenance (e.g., cytoplasmic transfer (CT) and SCNT), perturbed mitochondrial function may be intrinsic to stem cells derived from these sources.

[0151] In one aspect, as the parthenotes are uniparental, the possibility of heteroplasmy is minimized.

[0152] Other diseases and conditions treatable by cell therapy include, by way of example, spinal cord injuries, multiple sclerosis, muscular dystrophy, diabetes, liver diseases Including acute diseases (viral hepatitis, drug overdoses (acetaminophen) and others), chronic diseases (chronic hepatitis and others (generally leading to cirrhosis)), heritable liver defects (hemophilia B, factor IX deficiency, bulirubin metabolism defects, urea cycle defects, lysosomal storage disease, al-antitrypsin deficiency and others), heart diseases, cartilage replacement, bums, foot ulcers, gastrointestinal diseases, vascular diseases, kidney disease, retinal disease, corneal disease, urinary tract disease, and aging related diseases and conditions.

[0153] This methodology can be used to replace defective genes, e.g., defective immune system genes, cystic fibrosis genes, or to introduce genes which result in the expression of therapeutically beneficial proteins such as growth factors, lymphokines, cytokines, enzymes, etc.

[0154] For example, the gene encoding brain derived growth factor may be introduced into human pluripotent cells produced according to the invention, the cells differentiated into neural cells and the cells transplanted into a Parkinson's patient to retard the loss of neural cells during such disease.

[0155] Also, the subject pluripotent human ES cells, may be used as an in vitro model of differentiation, in particular for the study of genes which are involved in the regulation of early development. Also, differentiated cell tissues and organs produced using the subject ES
cells may be used in drug studies.

[0156] Further, the subject ES cells or differentiated cells derived therefrom may be used as nuclear donors for the production of other ES cells and cell colonies.

[0157] Still further, pluripotent cells obtained according to the present disclosure may be used to identify proteins and genes that are involved in embryogenesis. This can be effected, e.g., by differential expression, i.e., by comparing mRNAs that are expressed in pluripotent cells provided according to the invention to mRNAs that are expressed as these cells differentiate into different cell types, e.g., neural cells, myocardiocytes, other muscle cells, skin cells, etc. Thereby, it may be possible to determine what genes are involved in differentiation of specific cell types.

[0158] Further, ES cells and/or their differentiated progeny that have specific genetic defects, such as the genetic defect that leads to Duchene's Muscular Dystrophy, may be used as models to study the specific disease associated with the genetic defect.

[0159] Also, it is another object of the present disclosure to expose pluripotent cell lines produced according to the described methods to cocktails of different growth factors, at different concentrations and under different cell culture conditions such as cultured on different cell matrices or under different partial pressures of gases so as to identify conditions that induce the production and proliferation of desired differentiated cell types.

[0160] In one embodiment, a syntlietic cornea is disclosed which is produced in vitro, in the absence of a mechanical support for control of differentiation and/or proliferation (i.e., the absence of 3-D scaffolding). In one aspect, a synthetic cornea is disclosed, including, but not limited to, a cornea that is terminally differentiated in vitro.

[0161] In another embodiment, the cornea is produced from parthenogenetically activated lluman oocytes, where stein cells derivitized from the partlienogentically activated oocytes are artificially manipulated to produce the cornea.

[0162] In one aspect, the synthetic cornea is produced including culturing the isolated stem cells from parthenogenetically activated oocytes in media comprising serum replacement (M/SR), plasmonate, and at least one mitogen that activates the gp pathway and/or MAP kinase pathway on a fibroblast feeder layer treated with a DNA
inhibitor, culturing the mitogen treated cells in M/SR comprising plasmonate (M/SRP), without added mitogens, to near confluence, where 1/2 volume of the M/SRP is replaced with M/SR periodically until the near confluent cells develop pigmentation and a domed appearance, and transferring the pigmented/domed cells in M/SR to a gelatin coated substrate, where 1/2 volume of the M/SR is replaced with M/SR periodically until a floating cell mass develops, where the floating cell mass is the synthetic cornea. In a related aspect, the M/SR includes KO Hi glucose DMEM, streptomycin, non-essential amino acids, Glutamax-I, (3-mecaptoethanol, and Serum Replacement. In another related aspect, M/SRP
comprises the components of M1SR and plasmonate.

[0163] The following examples are intended to illustrate but not limit the invention.

Production of Human Parthenolzenic Embryogenic Stem Cells [0164] Materials and Metliods [0165] Donors voluntarily donated eggs and blood (for DNA analysis) with no financial paynient. Donors signed comprehensive informed consent docunients and were informed that all donated materials were to be used for research and not for reproductive purposes.
Before ovarian stimulation, oocyte donors underwent medical examination for suitability according to FDA eligibility determination guidelines for donors of human cells, tissues, and cellular and tissue-based products (Food and Drug Administration. (Draft) Guidance for Industry: Eligibility Determination for Donors of Human Cells, Tissues, and Cellular and Tissue Based Products (HCT/Ps) dated May 2004) and order N 67 (02.26.03) of Russian Public Health Ministry.` It included X-ray, blood and urine analysis, and liver function test.
Donors were also screened for syphilis, HIV, HBV, and HCV.

[0166] Oocytes were obtained using standard hormonal stimulation to produce superovulation in the subject donor. Each donor egg underwent ovarian stimulation by FSH
from the 3rd to the 13th days of their menstrual cycle. A total of 15001U of FSh was given.
From the 10t1i to the 14th day of the donor's menstrual cycle, gonadoliberin antagonist Orgalutran (Organon, Holland) was injected at 0.25 mg/day. From the 12th to the 14th day of the donor's menstrual cycle a daily injection of 751U FSH + 75ItJ LH
(Menopur, Ferring GmbH, Germany( was given, If an ultrasound examination displayed follicles between 18 and 20mm in diameter, a single 80001TJ dose of hGC (Choragon, Feiring GmbH, Germany) was administered on the 14th day of the donor's menstrual cycle. Trans-vaginal punction was performed 35 hours after hCG injection on approximately the 16th day.
Follicular fluid was collected from the antral follicles of anesthetized donors'by ultrasound-guided needle aspiration into sterile tubes.

[0167] Cumulus oocyte complexes (COCs) were picked fiom the follicular fluid, washed in Flushing Medium (MediCult) and then incubated in Universal IVF medium (MediCult, see Table 1) with a Liquid Paraffin (MediCult) overlay for 2 hours in a 20% 02, 5%
C02, at 37 C
humidified atmosphere.

Table 1. IVF media.
COMPOSITION
Calcium Chloride EDTA
Glucose Human Serum Albumin Magnesium Sulfate Penicillin G
Potassium Chloride Potassium di-Hydrogen Phosphate Sodium Bicarbonate Sodium Chloride Sodium Lactate Sodium Pyruvate Water [0168] Before activation, cumulus-oocyte complexes (COCs) were treated with SynVitro Hyadase (MediCult) to remove cumulus cells followed by incubation in Universal IVF
medium with a paraffin overlay for 30 minutes.

[0169] From this point onward, the culture of oocytes and embryos was performed in a humidified atmosphere at 37 C using O2-reduced gas mixture (90% N2 + 5% 02 +
5% C02), with the exception of the ionomycin treatment. The oocytes were activated by incubation in M ionomycin for 5 minutes in a CO2 incubator at 37 C in a gas environment of 20% 02, 5% CO2, followed by culture with 1 mM 6-dimethylaminopurine (DMAP) for 4 hours in IVF
medium, paraffin overlay, in a gas environment of 90% N2, 5% 02, and 5%COZ at 37 C.
Activation and cultivation were carried out in 4-well plates (Nunclon, A/S, Denmark) in 500 l of medium overlaid with liquid paraffin oil (MediCult, A/S, Denmark).

[0170] Activated oocytes were cultivated in IVF medium in a gas environment comprising 5% 02, 5% C02, and 90% N2, and embryos generated from the activated oocytes were cultured in the same gas mixture.

[0171] Activated oocytes were allowed to incubate in IVF under the above conditions until fully expanded blastocysts containing an inner cell mass (ICM) at a Blastocyst Scoring Modification of 1AA or 2AA (Shady Grove Fertility Center, Rockville, MD, and Georgia Reproductive Specialists, Atlanta, GA) was observed.

[0172] The zona pellucida was removed by 0.5% pronase (Sigma, St. Louis) treatinent.
The ICM from blastocysts was isolated by immuno-surgery where the blastocysts were incubated with horse antiseram to human spleen cells followed by exposure to guinea pig complement. Trophoectodem cells were removed from the ICM by gently pipetting the treated blastocysts.

[0173] For the derivation of phESC from whole blastocysts, the blastocysts were placed on a feeder layer in medium designed for culture of phESC (i.e., VitroHES
(Vitrolife) supplemented with ,4ng/ml hrbFGF, 5ng/ml hrLIF and 10% human umbilical cord blood serum). When blastocysts attached and trophoplast cells spread, the ICM became visible.
Through three to four days of additional culture, the ICM was isolated through mechanical slicing of the ICM from the trophoectoderm outgrowth using a finely drawn glass pipette.
Further, the IMC cells were cultured on a feeder cell layer of mitotically inactivated post natal human dermal fibroblasts, in VITROHESTM media (e.g., DMEM/high glucose medium, VitroLife, Sweden) supplemented with 10% human umbilical cord blood serum, 5 ng/ml human recombinant LIF (Chemicon Int'l, Inc., Temecula, CA), 4 ng/ml recombinant human FGF (Chemicon Int'l, Inc., Temecula, CA) and penicillin-streptomycin (100U/100 g) in a 96-well plate in 5% CO2 and 20% 02 at 37 C. This gas mixture was used to culture stem cells. Human fibroblast cultures were made using non-animal materials.
Inactivation of fibroblasts was carried out using 10 g/ml mitomycin C (Sigma, St. Louis, MO) for 3 hours.
[01741 In a separate method, immuno-surgery was performed by incubating blastocysts with horse antiserum to human spleen cells followed by exposure to rabbit complement. The trophectoderm cells were removed from the ICM through gentle pipetting of the treated blastocyts. Furtlier culturing of the isolated ICMs was performed on a feeder layer of neonatal human skin fibroblasts (HSF) obtained from a genetically unrelated individual (with parental consent) derived using medium containing human umbilical cord blood serum. The HSF feeder layer was mitotically inactivated using mitomycin C.

[0175] The medium for the culture of HSF consisted of 90% DMEM (high glucose, with L-glutamaine (Invitrogen), 10% human umbilical cord blood seruin and penicillin-streptomycin (100U/100mg) Invitrogen).

[0176] For the culture of ICM and phESC, VitroHES (Vitrolife) supplemented with 4ng/ml hrbFGF, 5ng/ml hrLIF and 10% human umbilical cord blood serum was used.
The ICM was mechanically plated on a fresh feeder layer and cultured for three to four days. The first colony was mechanically cut and replated after five days of culture. All subsequent passages were made after five to six days in culture. For early passages, colonies were mechanically divided into clumps and replated. Further passing of phESC was performed with collagenase IV treatment and mechanical dissociation. The propagation of phESC was performed at 37 C, 5% CO2 in a humidified atmosphere.

[0177] Oocyte activation [0178] From the initial 4 donors, activated oocytes were cultivated in IVF
medium in a gas environment comprising 5% 02, 5% C02, and 90% N2 and followed over five (5) days.
Table 2 shows the progress of maturation of the activated oocytes. Each oocyte was separated in a 4-well plate.

Table 2. Cultured Activated Oocytes.*

Day 1 Day 2 Day 3 Day 5 Nl 1 pronucleus (pn), 2 blastomers (bl) equal, 4 bl equal, 1 morula, 1 polar body (pb) fragmentation (fr)-0 /o fr-2% fr-15%
N2 0 pn, 4 bi not equal, 5 bl not equal, 4 bi not equal, 1 pb fr-4% fr-20% fr-40%
N3 1 pn, 2 bi not equal, 6 bl equal, early blastocysts 1 pb fr-0% fr-0%
N4 1 pn, 4 bl equal, 4 bl equal, Fully expanded 1 pb fr-10% fr-20% blastocyst with good ICM 1AA
*Cells were incubated in M1 media (MediCult) on the first day and M2 media (Medicult) on days 2-5. Media was changed everyday. M1 and M2 contain human serum albumin, glucose and derived metabolites, physiological salts, essential amino acids, non-essential amino acids, vitamins, nucleotides, sodium bicarbonate, streptomycin (40 mg/1), penicillin (40.000 IU/ 1) and phenol red.

[0179] Inner cell masses were isolated from N4 and transferred to human fibroblast feeder cells as outlined above. N1 and N2 degenerated on Day 6. Further, on Day 6, N3 produced fully expanded blastocyst with ICM 2AB. N3 was then transferred to human fibroblast feeder cells on Day 6. ICM from N4 was unchanged. N3 was used to isolate stem cells.
[0180] ICM cells were cultivated in NitroHES medium in a gas environment comprising 5% CO2 and 95% N2 and followed over forty-five (45) days. Table 2a shows the progress of N3 ICM cell cultivation.

Table 2a. Progress of N3-ICM Cultivation.*

Day 3 ICM transplanted on fresh feeder cells.
Day 8 Colony of cells divided mechanically into 6 pieces and cultivated in 3 wells of a 96-well plate-1 st passage.
Day 14 From five (5) colonies of 1 st passage, cells were mechanically divided, and 20 colonies of a 2nd passage were cultivated in 3 wells of a 24-well plate.
Day 20 Cells were plated in 35 mm dish-3rd passage.
Day 24 Five (5) 35 mm dishes were seeded with cells-4th passage. One dish was divided chemically with 5% pronase (Sigma) at room temperature.
Day 30 Twenty-five (25) 35 mm were seeded with cells-5th** passage.
Day 34 6th** cell passage.
Day 35 11 ampules were frozen from the 6th passage.
Day 37 7th** cell passage.
Day 44 12 ampules were frozen from the 7th passage.
Day 45 8th cell passage.
*Cells were grown on M2 media (MediaCult).
** These passages were made with pronase digestion.
[0181] Stem cell isolation.

[0182] From the oocyte from 5 donors, the use of MediCult media is followed by a culture under reduced oxygen allowed for the production of 23 blastocysts on the fifth or sixth day of culture. Eleven of the blastocysts had visible ICMs (Table 3).

Table 3. Generation of parthenotes and parthenolZenetic embryonic stem cell lines.
Donor Oocytes Oocytes Normally Parthenotes Blastocysts derived Lines Number harvested donated activated created With Without generated oocytes ICM visible ICM
1 8 4 4 4 2 - phESC-1 immunosurgery 2 15 8 8 8 3 3 phESC-3 phESC-4 pliESC-5 all from wliole blastocysts 3 27 14 121 112 3 2 phESC-6 from whole blastocysts 4 22 11 103 10 2 3 phESG7 from whole blastocysts 20 94 7 7 1 4 No cell line generated 1-two oocytes were not activated; '"- one oocyte degenerated after activation;
3- one oocyte was not activated; 4-two oocytes were at metaphase stage I and were discarded.

[0183] These results indicate an approximate 57.5% success rate in the formation of blastocysts from parthenogenetically activated oocytes.

[0184] Immunohistochemical staining [0185] For immunostaining, hES cell colonies and phESC cells on feeder layers were seeded onto micro cover glass, washed twice with PBS and fixed with 100%
methanol for 5 minutes at -20 C. Cells were washed twice with PBS + 0.05% Tween-20 and permeabilized with PBS + 0.1% Triton X-100 for 10 minutes at room temperature. After cell washing, non-specific binding was blocked by incubation with blocking solution (PBS +
0.05%
Tween-20 + four percent goat serum plus three percent human umbilical cord blood serum) for 30 minutes at room temperature (RT). Monoclonal antibodies were diluted in blocking solution and used for one hour at RT: SSEA-1 (MAB4301) (1:30), SSEA-3 (MAB4303) (1:10); SSEA-4 (MAB4304) (1:50), OCT-4 (MAB4305) (1:30), TRA-1-60 (MAB4360) (1:50), and TRA-1-81 (MAB4381) (1:50) from C1lemicon. After the cells were washed, secondary antibodies Alexa Fluor 546 (orange-fluorescent) and 488 (green-fluorescent) (Molecular Probes, Invitrogen) were diluted 1:1000 in PBS + 0.05% Tween-20 and applied for one hour at RT. Cells were washed and nuclei were stained with DAPI
(Sigma) 0.1 g/ml in PBS + 0.05% Tween-20 during ten minutes at RT. Cells were washed and mounted on slides with Mowiol (Calbiochern). Fluorescence images were visualized with a fluorescence microscope.

[0186] For the detection of mesodermal markers in three week old embryoid bodies or in contractile embryoid bodies, monoclonal mouse anti-desmina antibody anti-human alpha actinin antibody (Chemicon) as the muscle specific markers, and anti-human 1 antibody (R&D Systems), antihuman VE Cadherin (DC144) antibody (R&D Systems) as the endothelial markers were used.

[0187] For detection of the endodermal markers in embryoid bodies, monoclonal mouse anti-human alpha-fetoprotein antibody (R&D Systems) was used.

[0188] Alkaline phosphatase and telomerase activity [0189] Alkaline phosphatase and telomerase activity were performed according to the manufacturer's specifications with AP kit and TRAPEZE Kit (Chemicon).

[0190] Karyotyping [0191] To analyse the karyotype, hES cells were treated with 10 g/ml Demecolcine (Sigma) for two hours, harvested with 0.05% trypsin/EDTA (Invitrogen) and centrifuged at 700 x rpm for three minutes. The pellet was resuspended in 5 ml of 0.56% KCI, and incubated for 15 minutes at RT. After repeated centrifugation, the supematant was removed and cells were resuspended and fixed with 5 ml of an ice cold mixture of methanol/acetic acid (3:1) for five minutes at +4 C. The fixation of the cells was repeated twice, after that the cell suspension was placed onto microscope slides and the preparations were stained with Giemsa Modified Stain (Signia). Metaphases from cells prepared in this manner were analyzed by a standard G-banding metliod. Quantity of 5/1000 metaphase spreads were revealed and 63 metaphases were analyzed.

[0192] Embryoid body formation [0193] hES and phESC cell colonies were mechanically divided into clumps and placed in wells of a 24 well plate precoated with 1.5% agarose (Sigina) in medium containing 85%

Knockout DMEM, 15% human umbilical cord blood serum, 1 x MEM NEAA, 1 mM
Glutamax, 0.055 mM [3-mercaptoethanol, penicillin-streptomycin (50 U/50 mg), 4 ng/ml hrbFGF (all from Invitrogen, except serum). Human EBs were cultured for 14 days in suspension culture and placed on a culture dish to give outgrowth or cultivated in suspension for an additional week.

[0194] Neural differentiation was induced by the cultivation of two week old embryoid bodies attached to a culture dish surface over a period of a week in differentiation medium:
DMEM/F12, B27, 2 mM Glutamax, penicillin-streptomycin (100U/100 g) and 20 ng/ml hrbFGF (all from Invitrogen). Some embryoid bodies gave rise to differentiated cells with neural morphology, others were dissected and additionally cultured to produce neurospheres.
[0195] Rhythmically beating embryoid bodies appeared spontaneously following five days of culture after plating on an adllesive surface in the salne medium as was used for embryoid body generation.

[0196] Cornea formation [0197] hES were grown in Growth Medium with mitogens, LIF and bFGF (on a >40%
confluent mitomycin C treated human fibroblast feeder layer). Near confluent (i.e., when ES
lose clear colony boarders), culture medium is replaced with Growth Medium without addition of mitogens. Thereafter, 50% of the medium is replaced with EB medium every 2-3 days for a minimum of three weeks. At this time, pigmented cells develop in small balls or large domes and columns in the culture.

[0198] The medium was then removed from the culture and cells were vigorously washed with EB Medium to dislodge the desired cells. The EB Medium wash and harvested cells were then transferred to a separate culture vessel that had been coated with 0.1% gelatin.
After two days, 50% of the medium in the transferred culture was replaced with EB Medium.
Subsequently, 50% of the medium in the transferred culture was replaced every 3-4 days with EB Medium for a minimum of three weeks until small floating cell masses that resemble oil droplets became visible. At this point, care was taken not to disturb the floating cell mass or lens when medium is replaced. Fifty percent of the medium is removed and replaced every 3-4 days with a volume of EB medium sufficient to ensure the growing cornea was completely immersed in medium.

[0199] Growth Medium:
KO Hi Glucose DMEM
500 U/mi streptomycin 1% non-essential amino acids 2 mM Glutamax-I
0.1 mM (3-mercaptoethanol 8% Serum Replacement 8% Plasmonate (Beyer, Res Triangle Park) Mitogens:
lOng/ml LIF
5ng/ml bFGF
[0200] EB Medium=

KO Hi Glucose DMEM
500 U/mi streptomycin 1% non-essential amino acids 2 mM Glutamax-I
0.1 mM (3-mercaptoethanol 13% Serum Replacement [0201] Histological Examination [0202] A specimen (10 mm clear/white translucent tissue sphere) was placed in 70%
ethanol after being fixed in neutral buffered formalin (NBF). The sphere was bisected, and a portion was examined for gross description and a portion was examined by microscopy.
[0203] The specimen was stained with a battery of histological dyes, including mucin stains (e.g., periodic acid-Schiff [PAS]), biogenic amine stains, melanin stains, lipochrome pigment stains, stains for iron and calcium, urate stains, fat stains, connective tissue stains, giemsa stains, microorganism stains (e.g., acid fast bacilli, gomori methenamine silver stain, and the like). Subsequent to staining, the specimen was examined under light microscopy.
[0204] HLA typing [0205] Genomic DNA was extracted from donor blood, bES, phESC cells, and human newborn skin fibroblasts (NSFs) with Dynabeads DNA Direct Blood from Dynal (Invitrogen). HLA typing was performed by PCR with allele-specific sequencing primers (PCR-SSP, Protrans) according to the manufacturer's specifications. HLA class I genes (HLA A*,B*,Cw*) were typed with PROTRANS HLA A* B* Cw* defining A*01-A*80, B*07-B*83, Cw*01-Cw*18 regions. HLA class II genes (HLA DRB1*, DRB3*, DRB4*, DRB5*, DQA 1*, DQB1*) were analysed with PROTRANS HLA DRB 1* defining DRB 1*01-DRB 1* 16 (DRl -DRl 8), DRB3*, DRB4*, DRB5* regions and PROTRANS HLA
DQB1* DQA1* definingDQB1*02-DQB1*06 (DQ2-DQ9), DQAl*0101-DQAl*0601 regions. PCR amplification was achieved: at 94 C for 2 min; 10 cycles at 94 C
for 10 see, 65 C for 1 min; 20 cycles at 94 C for 10 see, 61 C for 50 see, 72 C for 30 sec. Amplified products were detected in 2% agarose gel.

[0206] Affimetrix SNP microarray analysis [0207] Genomic DNA was isolated from blood, cumulus cells, phESC and NSF by phenol/chloroform extraction method. These DNA samples obtained from four Caucasian subjects were genotyped with Affimetrix Mapping 50K Hind 240 Array (part of Affimetrix GeneChip Mapping 100K kit). Initially, the dataset contained 57,244 binary SNP
markers.
Since the number of markers is more than would be necessary to identify the equivalency of genomic samples and to study heterozygosity, 15 (chromosomes 1-15) out of 22 autosomal chromosomes were chosen. The shorter seven chromosomes were removed to reduce the chance that no marker, or only a single marker for a given chromosome, is selected during random sampling. The 1,459 markers were analyzed by Relcheck (version 0.67, Copyright (D
2000 Karl W. Broman, Johns Hopkins University, Licensed under GNU General Public License version 2 (June 1991)).

[0208] Genomic imprinting analysis [0209] Total nucleic acid was prepared as described Li et al. (J Biol Chem (2002) 277(16):13518-13527). RNA and DNA were extracted from cells using Tri-reagent (Sigma) or by using an RNA preparation kit from Qiagen (Valencia, CA).

[0210] Nortliern blots containing RNA from the various samples (see FIG. 3) were blotted onto filters by standard methods (See, e.g., Sambrook et al., Molecular Cloning: A
Laboratory Manual, 1989, 2nd ed, Cold Spring Harbor Press). The Northern filter was hybridized with single stranded oligonucleotide probes that hybridized specifically to the mRNAs. The oligonucleotide probes were end-labeled with [y32P]ATP (Amersham Biosciences). The filters were subsequently washed three times for 10 min each with 0.2 X

SSC (1 X SSC = 0.15 M NaCl and 0.015 M sodium citrate) containing 0.1% SDS at and analyzed by PhosphorImager (Molecular Dynamics). The sequences of the oligonucleotide probes were obtained from sequences based on the following Accession Nos.: NP002393 (Pegl_2 and Pegl A; for these genes, human PEG1 is transcribed from two alternative promoters, resulting in the transcription of two isoforms, of which only one (isoform 1_2) is imprinted. Paternal expression isofornl 1 occurs in conjunction with an unmethylated CpG island in exon 1 of the paternal allele, whereas the corresponding CpG
island in the maternal gene (isoform 1 A) is fully methylated. See, e.g., Li et al. (2002), supra); CAG29346 (SNRPN); AF087017 (H19); NR 001564 (inactive X specific transcripts-XIST); and P04406 (GAPDH).

[0211] DNA fingerprinting analysis [0212] Genomic DNA was isolated from blood, hES cells, and NSFs through a phenol/chloroform extraction, digested with Hinfl restriction enzyme (Fermentas) and loaded in a 0.8% agarose gel. Following electrophoresis, denatured DNA was transferred to a nylon membrane (Hybond N, Amersham) by Southern blotting and hybridized with 32P-labeled (CAC) 5 oligonucleotide probe. mData were analysed after membrane exposition on X-ray film (Kodak XAR) using Cronex intensifying screens.

[0213] Monolocus PCR genotyping [0214] 3' Apolipoprotein B hypervariable minisatellite locus (3'ApoB VNTR) [0215] Chromosomallocation: 2p23-p23 [0216] GenBank locus and locus definition: APOB, apolipoprotein B (including Ag(x) antigen) untranslated region [0217] Repeat sequence 5'-3': (TATAATTAAATATT TTATAATTAAAATATT)n (SEQ ID NO: 1) [0218] Allelic ladder size range (bases): 450 + 10 + 2 primer + links [0219] VNTR ladder size range (# of repeats, according to Ludwig et al, 1989):
30, 32, 34, 36,38,40,42,44,46,48,50,52 f0220] Other known alleles (# of repeats): 25, 27, 28, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49,51,53,54,55 [0221] Promega K562 DNA Allele sizes (# of repeats): 36/36 [0222] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 1' Elongation and primer linking 60 C, 2' Extension step: 72 C, 5' Hold step: 4 C, unlimited time The analysis may be done as described in Verbenko et al., Apolipoprotien B 3'-VNTR
polymorphism in Eastern European populations. Eur J Hum Gen (2003) 11(1):444-451. See Table 4.

Table 4. Allele Freguencies for Russian Populations Homozygotes 94 Heterozygotes 333 Allele Allele frequency Number ofAlleles Total samples 427 observed 25 0.001 1 30 0.079 75 32 0.071 68 33 0.001 1 34 0.238 227 35 0.004 4 36 0.393 375 37 0.001 1 38 0.036 36 39 0.001 1 40 0.014 13 42 0.001 1 44 0.042 41 45 0.006 6 46 0.033 31 48 0.067 64 50 0.011 10 52 0.001 1 [0223] D1S80 (pMCT118) hypervariable minisatellite locus (D1S80 VNTR) [0224] Chromosomal location: lp35-36 [0225] GenBaiilc locus and locus definition: Human D1S80 and MCTl 18 gene [0226] Repeat sequence 5'-3': (GAAGACAGACCACAG)n (SEQ ID NO: 2) [0227] Allelic ladder size range (bases): 387-762 [0228] VNTR ladder size range (# of repeats): 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41 [0229] Other known alleles (# of repeats): 13, 14, 15, 38, 39,>41 [0230] Promega K562 DNA Allele sizes (# of repeats): 18/29 [0231] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 60 C, 30"
Elongation 72 C, 45"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0232] The analysis may be done as described in Verbenko et al., Allele frequencies for D1S80 (pMCT1 18) locus in some Eastern European populations. J Forensic Sci (2003) 48(1):207-208. See Table 5.

Table 5. Allele Frequencies for Russian Populations Allele Allele frequency Number of Alleles Homozygotes 15 observed Heterozygotes 44 18 0.280 33 Total samples 59 20 0.017 2 21 0.009 1 22 0.042 5 23 0.017 2 24 0.390 46 25 0.017 2 26 0.025 3 28 0.068 8 29 0.009 1 30 0.034 4 31 0.059 7 33 0.017 2 34 0.008 1 36 0.008 1 [0233] D6S366 [0234] Chromosomal location: 6q21-qter [0235] GenBaiik locus and locus definition: NA
[0236] Allelic ladder size range (bases): 150-162 [0237] STR ladder size range (# of repeats): 12, 13, 15 [0238] Other known alleles (# of repeats): 10, 11, 14, 16, 17 [0239] Promega K562 DNA Allele sizes (# of repeats): 13/14 [0240] PCR protocol:

Thennal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 1' Elongation and primer linking 60 C, 2' Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0241] The analysis may be done as described in Efremov et al., An expert evaluation of molecular genetic individualizing systems based on the HUMvWFII and D6S366 tetranucleotide tandem repeats. Sud Med Ekspert (1998) 41(2):33-36. See Table 6.

Table 6. Allele Freguencies for Russian Populations Allele Allele frequency Number of Alleles observed 10 0.008 3 11 0.059 21 12 0.316 112 13 0.251 89 14 0.085 30 15 0.175 62 16 0.015 7 17 0.011 4 Total samples 177 [0242] D16S539 [0243] Chromosomal location: 16q24-qter [0244] GenBank locus and locus definition: NA
[0245] Repeat sequence 5'-3': (AGAT)n [0246] Allelic ladder size range (bases): 264-304 [0247] STR ladder size range (# of repeats): 5, 8, 9, 10, 11, 12, 13, 14, 15 [0248] Promega K562 DNAOO Allele sizes (# of repeats): 11/12 [0249] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 64 C, 30"
Elongation 72 C, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0250] The analysis has been done as described in GenePrint STR Systems (Silver Stain Detection) Technical Manual No. D004. Proinega Corporation, Madison, WI USA:

2001. See Table 7.

Table 7. Allele Freguencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.000 0 7 0.000 0 8 0.026 11 9 0.107 45 0.079 33 11 0.319 134 12 0.269 113 13 0.167 70 14 0.031 13 0.002 1 Homozygotes 57 Heterozygotes 153 Total samples 210 [0251] D7S820 [0252] Chromosomal location: 7q11.21-22 [0253] GenBank locus and locus definition: NA
[0254] Repeat sequence 5'-3' : (AGAT)n [0255] Allelic ladder size range (bases): 215-247 [0256] VNTR ladder size range (# of repeats): 6, 7, 8, 9, 10, 11, 12, 13, 14 [02571 Promega K562 DNA Allele sizes (# of repeats): 9/11 [0258] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 64 C, 30"
Elongation 72 C, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time The analysis has been done as described in GenePrintQ STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA: 1993-2001.
See Table 8.

Table S. Allele Frepuencies for D7S820 in Different Populations Allele Allele frequency for Number of Allele frequency Number of Caucasian-Americans Alleles observed for Russians Alleles observed 6 0.002 1 0.0012 1 7 0.010 4 0.0087 7 8 0.155 65 0.1928 155 9 0.152 64 0.1480 119 0.295 124 0.2524 203 11 0.195 82 0.2040 164 12 0.121 51 0.1580 127 13 0.057 24 0.0299 24 14 0.012 5 0.0050 4 Homozygotes 43 92 Heterozygotes 167 310 Total samples 210 402 [0259] Human von Willebrand factor gene hypervariable microsatellite locus II
(vWFII) [0260] Chromosomal location: l2p l 3.3-12p l 3.2 [0261] GenBank locus and locus definition: HUMvWFII, Human von Willebrand factor gene [0262] Repeat sequence 5'-3': (ATCT)n/(AGAT)n [0263] Allelic ladder size range (bases): 154-178 [0264] STR ladder size range (# of repeats): 9, 11, 12, 13 [0265] Other lcnown alleles (# of repeats): 8, 10, 14, 15 [0266] Promega K562 DNA Allele sizes (# of repeats): 13/13 [0267] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 1' Elongation and primer linking 60 C, 2' Extension step: 72 C, 5' Hold step: 4 C, unlimited time 102681 The analysis has been done as described in Efreinov et al., An expert evaluation of molecular genetic individualizing systems based on the HUMvWFII and D6S366 tetranucleotide tandeni repeats. Sud Med Ekspert (1998) 41(2):33-36. See Table 9.

Table 9. Allele Frequencies for Russian Populations Allele Allele frequency Number of AIleles observed 9 0.082 37 0.088 40 11 0.392 177 12 0.296 134 13 0.069 31 14 '0.058 26 0.015 7 Total samples 226 [0269] D 13 S317 [0270] Chromosomal location: 13 q22-q31 [0271] GenBanlc locus and locus definition: NA
[0272] Repeat sequence 5'-3': (AGAT)n [0273] Allelic ladder size range (bases): 165-197 [0274] STR ladder size range (# of repeats): 8, 9, 10, 11, 12, 13, 14, 15 [0275] Other known alleles (# of repeats): 7 [0276] Promega K562 DNA Allele sizes (# of repeats): 8/8 [0277] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 64 C, 30"
Elongation 72 C, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0278] The analysis has been done as described in GenePrintQ STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA:

2001. See Table 10.

Table 10. Allele Freguencies for D13S317 in Different Populations Allele Allele frequency for Number of Allele frequency for Number of Caucasian-Americans Alleles observed Russians Alleles observed 7 0.000 0 0 0 8 0.143 60 0.1393 112 9 0.052, 22 0.0883 71 10 0.052 22 0.0684 55 11 0.305 128 0.3706 298 12 0.307 129 0.2040 164 13 0.083 35 0.0871 70 14 0.057 24 0.0423 34 15 0.000 0 0 0 Homozygotes 61 90 Heterozygotes 149 312 Total samples 210 402 [0279] Human vonWillebrand factor gene hypervariable microsatellite locus (vWA) [02801 Chromosomal location: 12p 12pter [0281] GenBank locus and locus definition: HUMVWFA31, Human von Willebrand factor gene [0282] Repeat sequence 5'-3': (AGAT)n [0283] Allelic ladder size range (bases): 139-167 [0284] STR ladder size range (# of repeats): 14, 16, 17, 18 [0285] Other known alleles (# of repeats): 11, 12, 13, 15, 19, 20, 21 [0286] Promega K562 DNA Allele sizes (# of repeats): 16/16 [0287] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 1' Elongation and primer linking 60 C, 2' Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0288] The analysis has been done as described in GenePrint STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA:

2001. See Table 11.

Table 11. Allele Freguencies for HUMVWFA31 in Different Populations Allele Allele frequency for Number of Alleles Allele frequency for Number of Alleles Caucasian-Americans observed Russians observed 13 0.000 0 0.0025 2 14 0.131 56 0.0796 64 15 0.082 35 0.0920 74 16 0.211 90 0.2127 171 17 0.265 113 0.2836 228 18 0.202 86 0.2251 181 19 0.087 37 0.0833 67 20 0.021 9 0.0199 16 21 0.000 0 0.0012 1 Homozygotes 38 70 Heterozygotes 175 332 Total samples 213 402 [0289] Human c-fins proto-oncogene for CSF-1 receptor gene microsatellite locus(CSFIPO) [0290] Chromosomal location: 5q33.3-34 [0291] GenBank locus and locus definition: HUMCSF1PO, Human c-fins proto-oncogene [0292] Repeat sequence 5'-3': (AGAT)n [0293] Allelic ladder size range (bases): 295-327 [0294] STR ladder size range (# of repeats): 7, 8, 9, 10, 11, 12, 13, 14, 15 [0295] Other known alleles (# of repeats): 6 [0296] Promega K562 DNA Allele sizes (# of repeats): 9/10 [0297] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Incubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 64 C, 30"
Elongation 72 C, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0298] The analysis has been done as described in GenePrint STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA:

2001. See Table 12.

Table 12. Allele Freguencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.000 0 7 0.000 0 8 0.002 1 9 0.033 14 0.251 108 11 0.309 133 12 0.330 142 13 0.060 26 14 0.014 6 0.000 0 Homozygotes 47 Heterozygotes 168 Total samples 215 [0299] Human thyroid peroxidase gene microsatellite locus (TPOX) [0300] Chromosomal location: 2p25.1-pter [0301] GenBank locus and locus definition: HUMTPOX, Human thyroid peroxidase gene [0302] Repeat sequence 5'-3': (AATG)n [0303] Allelic ladder size range (bases): 224-252 [0304] STR ladder size razige (# of repeats): 6, 7, 8, 9, 10, 11, 12, 13 [0305] Other known alleles (# of repeats): none [0306] Promega K562 DNA Allele sizes (# of repeats): 8/9 [0307] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia Initial Iiicubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"

Primer linlcing 64 C, 30"
Elongation 72 C, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time [0308] The analysis has been done as described in GenePrint STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA:

2001. See Tab1e 13.

Table 13. Allele Freguencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 6 0.002 1 7 0.000 0 8 0.528 227 9 0.093 40 0.056 24 11 0.284 122 12 0.037 16 13 0.000 0 Homozygotes 76 Heterozygotes 139 Total samples 215 [0309] Human tyrosine hydroxylase gene microsatellite locus (THO1) [0310] Chromosomal location: 5q33.3-34 [0311] GenBank locus and locus definition: HUMTHOl, Human tyrosine hydroxylase gene {0312] Repeat sequence 5'-3': (AATG)n [0313] Allelic ladder size range (bases): 179-203 [0314] STR ladder size range (# of repeats): 5, 6, 7, 8, 9, 10, 11 [0315] Other known alleles (# of repeats): 9.3 [0316] Promega K562 DNA Allele sizes (# of repeats): 9.3/9.3 10317] PCR protocol:

Thermal cycler: DNA Technology Ltd., Russia InitialIncubation: 95 C, 2' Cycling for 30 cycles:
Denaturation 94 C, 45"
Primer linking 64 C, 30"
Elongation 72 C,, 30"
Extension step: 72 C, 5' Hold step: 4 C, unlimited time The analysis has been done as described in GenePrintOO STR Systems (Silver Stain Detection) Technical Manual No. D004. Promega Corporation, Madison, WI USA: 1993-2001.
See Table 14.

Table 14. Allele Freguencies for Caucasian-Americans Allele Allele frequency Number of Alleles observed 5 0.007 3 6 0.237 101 7 0.148 63 8 0.117 50 9 0.155 66 9.3 0.331 141 10 0.005 2 11 0.000 0 Homozygotes 50 Heterozygotes 163 Total samples 213 [0318] Results [0319] The hES cells from this method display many features that are typical for embryonic stem cells: cytoplasmic lipid bodies, small cytoplasmic/nuclear ratio and clearly distinguishable nucleoli. The hES cell colonies display similar morphology to that reported previously for human embryonic stem cells derived after in vitro fertilization. The cells were immunoreactively positive for alkaline phosphatase (Fig tA), octamer-binding transcription factor 4 mRNA (Oct-4) (Fig 1B), stage- specific embryonic antigen 1(SSEA-1) (Fig 1C),stage- specific embryonic antigen 3 (SSEA-3) (Fig 1D), stage-specific embryonic antigen 4 (SSEA-4) (Fig 1E), tumor rejection antigen 1-60 (TRA-1-60) (Fig 1F), tumor rejection antigen 1-81 (TRA-1-81) (Fig 1G), and negative for stage-specific embryonic antigen 1 (SSEA-1) (Fig 1C), (which is positive for mouse embryonic stem cells, but not for human).
Telomerase activity is often correlated with replicative inimortality and is typically expressed in germ cells, cancer cells, and a variety of stem cells, including stem cells, but absent in most somatic cell types. The cells prepared by this method after three months in in vitro proliferation maintained their undifferentiated morphology and displayed high levels of telomerase activity (Fig 2A). The pluripotency of the cells was investigated in vitro by embryoid body formation (Fig 2B, 2C), G-banded karyotyping shows that cells have normal human 46XX karyotype (Fig 2D).

[0320] DNA fingerprinting analysis was performed on the blood of the oocyte donor, on the ES cells, and on the HNSF feeder cells by Southern blotting and hybridization with a 32P
- labeled (CAC)s oligonucleotide probe (Fig 2E), and monolocus polymerase chain reaction (PCR) with different locuses.

[0321] For monolocus PCR, genotyping revealed identical alleles for all loci (but one, D7S820) between blood (donor) DNA and OL1 DNA. See Table 15.

Table 15. Monolocus PCR 1jenotypin~.

NN Locus definition Chromosomal location hES NSF Blood 1. 3'ApoB 2p24-p23 36/48 36/36 36/48 2. D1S80 1p35-36 18/24 22/31 18/24 3. D6S366 6q21-qter 13/15 17/17 13115 4. D16S359 16q24-qter 8/13 12/13 8/13 5. D7S820 7q11.21-22 11/11 9/10 10/11 6. vWFII 12p13.3-12p13.2 11/13 9/11 11/13 7. D135317 13q22-q31 9/12 11/12 9/12 8. vWA 12p12pter 14/18 17/18 14/18 9. CSFIPO 5q33.3-34 12/12 12/13 12/12 10. TPOX 2p25.1-pter 8/11 8/11 8/11 11. THOI 5q33.3-34 6/6 6/9,3 6/6 [0322] Heterozygosity (heterozygosis) of all heterozygous donor loci (but one, D7S820) was not changed.in hES loci. Homozygosity (homozygosis) of D7S8201ocus in hES
DNA is a result of mutation (insertion of one AGAT monomer in microsatellite repeat) due to slipped-strand mispairing during DNA replication and DNA repair.

[0323] These results are in accordance with those obtained with multilocus DNA
fingerprinting (when substantially identical fingerprint patterns for donor DNA and hES
DNA were found).

[0324] Figure 2E demonstrated heterozygosity of hES cells and their identity with the oocyte donor's blood, and there was not similarity between the hES cells and the feeder cells.
The DNA profile of hES cell line was confirmed by PCR-based haplotype analysis using polymorphic genes within the MHC class I and class II. Total genomic DNA from the oocyte donor blood cells, from hES cells, and feeder HNSFs were genotyped and compared. The data demonstrated that hES cells and cells from donor blood were indistinguishable from each other and therefore should be considered autologous, and both distinguished from DNA
of the feeder cells (Table 16).

Table 16. HLA Typing.

MHC I MHC II
HLA-A HLA-B HLA-C DRBl DQB1 DQA1 pHES-1 A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQA1*O1 A*02 B*35 Cw*0708 DRB1*13 DQB1*03 DQA1*0505 Donor A*01 B*15(63) Cw*04 DRBI*12 DQBI*06 DQAI*O1 A*02 B*35 Cw*0708 D.RB1*13 DQB1*03 DQA1*0505 HNSF A*25 B*15(62) Cw*12 DRB1*04 DQB1*06 DQA1*01 A*32 B*18 Cw*12 DRB1*15 DQB1*03 DQA1*03 [0325] DNA fingerprinting and HLA typing analysis confirmed that the hES cells are heterozygous and contain the whole donor genetic material. These results coincide with data fronl parthenogenetic monkey stem cell lines (Vrana et al., Proc Natl Acad Sci USA (2003) 100(Suppl 1): 11911-11916), and do not coincide with data from parthenogenetic mouse stem cell lines (Lin et al., Stem Cells (2003) 21:153-161), which contains half of the donor genetic material.

[0326] The phESC lines display a morphology expected in hES cells, forming colonies with tightly packed cells, prominent nucleoli and a small cytoplasm to nucleus ratio (FIG. 4).
These cells express traditional hES markers SSEA-3, SSEA-4, TRA-1-60, TRA-1-81, and OCT-4, and do not express SSEA-1, a positive marker for undifferentiated mouse embryonic stem cells (FIG. 4). The cells derived from all lines demonstrate higll levels of alkaline phosphatase and telomerase activity (FIG. 5 and FIG. 6). G-banded karyotyping showed that phESC lines have a normal human 46,XX karyotype, with the exception of the phESC-71ine (FIG. 7). Approximately 91% of cells from the phESC-7 line have a 47,XXX
karyotype and 9% of the cells have a 48,XXX,+6 karyotype. A different degree of X chromosome heteromorphism was observed in the lines; approximately 12% of the phESC-1 and phESC-6 lines; 42% for the phESC-5 line; and 70, 80, and 86 % for the cell lines phESC7, phESC-3, and phESC-4, respectively (FIG. 7).

[0327] Comparative DNA profiling of was performed on all the phESC lines, the donor somatic cells and the feeder cells. These studies used Affimetrix SNP
microarrays (Mapping 50K Hind 240 Arrays) to study chromosome changes and to confirm the genetic similarity of the phESC to the donor's somatic cells. All paired genotype relationships between phESC
lines and their associated donor somatic cells were identified as "full siblings", and all other combinations of pairs were identified as "unrelated". Internal controls identified the paired genotype relationship between split cultures derived from the same phESC line as "monozygotic twins" (Table 17, Database S 1).
Table 17. Database Sl.

Database Si Identif in DNA sam les from hESC and related donors genotype genotype putative inferred IBS IBS IBS LOD LOD LOD LOD
1 2 relationshi relationshi 0 1 12 n t ed MZtwins ar/off fullsibs halfsibs unrelated 1 2 unrelated unrelated 166 662 631 1459 -1503.03 -300.45 -23.15 -8.41 0 3 unrelated unrelated 241 616 602 1459 -1560.65 -434.85 -28.04 -12.22 0 1 4 unrelated unrelated 225 623 611 1459 -1535.94 -400.61 -31.39 -14.39 0 1 5 unrelated unrelated 225 623 611 1459 -1535.94 -400.61 -31.39 -14.39 0 1 6 Unrelated unrelated 243 644 572 1459 -1642.35 -445.78 -31.74 -14.54 0 1 7 unrelated unrelated 252 638 569 1459 -1641.11 -453.5 -29.25 -12.86 0 1 8 unrelated unrelated 250 643 566 1459 -1656.02 -460.02 -32.86 -15.32 0 9 unrelated unrelated 219 657 583 1459 -1605.31 -382.39 -27.37 -11.58 0 unrelated unrelated 158 707 594 1459 -1591.43 -279.21 -26.37 -10..89 0 11 Unrelated unrelated 193 668 598 1459 -1564.71 -354.76 -29.65 -13..31 0 12 unrelated unrelated 166 671 622 1459 -1523.1 -300.5 -30.53 -13..92 0 2 3 unrelated fullsibs 0 282 1177 1459 -440.02 -146.3 0 -167.42 -363.63 2 4 Unrelated unrelated 233 627 599 1459 -1569.66 -423.24 -28.24 -12.91 0 2 5 unrelated unrelated 233 627 599 1459 -1569.66 -423.24 -28.24 -12.91 0 2 6 unrelated unrelated 217 650 592 1459 -1584.75 -388.44 -22.62 -8.53 0 2 7 unrelated unrelated 243 650 566 1459 -1645.94 -437.91 -23.23 -8.72 02 8 unrelated unrelated 225 649 585 1459 -1603.18 -404.41 -27.04 -11.97 0 2 9 unrelated unrelated 210 639 610 1459 -1532.75 -360.46 -24.72 -9.89 0 2 SO unrelated unrelated 144 683 632 1459 -1491.18 -243.56 -16.82 -4.51 0 2 Si unrelated unrelated 172 680 607 1459 -1556.46 -310.03 -23.5 -9.7 0 2 12 unrelated unrelated 176 667 616 1459 -1538.57 -327.95 -27.31 -12..06 0 3 4 unrelated unrelated 336 457 666 1459 -1391.57 -599.92 -30.6 -14.62 0 3 5 unrelated unrelated 336 457 666 1459 -1391.57 -599.92 -30.6 -14.62 0 3 6 Unrelated unrelated 322 482 655 1459 -1415.98 -571.23 -26.08 -11.86 0 3 7 unrelated unrelated 369 442 648 1459 -1432.05 -664.95 -27.39 -11.93 0 3 8 unrelated unrelated 334 483 642 1459 -1449.86 -597.75 -31.68 -15.14 0 3 9 unreiated unrelated 307 493 659 1459 -1395.19 -530.45 -24.56 -10 0 3 10 unrelated unrelated 215 623 621 1459 -1503.92 -364.97 -17.26 -4.43 0 3 11 unrelated unrelated 264 582 613 1459 -1531.91 -473.48 -28.41 -12.,81 0 3 12 unrelated unrelated 254 595 610 1459 -1544.73 -460.57 -29.92 -13..88 0 4 5 unrelated MZ twins 0 0 1459 1459 0 -379.58 -45.47 -401.67 -677.74 4 6 unrelated unrelated 334 475 650 1459 -1436.59 -599.55 -32.73 -15.19 0 4 7 unrelated unrelated 365 439 655 1459 -1418.34 -656.01 -31.6 -14.56 0 4 8 unrelated unrelated 329 486 644 1459 -1450.75 -586.4 -32.06 -14.88 0 4 9 unrelated unrelated 332 466 661 1459 -1395.18 -590.12 -28.69 -12.94 0 4 10 unrelated unrelated 245 606 608 1459 -1542.32 -438.93 -28.75 -12..74 0 4 11 unrelated unrelated 273 569 617 1459 -1530.97 -492.84 -29.03 -12..34 0 4 12 unrelated fullsibs 0 224 1235 1459 -326.17 -162.34 0 -183.44 -393.46 5 6 unrelated unrelated 334 475 650 1459 -1436.59 .-599.55 -32.73 -15.19 0 5 7 unrelated unrelated 365 439 655 1459 -1418.34 -656.01 -31.6 -14.56 0 5 8 unrelated unrelated 329 486 644 1459 -1450.75 -586.4 -32.06 -14.88 0 5 9 unrelated unrelated 332 466 661 1459 -1395.18 -590.12 -28.69 -12.94 5 10 unrelated unrelated 245 606 608 1459 -1542.32 -438.93 -28.75 -12..74 0 5 11 unrelated unrelated 273 569 617 1459 -1530.97 -492.84 -29.03 -12..34 0 5 12 unrelated fullsibs 0 224 1235 1459 -326.17 -162.34 0 -183.44 -393.46 6 7 unrelated full sibs 45 176 1238 1459 -277.78 -217.21 0 -165.72 -390.62 6 8 unrelated full sibs 44 187 1228 1459 -289.8 -201.32 0 -153.75 -365.51 6 9 unrelated unrelated 333 481 645 1459 -1436.5 -595.4 -30.3 -13.77 0 6 10 unrelated unrelated 240 601 618 1459 -1518.17 -425.03 -27.11 -11..53 0 6 11 unrelated fullsibs 0 164 1295 1459 -209.27 -191.66 0 -213.25 -440.56 6 12 unrelated unrelated 234 615 610 1459 -1547.15 -416.14 -30.21 -13..64 0 7 8 unrelated full sibs 38 225 1196 1459 -326.62 -150.16 0 -121.55 -334.09 7 9 unrelated unrelated 359 473 627 1459 -1479.28 -642.41 -30.61 -14.47 0 7 10 unrelated unrelated 252 623 584 1459 -1598.35 -443.81 -28.88 -13.,09 0 7 11 unrelated full sibs 0 230 1229 1459 -318.49 -137.93 0 -159.55 -389.58 7 12 unrelated unrelated 265 583 611 1459 -1539.33 -472.91 -30.55 -13..87 0 8 9 unrelated unrelated 347 480 632 1459 -1472.41 -625.68 -30.93 -14.31 0 8 10 unrelated unrelated 244 614 601 1459 -1561.3 -434 -28.07 -12..37 0 8 11 unrelated fullsibs 0 175 1284 1459 -223.73 -178.56 0 -200.12 -428.04 8 12 unrelated unrelated 236 610 613 1459 -1539.08 -417.14 -29.32 -13..14 0 9 10 unrelated fulisibs 0 228 1231 1459 -315.15 -152.88 0 -174.27 -392.91 9 11 unrelated unreiated 269 M21 623 1459 -1502.69 -479.57 -28.47 -12..55 0 9 12 unrelated unrelated 245 602 1459 -1557.25 -438.53 -26.07 -11..15 0 10 11 unrelated unrelated 187 635 637 1459 -1478.7 -328.06 -25.52 -10.6 0 10 12 unrelated unrelated 181 662 616 1459 -1534.36 -329 -25.2 -10.6 0 DNA samples were numbered as follows: 1-human neonatal slcin fibroblasts; 2-phESC-71ine donor; 3-phESC-71ine; 4-phESC-1 line; 5-phESC-1 line; 6-phESC-3 line; 7-phESC-41ine; 8-phESC-5 line; 9-phESC-6 line; 10-phESC-61ine donor; 11-phESC-3 to phESC-5 lines donor; and 12-phESC-1 line donor.

The result shows that only one pair (sample 4-5), has been identified as monozygotic (MZ) twins. Ten other pairs (samples 2-3, 4-12, 5-12, 6-7, 6-11, 7-8, 7-11, 8-11, 9-10) have been identified as full siblings, and all the other combination of pairs have been identified as unrelated. The IBS
columns in the output display the rnimber of marlcers at which the pair are both typed and share 0, 1, or 2 alleles identical by state (For MZ twins under ideal conditions of no genotyping errors, all markers must be placed under IBS=2). The output does not display P (observed markers I given relationship) directly, but it displays LOD score - loglo {P(observed markers I putative relationship/P(observed marlcers I relationship for which maximum likelihood was obtained and thus the call was made)} as a measure of similarity. The smaller the LOD
score is, the less likely the putative relationship between two sainples it.

[0328] Comparative analysis of 1,459 SNP markers revealed phESC heterozygosity and showed that changes had occurred in the phESC cell genotype in comparison to the related donor somatic cell genotype. Sorlie segments of the somatic cell genome that had formerly been heterozygous became homozygous in the related phESC line genome. This heterozygous to homozygous pattern occurred in 11-15% of the phESC-1, PhESC-3, phESC-4, phESC-5 and phESC-6 lines, and was 19% for the phESC7 line (Database S2).
Moreover, genetic differences were observed between the pIiESC and phESC-5 lines that had been derived from the same oocyte donor (Table 18, Database S2).
Table 18 Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines y L L
'r ~ .~. cC-C C '~" C C
~ ~~c ~ R~ a~"i o a ~ a c o 0 o c a ~ a' b a R ~` U U ~ U U
o. . c c.
SNPA- A A B A A A B B B B
1 1697748 rs10752719 3744122 3.744122 0.436 B B B B B B B B B B
SNP_A- A A A A A A A A A A
1 1743594 rs806104 5977200 5.9772 0.631 B B A B B B B B A A
SNP_A- A A B B B B A A A A
1, 1687843 rs301791 8402638 8.402638 0.274 B B B B B B B B A B
SNP_A- B B A A A A A A A A
1 1647681 rs1474868 11978430 11.97843 0.333 B B A A A A A A A A
SNP_A- A A A A A A A A A A
1 1673737 rs1417144 14211391 14.211391 0.548 A A B B B B A A B B
SNP_A- B B B B B B B B B B
1 1747116 rs860379 18414756 18.414756 0.25 B B B B B B B B B B
SNP_A- A A B B B B A A A A
1 1662223 rs10492997 19514677 19.514677 0.631 A A B B B B B B A A
SNP_A- B A A A A A A A A A
1 1662225 rs559346 28077956 28.077956 0.583 B B B B B B B B A B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines , ' "L' ~ ~ q ^ C
~ =ce R ~ ' ~ .,c~tt e ~ O M , h u a ~ ~ d V '~ C U V ro V V V 7 z s e~'7 e~'6 a~ ~ G "~ G RCs. C ~ tY N
v~ a g ~ a w U C.
SNP_A- A A A B A A A A A A
1 1646469 rs4949455 31783886 31.783886 0.382 A B B B B B B B A A
SNP_A- B B B B B B B B B A
1 1695076 rs6661190 33872782 33.872782 0.274 B B B B B B B B B B
SNP_A- B B B B B B B B B B
1 1679571 rs4653029 34558585 34.558585 0.274 B B B B B B B B B B
SNP_A- A A A A A A A A A A
1 1675060 rs7531479 36798680 36.79868 0.714 A A A A A A A A A A
SNP_A- A A A A B A A A B B
1753902 rs1010805 37858235 37.858235 0.738 A A B A B B A A B B
SNPA- A A A A B A A A B B
1691977 rs6693076 39972196 39.972196 0.441 A A B A B B B B B B
SNP_A- B B A A B A B B B B
1723259 rs407752 40472948 40.472948 0.333 B B B A B B B B B B
SNP_A- A A A A A A A A B B
1 1692103 rs7515340 41055964 41.055964 0.381 B B A A A A A A B B
SNP_A- B B B B B B A A B A
1 1696731 rs4660575 41902429 41.902429 0.429 B B B B B B A A B B
SNP_A- A A A A A A A A A A
1 1701070 rs1408412 42787470 42.78747 0.679 A A A A A A A A A A
SNP_A- A A A A A A A A B A
1 1729559 rs1771551 45552736 45.552736 0.738 A A A A A A A A B B
SNPA- A A A A A A B B B A 1 1670587 rs2245122 47358015 47.358015 0.598 A A A A
A A B B B B
SNP_A- A A B B B B B B B B
1 1711898 rs1875645 50501900 50.5019 0.524 B B B B B B B B B B
SNPA- B B B B B B B B B B
1 1645411 rs625643 54349188 54.349188 0.25 B B B B B B B B B B

1 1718210 r810493206 56531172 56.531172 0.488 A A B B B B B B A B
SNP_A- A A A A B A B B B A
1 1752670 rs1831870 57339224 57.339224 0.524 B B B A B B B B B B
SNP_A- A A A A A A A A B A
1 1669308 rs852766 57998529 57.998529 0.564 A A A A A A A A B B
SNP_A- A A A A A A A A A A
1 1681141 rs1969772 58917123 58.917123 0.738 A A A A A A B B A B
SNP_A- A A A A A A A A A A
1 1690420 rs10489908 61576784 61.576784 0.738 A A A A A A A A A A 11 SNP_A- A
A A A A A B B A A

1 1727043 rs2765249 62441479 62.441479 0.75 A A A A A A B B A B
SNPA- - B B B B B B A A A A
1 1646105 rs3861943 63439667 63.439667 0.405 B B B B B B B B A B
SNP_A- B B B B B B A A B A
1 1654674 j rs592298 64000081 64.000081 0.25 B B B B B B B B B B

Database S2 Heterozygosity ot p1iESC (Abbreviated as "pC") Lines ~ y ~ C C C ~ O O
~ ~ C C G ~ `n '-1 o M eF ~ ~ ~O G t i C
q, R
rAG

SNP_A- A A B B B B B B A A
1 1708628 rs746633 64503887 64.503887 0.692 A A B B B B B B A B
SNP A B B B B B B B B B A
1 1713897 rs1171279 65700514 65.700514 0.345 B B B B B B B B B B
SNP A- A A A B A A A A A A
1 1717648 rs1280310 66928844 66.928844 0.655 B B B B A'B B B A B
SNP A- A A A A B A A A B B
1 1712508 rs1408956 67849084 67.849084 0.536 B B B A B B B B B B
SNP_A- A A A A A A A A A A
1 1688631 rs1413953 70834525 70.834525 0.571 B B A A A A B B A B
SNP_A- A A A A A A A A B B
1 1720162 rs1338655 73569634 73.569634 0.429 B B A A A A A A B B
SNP_A- A A B B B B B B A A
1 1697494 rs10493539 74427598 74.427598 0.25 A A B B B B B B A B
SNP_A- B B B B B B A A B A
I 1649261 rs277355 75002805 75.002805 0.345 B B B B B B B B B B
SNP_A- A A A B A A A A B B
1 1744876 rs1250876 75905253 75.905253 0.345 B B B B A B B B B B
SNP A- A A A A A A A A A A
1 1739854 rs3928852 76926021 76.926021 0.607 A A A A A A B B A A
SNP A- A A A A A A A A A A
1 1687047 rs10493596 77438262 77.438262 0.718 A A A A A A B B A A
SNP_A- B B A A A A A A B B
1 1732619 rs1248480 79071260 79.07126 0.357 B B A A A A B B B B
SNP_A- A A A B A A B B A A
1 1664985 rs2127436 79792017 79.792017 0.488 B B B B A B B B A B
SNP A- A A A B A A A A A A
1 1644541 rs2389016 80511350 80.51135 0.738 A A B B A B B B A B
SNP A- A A A A A A A A A A
1 1645927 rs10518660 82094088 82A94088 0.738 B B A A A A A A A A
SNP_A- B B A A A A A A A A
1 1693780 rs6598991 82697988 82.697988 0.524 B B B A B B A A A A
SNP_A- B B A A A A B B B A
1 1674234 rs2268667 85505767 85.505767 0.321 B B B A B B B B B B
SNP A- A A A A A A A A B A
1 1752288 rs306322 88673430 88.67343 0.726 A A A A A A B B B B
SNP_A- A A B B B B A A B A
1 1736094 rs1831298 90211840 90.21184 0.262 B B B B B B A A B B
SNP A- B B A B A A B B B B
1 1711115 rs4233429 90811924 90.811924 0.25 B B B B B B B B B B
SNP_A- A A A A A A A A B B
1 1714794 rs665484 91375951 91.375951 0.512 B B A A A A A A B B
SNP_A- B B A B A A A A B A
1 1675488 rs490800 92304926 92.304926 0.369 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines Q~, ' a R~ d ~ n ~ Vo. a a o c o n r U=4 SNP A- A A A A A A B B B B
1 1656572 rs6703310 93500761 93.500761 0.393 B B B A B B B B B B
SNP A- B B B B B B A A A A
1 1755223 rs223237 96276742 96.276742 0.476 B B B B B B A A A A
SNP A- A A A A A A A A A A
1 1691383 rs1911500 98291841 98.291841 0.738 A A A A A A B B A B
SNP A- A A A A A A A A A A
1 1725993 rs1838587 101983453 101.983453 0.525 A A B A B B B B A B
SNP A- B B A A A A A A B B
1 1689489 rs7521799 102944538 102.944538 0.619 B B B A B B A B B B
SNP A- A A A A A A B B A A
1 1684273 rs1576516 104210964 104.210964 0.452 B B A A A A B B A A
SNP A- B B B B B B A A B B
1 1733369 rs1919894 107240697 107.240697 0.381 B B B B B B A B B B
SNP A- A A A A A A A A B A
1 1715038 rs10494081 108114145 108.114145 0.667 A A A A A A A B B B
SNP A- B B A B A A B B B A
1 1699288 rs2026485 108978565 108.978565 0.333 B B B B B B B B B B
SNP A- A A A B A A A A A A
1 1750726 rs6682717 110527665 110.527665 0.441 A A B B B B A B A A
SNP A- A A B B B B B B A A
1 1648811 rs694180 111438255 111.438255 0.464 B B B B B B B B A B
SNP A- A A A A A A B A B B
1 1753842 rs1936061 112187978 112.187978 0.595 A A A A A A B B B B
SNP A- B B B B B B A A B B
1 1689065 rs2359417 113685242 113.685242 0.452 B B B B B B A B B B
SNP A- B B B B B B B B B B
1 1746401 rs3767824 118152606 118.152606 0.429 B B B B B B B B B B
SNP A- B A B B B B B B B B
1 1688653 rs1766803 119095860 119.09586 0.366 B B B B B B B B B B
SNP A- A A B B B A B B B A
1 1708513 rs477992 119969618 119.969618 0.286 A B B B B B B B B B
SNP A- A A A A A A B A A A
1 1701244 rs10494240 143040559 143.040559 0.321 B B A A A A B B A B
SNP A- B B B B B B A A B B
1 1706430 rs10494267 148366991 148.366991 0.321 B B B B B B B B B B
SNP A- B B B B B A A A A A
1 1680305 rs2879490 149760236 149.760236 0.381 B B B B B B A A A A
SNP A- B B A A A A A A A A
1 1723421 rs10494303 150706096 150.706096 0.571 B B A A A B B B A A
SNP A- A A A A A A A A A A
1 1681003 rs884664 151516798 151.516798 0.702 A A A A A B A A A A
SNP A- A A A A A A B B B A
1 1667931 rs10494315 154072954 154.072954 0.655 B B A A A B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L I..
, p ~ ,L. K cC^a q ~ C C
F~ Q z c. o. .ci d N ,.. ~ m t ~n ~ ~o b c~ ,oo n o a c n n o r ~ ~ s a F~L Cj U 3 V U

SNP A- B B B B B B B B B A
1 1647211 rs919477 155585918 155.585918 0.25 B B B B B B B B B B
SNP A- B B B B B B B B B B
1 1662451 rs1149392 157241261 157.241261 0.286 B B B B B B B B B B
SNP A- A A B B B B A A A A
1 1695012 rs6683968 158923070 158.92307 0.571 A A B B B B A A A A
SNP A- A A A A A A A A A A
1 1716490 rs869513 159832184 159.832184 0.607 A A A A A A A A A A
SNP A- A A A A A A B B B B
1 1727494 rs4656422 161688624 161.688624 0.25 B B A A B B B B B B
SNP A- A A B B B B A A B B
1 1646555 rs4657482 162563307 162.563307 0.405 B B B B B B B B B B
SNP A- A A A A A A A A A A
1 1743854 rs2093658 164086850 164.08685 0.317 A A A A B B A A A A
SNP A- B B B B B B A A A A
1 1681011 rs1358948 165590931 165.590931 0.31 B B B B B B B B A B
SNP A- B B B B B B B B B A
1 1751990 rs2205848 166407951 166.407951 0.31 B B B B B B B B B B
SNP A- A A B B B B B B B B
1 1736240 rs10494487 167046739 167.046739 0.298 B B B B B B B B B B
SNP A- A A A A A A A A B A
1 1674510 rs3753538 168481215 168.481215 0.691 A A A A A A A A B B
SNP A- A A B B B B A A B B
1 1719434 rs10489280 169204277 169.204277 0.488 A A B B B B A A B B
SNP_A- A A A A A A A A A A
1 1753950 rs989423 171514180 171.51418 0.75 A A A A A A A A A A
SNP A- A A B B A A A A A A
1 1722081 rs1359587 172487558 172.487558 0.691 B B B B B B B B A B
SNP A- A A A A A A A A B B
1 1694706 rs2861746 173128066 173.128066 0.452 B B A A A A B B B B
SNP A- B B B B B B B B A A
1 1733825 rs2493119 175995013 175.995013 0.333 B B B B B B B B A B
SNP A- A A A A A A A A A A
1 1671505 rs1281294 178629596 178.629596 0.714 A A A A A A A A A A
SNP A- A A A B A A A A B B
1 1694118 rs2274984 179839103 179.839103 0.524 B B B B B B A A B B
SNP A- B B B B B B B B B A
1 1644471 rs1184639 180355276 180.355276 0.357 B B B B B B B B B B
SNP A- A A B B B B A A B B
1 1711261 rs2840274 180942462 180.942462 0.429 A A B B B B A B B B
SNP A- A A A A A A B A B A
1 1706912 rs170885 181673406 181.673406 0.512 B B A A A A B B B B
SNP A- A A A B A A A A A A
1 1703470 rs10489701 182242226 182.242226 0.595 A A B B B B A A A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines Fl Q z G c. .C Q ~ =-~ . ~o m ~t ~n 3 ~o ,o~ t ~ ,b z ~ ta a~ u ~-' Q. u U U U U U U
C4 v a L o a a a a o c c c ~
~ b a o Ft Cj U : U U
a a a S11P p,- B B A A A A A A B A
1 1696277 rs10489756 182835425 182.835425 0.262 B B B A B B A A B B
SNP_A- A A B B B B B B A A
1 1744486 rs726706 183604111 183.604111 0.429 B B B B B B B B A B
SNP A- A A A A A A A A A A
1 1693312 rs7543266 184360480 184.36048 0.595 A A A A A A A A A A
SNP'A- B B B B B B B B A A
1 1739170 rs6665263 185050414 185.050414 0.452 B B B B B B B B A A
SNP_A- A A B B B B B B B A
1 1726093 rs10494626 186275233 186.275233 0.464 A A B B B BB B B B
SNP_A- A A A A A A A A A A
1 1658415 rs815160 186988747 186.988747 0.427 B B A A A A A A A A
SNP_A- A A A B A A B B B B
1 1666089 rs1563191 187849406 187.849406 0.333 B B B B B B B B B B
SNP_A- B B B B B B B B B B
1 1753798 rs1338034 188358939 188.358939 0.393 B B B B B B B B B B
SNP_A- A A B B B B B A B B
1 1688981 rs4657868 190164348 190.164348 0.524 B B B B B B B B B B
SNP_A- B B B B B B A A B B
1723115 rs10494707 191296870 191.29687 0.357 B B B B B B A B B B
SNP_A- B B B B B B B B A A
1 1651749 rs822456 191826836 191.826836 0.439 B B B B B B B B A B
SNPA- A A B B B B A A B B
1 1642592 rs10494728 192402426 192.402426 0.25 B B B B B B A B B B
SNP_A- A A A A A A B B A A
1 1658925 rs3762271 193802099 193.802099 0.6 B B A A A A B B A B
SNP_A- A A A B A A A A A A
1 1687705 rs1927246 195048356 195.048356 0.702 B B B B B B A A A B
SNP_A- A A A A A A B B B A
1 1725025 rs10494808 196821529 196.821529 0.548 B B A A A A B B B B
SNP_A- B B A A A A A A A A
1665029 rs6667172 197375495 197.375495 0.5 B B A A A A A B A B
SNP_A- A A B B B B B B B B
1 1747494 rs832174 197990176 197.990176 0.25 A A B B B B B B B B
SNPA- A A A A A A A A B A
1 1651207 rs7555556 199822633 199.822633 0.293 B B B B B B A B B B
SNP A- A A A A A A A A A A
1 1714962 rs10494844 200501548 200.501548 0.75 A A A A A A A B A A
SNP A- B B B B B B A A A A
1 1724123 rs10494852 201189443 201.189443 0.655 B B B B B B A B A A
SNPA- A A B B B B B B B B
1 1673439 rs311286 203999303 203.999303 0.286 B B B B B B B B B B
SNP A- B B A A A A B B A A
1 1669116 rs684431 204553812 204.553812 0.381 B B A B A B B B B B

L Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L

~ ~~ b R ce ~ v ~ c *; o c c ~ c. c o ~;
~ .. c a W U c o c SNP_A- A A A A A JA B B A A
1 1650733 rs2358452 208747444 208.747444 0.707 A A A A A A B B A A
SNP_A- A A B B B B B B A A
1 1651975 rs340840 210516282 210.516282 0.393 B B B B B B B B A A
SNP_A- A A A A A A A A A A
1 1683565 rs10494987 211525052 211.525052 0.691 B B A A A A A A A A
SNP_A- A A B A B A A A A A
1750462 rs10495003 212237742 212.237742 0.417 B B B B B B A B A A
SNP_A- B B A A A A B B A A
1 1683969 rs6604634 213109650 213.10965 0.524 B B A A A A B B A A
SNP_A- A A A A A A B B A A
1 1731002 rs10495045 213806233 213.806233 0.714 A A A B A B B B B B
SNP_A- A A A A A A A A A A
1 1677675 rs618171 215537693 215.537693 0.631 B B A A A A A A B B
SNP_A- B B B B B B A A A A
1 1703136 rs10495156 217494419 217.494419 0.298 B B B B B B A A B B
SNP_A- B B B A B A B B B B
1 1711849 rs1338077 218118775 218.118775 0.321 B B B B B B B B B B
SNP_A- A A A A A A B B B B
1755399 rs4481859 219121051 219.121051 0.512 B B A A A A B B B B
SNP_A- A A A A A A A A A A
1739524 rs10495236 221802391 221.802391 0.691 B B A B A B B B B B
SNP_A- A A B A B A A A A A
1 1710164 rs710805 225430849 225.430849 0.429 B B B B B B B B A A
SNP_A- B B A A A A B B B B
1 1688357 rs1998067 226545242 226.545242 0.298 B B A A A A B B B B
SNP_A- A A A A A A A A A A
1 1732138 rs9286801 229119361 229.119361 0.476 A A A A A A A A A A
SNP_A- A A A A A A A A A A
1 1747040 rs1892298 230387334 230.387334 0.714 A A A A A A A B A A
SNP A- A A B A B A A A A A
1 1717898 rs2463190 232711157 232.711157 0.441 B B B B B B A A A A
SNP_A- A A A A A A B A A A
1 1710935 rs819639 233219640 233.21964 0.56 B B A A A A B B A A
SNP_A- A A A A A A B A A A
1 1755297 rs2819774 234214896 234.214896 0.691 A A A A A A B B B B
SNP_A- B B A A A A A A A A
1 1677233 rs6685861 235621137 235.621137 0.357 B B A A A A A B A A
SNP_A- B B B B B B B B A A
1 1679485 rs732160 236262770 236.26277 0.298 B B B B B B B B B B
SNP_A- A A A A A A A A A A
1 1679759 rs1039529 238918670 238.91867 0.619 A A A A A A A A A A
SNP_A- B A A A A A A A A A
1 1664943 rs879725 240732087 240.732087 0.464 B B A A A A A B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
q ^ C
eC c7 ~ ,t y 11 o M <1' V1 "O o h O
~" ~ v wL Cj a n o. -1 n o a ~
~ b aSNP A- B A A B A JA A A A A
I 1724627 rs1093961 241902498 241.902498 0.415 B B B B B B A B B B
SNP A- B B A A A A B A A A
1 1672603 rs3844080 243632874 243.632874 0.655 B B A A A A B B A A
SNP A- B B B B B B A A B B
2 1753456 rs10519439 108913 0.108913 0.274 B B B B B B B B B B
SNP_A- A A B B B B A A B B
2 1746820 rs6759198 2342478 2.342478 0.56 A A B B B B B B B B
SNP A- A A A A A A A A A A
2 1697325 rs2119075 4395806 4.395806 0.607 A A A B B B B B B B
SNP A- B B B B B B B B A A
2 1740868 rs963964 5206872 5.206872 0.321 B B B B B B B B B B
SNP_A- B B B B B B B B B B
2 1677893 rs1429220 5881639 5.881639 0.369 B B B B B B B B B B
SNP A- B B A A A A B B A A
2 1650909 rs6727796 7605796 7.605796 0.512 B B A A A A B B B B
SNP A- B B B B B B A A A A
2 1663651 rs9287698 8437894 8.437894 0.281 B B B B B B B B A A
SNP A- A A A A A A B B B B
2 1647101 rs2271333 9323848 9.323848 0.5 B B A A A A B B B B
SNP A- B B A A A A B A B B
2 1717786 rs2241113 10226344 10.226344 0.31 B B B B B B B B B B
SNP A- B B A A A A B B B B
2 1706150 rs1686426 10899146 10.899146 0.5 B B B B B B B B B B
SNP A- B B A A A A A A A A
2 1676173 rs4669806 12151350 12.15135 0.619 B B A A A A A A B B
SNP A- B B A A A A B B A A
2 1664687 rs625842 12779571 12.779571 0.583 B B A A A A B B B B
SNP A- A A A A A A B B A A
2 1696327 rs7568703 15041402 15.041402 0.571 A A B B B B B B A A
SNP A- B B B B B B B B B B
2 1683239 rs4668968 15835884 15.835884 0.369 B B B B B B B B B B
SNP A- A A A A A A A A A A
2 1677981 rs9306902 16971747 16.971747 0.631 A A A A A A A A A A
SNP A- A A A A A A A A A A
2 1714454 rs10495699 19918971 19.918971 0.56 B B B B A B A B B B
SNP A- A A A A A A B A A A
2 1668860 rs10495705 20662972 20.662972 0.564 A A A A A A B B A A
SNP A- A A B B B B B B A A
2 1693698 rs7594267 23344557 23.344557 0.571 A A B B B B B B A A
SNP A- A A A A A A A A A A
2 1751070 rs1275963 26804398 26.804398 0.643 B B A A A A A A A A
SNP A- A A A A A A B A B B
2 1684619 rs2014701 30210694 30.210694 0.631 A A A A A A B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
'.~m'~j r1 O M V U1 Z ~O o h O
u V V ~ V U
ai ,~ e3 eC L ~ C. C+. G 7 G ~D 4 l ~
.. a c w U n ~ c o SNP_A- B B A A A JA B B A A
2 1648557 rs10490360 32207919 32.207919 0.441 B B A A A A B B B B
SNP_A- A A A A A A A A B B
2 1671421 rs219145 33123165 33.123165 0.634 A A A A A A A A B B
SNP_A- B B B B B B B B B B
2 1696185 rs10495796 34029149 34.029149 0.274 B B B B B B B B B B
SNP A- A A A A A A A A A A
2 1642658 rs2049638 34866446 34.866446 0.738 A A A A A A A B B B
SNP A- A A A A A A A A A A
2 1696029 rs1401242 35923474 35.923474 0.417 B B B B A B A B B B
SNP A- B B B B B B A A B B
2 1748242 rs2161905 36427824 36.427824 0.286 B B B B B B A B B B
SNP A- A A A A A A A A A A
2 1660238 rs975315 38407251 38.407251 0.631 B B A A A A A B A A
SNP A- B B A A B A B B B B
2 1719460 rs9309043 39939220 39.93922 0.643 B B B B B B B B B B
SNP_A- A A A A B A A A B B
2 1714203 rs2059338 41186539 41.186539 0.714 B B B B B B A B B B
SNP A- A A B B B B B B B B
2 1690204 rs10495900 43528810 43.52881 0.369 B B B B B B B B B B
SNP A- B B A A A A A A B B
2 1740164 rs4276071 44121457 44.121457 0.417 B B A A A A B B B B
SNP_A- B B B B B B A A A A
2 1685265 is6708061 44721790 44.72179 0.357 B B B B B B A A B B
SNP A- B B B B B B A A A A
2 1680505 rs6737073 45442330 45.44233 0.286 B B B B B B A A B B
SNP A- A A A A A A A A A A
2 1680749 rs935661 45967008 45.967008 0.56 B B B A B B B B B B
SNPA- A A A A A A A A A A
2 1721531 rs7589621 46494033 46.494033 0.738 B B A A A A A A A A
SNP A- A A A A A A A A A A
2 1734011 rs6544955 47235732 47.235732 0.643 A A A A A A A A A A
SNP A- A A B B B B B B B B
2 1699364 rs10495972 49412546 49.412546 0.298 B B B B B B B B B B
SNP_A- A A A A A A B B B B
2 1696353 rs10495987 50064931 50.064931 0.286 B B A A A A B B B B
SNP_A- A A A A A A A A A A
2 1646009 rs10490176 50979585 50.979585 0.738 B B A A A A A A A A
SNP A- A A B B B B B B A A
2 1676509 rs1160297 53148971 53.148971 0.321 B B B B B B B B B B
SNP A- B B A A A A B B A A
2 1742892 rs843622 54460133 54.460133 0.524 B B A A A A B B A A
SNP A- A A B B B B A A A A
2 1704006 rs5008666 59390639 59.390639 0.65 A A B B B B A A A B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines .^
et Ifi ~ ~O O l~ O
~ O' O. R T7 7 O+ R. R. b c h ~ ~ c c f~ R U CJ U
V o a c.
SNP A- A A B B B B A A A A
2 1673301 rs1517401 63452358 63.452358 0.738 A A B B B B B B A A
SNP_A- B B B B B B B B B B
2 1711471 is2581047 64219699 64.219699 0.286 B B B B B B B B B B
SNP_A- B B A A A A A A A A
2 1652253 rs2971828 66466238 66,466238 0.667 B B A A A A A A A A
SNP_A- A A A A A A B B A A
2 1722279 rs9309400 67746695 67.746695 0.738 B B A A A A B B A A
SNP_A- B B B B B B B B A A
2 1656216 rs10496165 68531740 68.53174 0.333 B B B B B.B B B A B
SNP_A- B B A A A A B B B B
2 1703772 rs2312209 69633766 69.633766 0.524 B B A A B B B B B B
SNP_A- A A A A A A A A A A
2 1753748 rs10489986 70719802 70.719802 0.75 A A A A A A B B A A
SNP A- A A B B B B A A B B
2 1723065 rs6724782 73591645 73.591645 0.286 A B B B B B B B B B
SNP_A- B B A A A A A A B B
2 1665193 rs730148 76269470 76.26947 0.408 B B A A B B A A B B
SNP_A- B B A A A A A A B B
2 1718918 rs 1446707 77141310 77.14131 0.429 B B A A A A A A B B
SNP_A- A A B B B B A A A A
2 1749208 rs4852483 79513076 79.513076 0.75 A B B B B B A A A A
SNP A- B B A A A A B B B B
2 1745171 rs216616 80715814 80.715814 0.298 B B A A A A B B B B
SNP_A- B B B B B A A A B A
2 1750234 rs9309572 81381197 81.381197 0.321 B B B B B B A A B B
SNPA- A A B B B B B B A A
2 1728812 rs7577293 85846940 85.84694 0.274 A B B B B B B B A B
SNP_A- A A A A A A A A A A
2 1676217 rs9308826 99738211 99.738211 0.738 A A A A A A A A A A
SNP_A- A A A A A A A A B A
2 1655416 rs9308849 101983905 101.983905 0.714 A A A A A A A B B B
SNP A- A A B B B A B B B B
2 1655538 rs956966 103046093 103.046093 0.512 A A B B B B B B B B
SNP_A- A A A A A A A A A A
2 1690274 rs1869070 106074094 106.074094 0.714 A A A A A A B B B B
SNP_A- A A A A A A B B A A
2 1742362 rs1398132 106705516 106.705516 0.607 B B A A A A B B B B
SNP_A- B B A A A A A A A A
2 1654768 rs826690 108705477 108.705477 0.429 B B A A B B B B B B
SNP A- A A A A A A A A A A
2 1709888 rs1469529 109207139 109.207139 0.583 B B A A B B B B A A
SNP_A- B B A A A A A A A A
2 1671489 rs3961919 112959552 112.959552 0.298 B B A A B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ .~". .~". ~ C"'~6 ^ O q C3 c3 ~ Qt y r{ O M 'd' ~l1 ~ ~O O ~ O
U a M r A d v ~ ~ u u u u u' ~ F~y ~ R R ~ ~ R"'i G G G G ~C G r;
~ w V U U U
c. .. a c SNP A- A A A A A A A A A A
2 1720080 rs2166965 114191141 114.191141 0.679 A A A A B B A A A A
SNP_A- A A A A A A A A A A
2 1712138 rs1346762 114988791 114.988791 0.72 A A A A A A A A A A
SNP-A- A A A A A A A A A A
2 1752188 rs9284719 118395025 118.395025 0.595 B B A A A A A A A A
SNP A- A A A A A A B B A A
2 1685413 rs1370380 120731125 120.731125 0.286 B B A A A A B B B B
SNP A- A A A A A A A A A A
2 1721631 rs4848174 122659698 122.659698 0.655 A A A A B BB B A A
SNP_A- A A B B B B B B A A
2 1707304 rs1215318 125809045 125.809045 0.536 A A B B B B B B B B
SNP_A- A A A A A A A A A A
2 1673583 rs548032 127461866 127.461866 0.631 A A A A A A A A B B
SNP_A- A A A A A A A A A A
2 1671177 rs2124432 128900396 128.900396 0.61 B B A A A A A A A A
SNP A- B B A B A A A A B B
2 1676259 rs10496731 135431360 135.43136 0.488 B B B B B B B B B B
SNP A- A A A A A A A A A A
2 1689435 rs10496750 137176540 137.17654 0.667 B B B A B B A A B B
SNP-A- B B B B B B B B B B
2 1695208 rs10490739 137712397 137.712397 0.287 B B B B B B B B B B
SNP_A- A A B B B B A A A A
2 1651715 rs3884566 139082237 139.082237 0.357 B B B B B B B B B B
SNP-A- B B B B B B B B A A
2 1665733 rs3922799 139592638 139.592638 0.476 B B B B B B B B A A
SNP_A- A A A A A A B B B B
2 1713885 rs838042 140153918 140.153918 0.262 A A B A B B B B B B
SNP_A- A A B B B B A A A A
2 1663529 rs1518441 140908218 140.908218 0.286 A A B B B B B B B B
SNP-A- B B A A A A A A B B
2 1643152 rs10496859 141502410 141.50241 0.536 B B A A A A A A B B
SNP_A- B B B B B B B B B B
2 1689866 rs355562 142245134 142.245134 0.321 B B B B B B B B B B
SNP A- A A A B A A A A A A
2 1688373 rs7560400 143121832 143.121832 0.75 A A B B B B B B A A
SNP_A- A A A B A A A A A A
2 1725903 rs1437717 146329325 146.329325 0.571 B B B B B B B B A A
SNP_A- A A A B A A A A A A
2 1729119 rs1528842 148291308 148.291308 0.75 B B B B B B A A A A
SNP A- A A A A A A B B A A
2 1716616 rs6734792 151450390 151.45039 0.738 A A A A A A B B A A
SNP_A- B B A A A A A A A A
2 1645341 rs9287956 151979514 151.979514 0.464 B B A A A A B B B B

Database S2 Heterozygosily of phESC (Abbreviated as "pC") Lines L L L
~ E3 G .¾ r~ N O M !!' N ~O O li O
cn d O p, ti V V V V C>
cn a d cv ea L ~ a e a o a o a r a c ~x U o d a SNP A- B B B B B B A A A A
2 1711079 rs1370502 153235438 153.235438 0.667 B B B B B B A A B B
SNP A A A A A A A B B B B
2 1751360 rs10497129 153977886 153.977886 0.31 B B A A A A B B B B
SNP A- A A A A A A B B A A
2 1682179 rs1469155 155088509 155.088509 0.726 A A A A A A B B B B
SNP A- B B A B A A A A A A
2 1729675 rs6750583 159423695 159.423695 0.738 B B B B A B B B B B
SNP A- A A B B B B A A B B
2 1710753 rs997163 161593412 161.593412 0.366 A A B B B B A A B B
SNP A- B B A B A A A A B B
2 1657420 rs1227921 162517707 162.517707 0.512 B B BB A B B B B B
SNP_A- B B A A B A A A B B
2 1681353 rs1446471 164812395 164.812395 0.345 B B B A B B A A B B
SNP A- A A A A A A A A B A
2 1755647 r810497261 166152395 166.152395 0.702 B B A A A A B B B B
SNP A- A A A A A A A A B A
2 1656096 rs9287874 167411538 167.411538 0.738 A A A A A A B B B B
SNP A- B B B B B B A A B B
2 1673653 rs2278785 168822282 168.822282 0.381 B B B B B B A A B B
SNP A- A A A A A A A A A A
2 1702574 rs830995 169955143 169.955143 0.702 A A A A A A B B A B
SNP A- B B B B B B A A B B
2 1645337 rs961313 170759024 170.759024 0.274 B B B B B B B B B B
SNP A- A A A A A A A A B B
2 1687817 rs731693 171622741 171.622741 0.667 A A A A A A B B B B
SNP A- B B B B B B B B B A
2 1749036 rs4095835 172330518 172.330518 0.429 B B B B B B B B B B
SNP A- B B A B A A A A B B
2 1683223 rs7575189 173840675 173.840675 0.512 B B B B A B B B B B
SNP A- A A A A B A A A B B
2 1743510 rs2119137 174843221 174.843221 0.333 B B B A B B B B B B
SNP A- A A A B A A A A A A
2 1673703 rs1993385 175563974 175.563974 0.476 A A B B A B B B A B
SNP A- B B A A A A A A A A
2 1730586 rs9287989 176543248 176.543248 0.643 B B A A A A A A A B
SNP A- A A B B B B A A A A
2 1676261 rs6722762 177140660 177.14066 0.345 B B B B B B B B A B
SNP_A- A A A B A A A A A A
2 1668972 rs10497467 177733918 177.733918 0.75 A A B B A B B B A A
SNP_A- A A B B B B A A A A
2 1643400 rs2008999 179796838 179.796838 0.643 A A B B B B A A A A
SNP A- A A A A A A B B B B
2 1721647 rs259845 180560120 180.56012 0.75 A A A A A A B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines , Py ^ ~ =E ~ C ~ C A
c ~ ~ Z a & a!~ <C ~ .r o cn ~F v 5 c o r o u Uj ai .'ap ~ ca v a ~, C. O d G~ C. b p, h a c k V U~ ; c a SNP_A- B B B B B B B B B B
2 1643999 rs9288052 181299542 181.299542 0.488 B B B B B B B B B B
SNP_A- B B A A A A A, A A A
2 1668465 rs288332 183450856 183.450856 0.262 B B A A A A A A A B
SNP A- B B B B B B A A A A
2 1723211 rs1454042 184407382 184.407382 0.357 B B B B B B B B A B
SNP_A- A A A A A A A A A A
2 1668055 rs10490389 186428458 186.428458 0.702 A A A A A A A A A A
SNP_A- B B B B B B A A B B
2 1678177 rs2044683 187026818 187.026818 0.366 B B B B B B B B B B
SNP_A- B B B B B B B B A A
2 1728072 rs840611 188023952 188.023952 0.583 B B B B B B B B A A
SNP_A- A A B B B B A A A A
2 1750900 rs10497725 192818722 192.818722 0.667 A A B B B B A A A B
SNP_A- B B B B B B B B B A
2 16429S8 is10497744 194316402 194.316402 0.31 B B B B B B B B B B
SNP A- A A A B A A A A A A
2 1669242 rs1350208 198911771 198.911771 0.571 B B B B B B A A A B
SNP_A- B B B B B B B B A A
2 1673517 rs10497821 '199463403 199.463403 0.31 B B B B B B B B A B
SNP_A- A A B B B B B B B A
2 1645863 rs1376877 204097596 204.097596 0.607 A A B B B B B B B B
SNP-A- A A A A A A A A A A
2 1650883 rs6707500 204941128 204.941128 0.667 B B A A A A A A A A
SNP_A- B B A A A A B B B B
2 1757786 rs10490293 206049378 206.049378 0.274 B B A A A A B B B B
SNP_A- B B A A A A A A A A
2 1752790 rs10490474 207934338 207,934338 0.571 B B B A B B B B A A
SNP A- A A B B B B A A A A
2 1642246 rs10497888 208586741 208.586741 0.679 A A B B B B A A A A
SNPA- A A A A A A A A B A
2 1644145 rs1607181 209364109 209.364109 0.655 A B A A A A B B B B
SNP A- A A B B B B A A A A
2 1669816 rs1816532 212093746 212.093746 0.75 A A B B B B A A A A
SNP A- B B B B B B B B B A
2 1661335 rs1402769 212906949 212.906949 0.274 B B B B B B B B B B
SNP_A- A A B B B B A A A A
2 1720206 rs10497986 213664725 213.664725 0.702 A A B B B B B B A A
SNP_A- A A A B A A A A A A
2 1701518 rs9283527 214674151 214.674151 0.417 A A B B B B A A A A
SNP_A- A A B B B B A A B A
2 1692929 rs2166459 215505298 215.505298 0.31 A B B B B B A A B B
SNP_A- B A A A A A A A A A
2 1755667 rs1250225 216151895 216.151895 0.744 B B A A A A A A A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines Q~ 6 ~ ~~a c~ 3 0 0 o n e! y r+ o cn ~ ~ 5 ~ o ~ o y e v V Qo~ w' a n o a a w V c , c. a.
SNP-A- B B A A A A B B B B
2 1705890 rs1110998 217169458 217.169458 0.429 B B B A B B B B B B
SNP_A- B A B B B B B B A A
2 1743410 rs6719545 218277340 218.27734 0.286 B B B B B B B B A B
SNP A- A A B B B B A A B B
2 1728154 rs1344645 219363524 219.363524 0.405 A B B B B B A A B B
SNP A- A A A A A A B B B B
2 1726837 rs715345 220649461 220.649461 0.274 A A B B B B B B B B
SNP-A- A A A A A A B A A A
2 1721280 rs1356399 221348562 221.348562 0.702 A A B B B B B B A A
SNP_A- B B B B B B B B B A
2 1655920 rs1430234 222049201 222.049201 0.274 B B B B B B B B B B
SNP A- B A A A A A A A A A
2 1711521 rs4673013 222802583 222.802583 0.619 B B B B B B A A A B
SNP_A- A A A A A A B B B B
2 1695224 rs1961637 223730613 223.730613 0.452 A B B B B B B B B B
SNP-A- A A B B B B B B B B
2 1713318 rs10498158 224777152 224.777152 0.417 A B B B B B B B B B
SN? A- B A A A A A B A B A
2 1702406 rs10498171 225622115 225.622115 0.524 B B A A A A B B B B
SNP A- A A A A A A A A A A
2 1643000 rs1835533 226193946 226.193946 0.738 A A A A A A A A A A
SNP-A- A A A A A A B B B A
2 1739924 rs1522804 226814661 226.814661 0.548 A B B B B B B B B B
SNP-A- A A A A A A A A A A
2 1683533 rs1950134 227888457 227.888457 0.714 A A A A A A A A A A
SNP-A- A A A A A A A A A A
2 1663421 rs1524023 228615089 228.615089 0.75 A A A A A A A A A A
SNP_A- B B A A A A B B B A
2 1707748 rs6759815 229797926 229.797926 0.571 B B A A A A B B B B
SNP-A- B B B B B B A A A A
2 1661533 rs4973304 230936568 230.936568 0.298 B B B B B B A A A B
SNP_A- B A A A A A B A A A
2 1727506 rs10498257 231818543 231.818543 0.702 B B B B B B B B A A
SNP A- B A B B B B B A A A
2 1728658 rs3791711 233258388 233.258388 0.524 B B B B B B B B A B
SNP-A- B A A A A A B A A A
2 1747120 rs1880747 235240125 235.240125 0.512 B B A A A A B B A A
SNP-A- A A A A A A A A A A
2 1738177 rs103718 239180488 239.180488 0.441 A A A A A A B B A A
SNP-A- A A B B B B A A B B
3 1675236 rs1516342 147906 0.147906 0.262 B B B B B B A B B B
SNP_A- A A A A A A A A A A
3 1754907 rs10510204 981912 0.981912 0.405 A A A A A A A B A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ '; ~ ~ ~ov q 3 0 0 ro o o o c ~ ~ ro c c SNP A- A A A A A A A A A~A
3 1726483 rs1720194 2366613 2.366613 0.631 A A A A A A A A A A
SNP A- A A A B B A B A A A
3 1717220 rs1508734 3538991 3.538991 0.607 B B B B B B B B B B
SNP A- B B A A A A A A A A
3 1668475 rs4684484 5437541 5.437541 0.441 B B A A A A A A A A
SNP_A- A A A A A A A A A A
3 1646075 rs9311817 6172932 6.172932 0.72 B B A A A A A A B B
SNPA- B B B B B B A A A A
3 1658187 rs1450097 7520521 7.520521 0.293 B B B B B B B B B B
SNP_A- A A A A A A A A A A
3 1718736 rs486012 9016299 9.016299 0.56 A A A A A A B B A B
SNP_A- A A A B B A A A A A
3 1679373 rs2160871 10421826 10.421826 0.75 B B B B B B A A A B
SNP-A- A A A A A A A A A A
3 1649097 rs6792718 11409380 11.40938 0.429 B B A A A A A A A A
SNP A- B B B B B B B B B B
3 1713577 rs172429 14880517 14.880517 0.25 B B B B B B B B B B
SNPA- A A B B B B A A A A
3 1719120 rs1983085 15504547 15.504547 0.56 A A B B B B B B A A
SNP_A- A A A A A A A A B B
3 1701284 rs2733528 17211259 17.211259 0.571 B B A A A A B B B B
SNP_A- A A A B B A A A B A
3 1653347 rs336615 18605807 18.605807 0.619 A A B B B B B B B B
SNP_A- A A A A A A A A B B
3 1753110 rs2053506 19350795 19.350795 0.595 A A A A A A A A B B
SNP A- A A A A A A A A A A
3 1649119 rs6770717 20406548 20.406548 0.726 B B A A A A A A A A
SNP_A- B B A B B A A A B A
3 1685927 rs365392 21465872 21.465872 0.583 B B B B B B B B B B
SNPA- A A B B B B B B B A
3 1738848 rs3732395 23209622 23.209622 0.378 A B B B B B B B B B
SNP_A-' B A A A A A A A A A
3 1730534 rs10510568 25577736 25.577736 0.679 B B A A A A B B A B
SNP-A- B B A A B A A A B A
3 1725077 rs9284859 26883268 26.883268 0.655 B B B B B B B B B B
SNP_A- B A B B B B B B A A
3 1647333 rs7639905 27951868 27.951868 0.429 B B B B B B B B A A
SNP_A- B A A A A A A A B A
3 1744932 rs9310901 29477393 29.477393 0.274 B B A A A A B B B B
SNP_A- A A A A A A B B B B
3 1741570 rs795347 30720945 30.720945 0.369 A B B B B B B B B B
SNP_A- B B B B B B B B A A
3 1747050 rs347163 32435579 32.435579 0.393 B B B B B B B B B B

Database S2 Heterozygosity of pbESC (Abbreviated as "pC") Lines = o p ..
; ~ "a COD N ~ a~~i ~ c * c a c o 0 o n a" ` a n ~ U ~ ~ 4 a SNP_A- B A A A A A A A B B
3 1735191 rs1376015 35274750 35.27475 0.595 B B B B B B B B B B
SNP A- B B A A A A B B A A
3 1717686 rs10510667 35834447 35.834447 0.476 B B A A A A B B B B
SNP A- A A A A A A A A A A
3 1643995 rs10510695 37621200 37.6212 0.738 A A A A A A A A A A
SNP_A- A A A A A A A A A A
3 1649705 rs2220345 41411812 41.411812 0.429 A B A A A A B B B B
SNP_A- B A A A A A A A A A
3 1699750 rs531888 43047989 43.047989 0.476 B B B B B B B B A A
SNP_A- A A A A A A B B A A
3 1722715 rs2742393 45732421 45.732421 0.417 A A B B B B B B A A
SNP_A- B B A A A A B B A A
3 1694360 rs7620394 55206368 55.206368 0.345 B B A A A A B B B B
SNP-A- B B A A A A A A A A
3 1643909 rs6445844 57028961 57.028961 0.726 B B B B B B B B A A
SNP_A- B B A A A A A A A A
3 1652229 rs10510803 59329572 59.329572 0.488 B B B B B B B B B B
SNP_A- B B A A A A A A A A
3 1669748 rs3843360 60016727 60.016727 0.393 B B B B B B B B A A
SNP_A- B B B B B B A A A A
3 1678019 rs1996520 61592725 61.592725 0.488 B B B B B B B B B B
SNP-A- A A A A A A A A A A
3 1665709 rs7650561 62466087 62.466087 0.643 A A B B B B A A B B
SNP_A- B B B B B B A A B A
3 1684953 rs10510929 64709076 64.709076 0.583 B B B B B B A A B B
SNP_A- A A B B B B A A B B
3 1688393 rs725160 66943022 66.943022 0.464 A A B B B B B B B B
SNPA A A A A A A A A A A
3 1678015 rs4145917 68099517 68.099517 0.679 B B A A A A A A A A
SNP_A- A A A A A A A A B B
3 1707438 rs2872939 69802192 69.802192 0.405 B B A A A A B B B B
SNP A- A A A A A A A A A A
3 1663707 rs10510996 70545357 70.545357 0.75 A A A B B B A A A B
SNP A- A A B B B B B B A A
3 1650625 rs830644 71748249 71.748249 0.5 B B B B B B B B A B
SNP_A- B B B B B B A A A A
3 1713028 rs4677226 73154304 73.154304 0.613 B B B B B B B B A A
SNP_A- A A A A A A B A A A
3 1685633 rs1107768 73959415 73.959415 0.726 B B A A A A B B A A
SNP_A- A A B B B B A 'A B B
3 1722733 rs10511039 76184447 76.184447 0.583 A A B B B B A A B B
SNP_A- A A A A A A A A B A
3 1648479 rs251552 76852596 76.852596 0.539 B B A A A A A B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines p L
Fj Q Z '. ~ .r~' c~ ^ 7 6i C
p=p, .p ~ vl eil O M ~I' ~fi ' ^.i \O . O l~ v0 u ~ .C ii m ~ d '.J M .y V V V y V ~ ~:
~ ~Y ~ a a L a o, a a ~ w o c t W V U~ ~ ~ ~
SNP_A- B B B B B B B A B B
3 1642486 rs9309840 80029943 80.029943 0.588 B B B B B B B B B B
SNP A- B B B B B B B B A A
3 1685115 rs2639611 81623522 81.623522 0.274 B B B B B B B B A A
SNP A- B A B B B B B B A A
3 1642250 rs9309888 82418655 82.418655 0.262 B B B B B B B B A B
SNP_A- B A B A B A A A A A
3 1732971 rs10511085 85614577 85.614577 0.619 B B B B B B A A A B
SNP_A- B B B B B B A A B B
3 1731608 rs1509783 87634505 87.634505 0.476 B B B B B B A B B B
S N ' P - A - A A B B B A A A A A
3 1721601 rs9310061 88146455 88.146455 0.631 A A B B B B A A A B
SNP_A- A A A A A A A A A A
3 1715294 rs724972 89664098 89.664098 0.607 A B A A A A A A A A
SNP_A- B B A A A A A A B A
3 1648583 rs10511152 96638708 96.638708 0.381 B B A A A B A B B B
SNP_A- B A B B B B B B B B
3 1701406 rs3856571 99031739 99.031739 0.298 B B B B B B B B B B
SNP A- A A A A A A A A B A
3 1643841 rs10511169 100116062 100.116062 0.691 A A A A A A A B B B
SNP A- A A A A A A A A B A
3 1697988 rs2700633 100643241 100.643241 0.643 A B A A A A A A B B
SNP_A- A A A A A A A A A A
3 1740468 rs10511183 102046105 102.046105 0.738 A A A A A A A A A A
SNP A- B B B B B B A A B A
3 1746982 rs974059 103277828 103.277828 0.25 B B B B B B A B B B
SNP A- A A A A A A A A A A
3 1687227 rs1391423 103923668 103.923668 0.732 A A A A A A A A A A
SNP_A- B A A A A A A A A A
3 1677819 rs10511221 105099054 105.099054 0.726 B B A A B B A A A B
SNP-A- A A A A A A B B A A
3 1663937 rs6783422 106031580 106.03158 0.393 A A A A A A B B A A
SNP A- A A A A A A B A A A
3 1674588 rs10511243 106653352 106.653352 0.667 A A A A A A B B A B
SNP-A- B A A A A A A A A A
3 1652015 rs2222039 108202685 108.202685 0.691 B B A A A A A A A A
SNP_A- 13 A B B B B A A A A
3 1722407 rs1525873 111232702 111.232702 0.702 B B B B B B A A A B
SNP_A- B A A A A A A A A A
3 1674512 rs1512514 111766406 111.766406 0.488 B B A A A'A A A A A
SNP_A- A A B B A A A A A A
3 1747616 rs1797626 114308943 114.308943 0.702 A A B B B B A A A A
SNP_A- B A A A A A B B B B
3 1668954 rs1553209 116705663 116.705663 0.476 B B A A A A B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines p .7- ~ ~3 ,p . .e~ 'v--I O M 'cY Ul ~D O l~ O
a p., a a~ ~ o 0 o V v o c o p r;
U ~CG ~ ~~e F ~ n a ~ a c z ~ A' A ~ V a a n SNP_A- B B A A, A A B A A A
3 1674292 rs7621196 117804184 117.804184 0.321 B B A A A A B B A B
SNP_A- A A B B B B B B_ B B
3 1643903 rs1218621 118459636 118.459636 0.31 A A B B B B B B B B
SNP A- B A A A A A A A A A
3 1728638 rs950649 121567065 121.567065 0.691 B B A A A A A A A A
SNP_A- B A A A A A A A A A
3 1730195 rs2126140 122627958 122.627958 0.5 B B B A B B B B A A
SNP A- B A A A A A A A B A
3 1741126 rs10511409 123610479 123.610479 0.738 B B A A A A B B B B
SNP_A- A A B B B B A A A A
3 1739520 rs1373606 125496637 125.496637 0.342 A A B B B B A A A A
SNP_A- A A A A A A B B A A
3 1727336 rs1374804 127391196 127.391196 0.524 A B B A B B B B A A
SNP A- A A A A A A A A A A
3 1683659 rs2718880 132343455 132.343455 0.75 A A A A A A B B A A
SNP-A- B B A A A A A A B B
3 1747192 rs1553975 132999274 132.999274 0.369 B B B A B B B B B B
SNP-A- A A A A A A A A A A
3 1744702 rs2310229 133541978 133.541978 0.691 A A A A A A A A A A
SNP A- A A A A A A A A A A
3 1730051 rs711923 136539253 136.539253 0.744 A A A A A A A A A A
SNP A- A A A A A A A A'B A
3 1654278 rs838623 144671624 144.671624 0.619 A A A A A A A A B B
SNP_A- A A A A A A A A A A
3 1730514 rs4610179 146387799 146.387799 0.726 B B A A A A A A A A
SNP_A- B B B B B B A A A A
3 1700733 rs4592991 147111601 147.111601 0.393 B B B B B B A A B B
SNP_A- A A B B B B B B A A
3 1744174 rs7645488 149410366 149.410366 0.31 B B B B B B B B B B
SNP_A- A A B B B B A A A A
3 1718574 rs2130319 150976344 150.976344 0.333 B B B B B B A A B B
SNP-A- A A B B B B A A A A
3 1718772 rs7648424 151906089 151.906089 0.488 B B B B B B A B B B
SNP-A- B B B B B B B B A A
3 1663723 rs10513399 152600180 152.60018 0.488 B B B B B B B B B B
SNP A- A A A A A A B B B B
3 1746211 rs2418925 155234610 155.23461 0.524 A A B B A B B B B B
SNP_A- A A A A A A A A A A
3 1658251 rs6772323 157710345 157.710345 0.667 A A A A A A A A A A
SNP_A- A A B B B B B A A A
3 1736960 rs4679851 160261035 160.261035 0.274 B B B B B B B B B B
SNP-A- B B A A A A B A A A
3 1716368 rs10513549 161237209 161.237209 0.25 B B B B A B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines S ~ 5 n~ ~ 3 0 0 er tn z 10 ~ ~
n a a o c o o r rZ
" '~ .Q A ~+ W t V a ' c o SNP A- A A B B B B B B B B
3 1726685 rs336583 162564683 162.564683 0.417 A A B B B B B B B B
SNP A- A A A A A A B A A A
3 1721879 rs7635791 163720371 163.720371 0.655 A A B B A B B B B B
SNP_A- A A A A A A B A A A
3 1745785 rs9290201 164397051 164.397051 0.31 B B B B A B B B B B
SNP A- B B A A A A A A A A
3 1697475 rs4352381 165179142 165.179142 0.369 B B A A A A A B B B
SNP_A- A A A A A A B B B B
3 1748578 rs2643191 165861395 165.861395 0.524 A A' A A A A B B B B
SNP_A- A A A A A A B B A A
3 1687865 rs1371900 167443656 167.443656 0.286 B B B B A B B B B B
SNP_A- A A A A A A A A A A
3 1680949 rs1877269 170109722 170.109722 0.548 B B B B A B B B B B
SNP_A- A A A A B A A A A A
3 1731022 rs8192675 172207585 172.207585 0.732 B B B B B B A A A A
SNP A- A A A A A A B B A A
3 1656780 rs7627220 173288405 173.288405 0.441 B B A A A A B B B B
SNP_A- B B A A A A B B B B
3 1720350 rs792354 174456847 174.456847 0.357 B B A A A A B B B B
SNP_A- A A B B B B B B B B
3 1662989 rs1377828 177727744 177.727744 0.286 A A B B B B B B B B
SNPA- A A B B B B A A A A
3 1651103 rs2160836 179192927 179.192927 0.662 B B B B B B A A A A
SNP_A- A A A A A A A A A A 3 1699226 rs6762743 180494702 180.494702 0.667 A A
A A A A A A B B
SNP_A- A A A A A A B B A A
3 1655724 rs262958 184975690 184.97569 0.583 B B A A A A B B B B
SNP_A- A A A A A A A A A A
3 1726281 rs10513799 186032241 186.032241 0.75 B B A A A A B B B B
SNP-A- A A A A A A A A A A
3 1649485 rs1962838 189742951 189.742951 0.405 B B B B B B A A B B
SNP A- A A B B B B A A B B
3 1756920 rs2378464 190305279 190.305279 0.262 B B B B B B B B B B
SNP-A- B B A A A A B B A A
3 1734403 rs3773928 191066407 191.066407 0.405 B B B B B B B B B B
SNP_A- A A A A A A B B B B
3 1720858 rs1405036 192749559 192.749559 0.262 B B B B B B B B B B
SNP_A- A A A A A A A A A A
3 1706600 r81403033 193538911 193.538911 0.441 B B A A A A B B B B
SNP_A- A A B B B B A A B B
3 1643612 rs587612 195020261 195.020261 0.369 A A B B B B A A B B
SNP_A- A A A A A A A A B B
4 1669560 rs1059159 5647306 5.647306 0.683 B B A A A A A A B B

Database S2 Heterozygosity of PhESC (Abbreviated as "pC") Lines Q 'ea 'a ~ ~'y n c en et vl 3 e o t o a ~ o 6 u ro U U
a a a SNP A- A A A A A A A A A A
4 1743690 rs10489076 9947117 9.947117 0.691 B B A A A A B B A B
SNP_A- A A A A A A A A B B
4 1736300 rs959233 10578428 10.578428 0.452 A A A A A A B B B B
SNP A- A A A A A A B B B A
4 1750658 rs10516254 12310930 12.31093 0.714 A A B B B B B B B B
SNP A- A A A A A A A A A A
4 1712820 rs10489092 13327021 13.327021 0.286 B B A A A A B B A B
SNP A- A A A A A A B B B B
4 1709160 rs10488982 14088975 14.038975 0.5 B B B A B B B B B B
SNP A- B B A B A A A A B B
4 1748456 rs1496747 16275503 16.275503 0.476 B B B B B B B B B B
SNP A- A A' A A A A A A A A
4 1674656 rs10516339 19549340 19.54934 0.725 A B A A A A A A A, A
SNP A- B B B B B B B B B B
4 1659171 rs6834573 20123113 20.123113 0.298 B B B B B B B B B B
SNP A- B B A B A A B B A A
4 1687559 rs10516397 21369936 21.369936 0.405 B B B B B B B B A A
SNP A- B A A B A A B B B A
4 1695570 rs2036713 22984189 22.984189 0.357 B B B B B B B B B B
SNP A- B A B B B B A A B B
4 1649429 rs1527354 24561836 24.561836 0.655 B B B B B B A A B B
SNP A- B B B B B B B B B B
4 1710973 rs7697266 25453418 25.453418 0.393 B B B B B B B B B B
SNP A- A A A A A A A A A A
4 1748352 rs9291495 27032051 27.032051 0.75 A A A A A A A A A B
SNP A- B B B B B B B B A A
4 1737486 rs1397438 28093488 28.093488 0.463 B B B B B B B B A A
SNP A- A A A A A A A A A A
4 1660740 rs939573 28670407 28.670407 0.75 A A A A A A A A A A
SNP A- B B A B A A B B B A
4 1659069 rs1441691 29221732 29.221732 0.274 B B B B B B B B B B
SNP A- A A A A A A A A A A
4 1731582 rs2571468 29891942 29.891942 0.667 A A B A B B B B A A
SNP A- A A A B A A A A A A
4 1666099 rs412253 31119019 31.119019 0.72 A A B B B B B B A A
SNP A- B B A A A A B B A A
4 1659419 rs10517232 31725815 31.725815 0.321 B B A A A A B B A A
SNP A- A A B B B B B B B B
4 1743944 rs2588544 36822899 36.822899 0.281 A B B B B B B B B B
SNP A- A A A A A A A A A A
4 1650541 rs7693744 42094241 42.094241 0.488 A, A B A A B A B A A
SNP A- A A A A A A A A A A
4 1651577 rs10517054 42743857 42.743857 0.726 A A A A A A A A A A

Database S2 Reterozygosity of phESC (Abbreviated as "pC") Lines L y, }.
~ p Ft " ~ 't^ tc C C C
p, f=y ~7, CC ~C 'y "a ~O M !S' VI y ~O v0 li ~p o Q r c c c GC
SNP-A- B B B B B B B B B B
4 1708293 rs10517094 44153139 44.153139 0.31 B B B B B B B B B B
SNP-A- A A A A A A A A B A
4 1672145 rs10517121 44712712 44.712712 0.583 A A B A A B A B B B
SNP_A- A A A A A A B A A A
4 1742914 rs1552419 45366813 45.366813 0.583 A B A A A A B B A A
SNP-A- B B B B B B B A A A
4 1741538 rs279842 46181884 46.181884 0.439 B B B B B B B B A B
SNP-A- B B B B B B B B B B
4 1726797 rs3934674 46854066 46.854066 0.305 B B B B B B B B B B
SNP_A- A A A A A A A A B A
4 1734487 rs6447614 47908885 47.908885 0.549 A B A A A B A A B B
SNP-A- A A A A A A A A A A
4 1659623 rs6850277 54268853 54.268853 0.667 B B A A A A A B A A
SNP A- B B B B B B B A A A
4 1724073 rs2726610 55528245 55.528245 0.548 B B B B B B B B A B
SNP A- A A A A A A A A A A
4 1643184 rs4580704 56167635 56.167635 0.643 B B A A A A A A A B
SNP A- A A B B A A A A B B
4 1647321 rs10517400 58338522 58.338522 0.679 B B B B B B B B B B
SNP A- A A B B B B A A B B
4 1685901 rs10517453 60065841 60.065841 0.679 A A B B B B B B B B
SNP_A- B B B B B B B B A A
4 1660836 rs2129274 61712878 61.712878 0.613 B B B B B B B B A A
SNP_A- A A A A A A B B B B
4 1712860 rs2345043 62476674 62.476674 0.619 A A A A A A B B B B
SNP_A- A A A A A A B B A A
4 1706808 rs2199219 63012534 63.012534 0.321 B B A A A A B B A B
SNP-A- B B B B B B A A A A
4 1657186 rs7674285 65578799 65.578799 0.536 B B B B B B A A A A
SNP-A- A A A A A A A A A A
4 1701798 rs1450036 67486005 67.486005 0.619 A A A A B B A A A B
SNP-A- A A A A A A A A A A
4 1734479 rs2736466 70507268 70.507268 0.679 B B A A A A A A B B
SNP-A- B B A A A A A A A A
4 1645045 rs3775745 71293834 71.293834 0.536 B B A A A A A A B B
SNP-A- B B A A A A B B A A
4 1741102 rs7678694 75663264 75.663264 0.476 B B A A A A B B A A
SNP-A- A A A A A A A A A A
4 1670999 rs925454 77604654 77.604654 0.595 A A A A B B A A B B
SNP-A- A A A A A A A A A A
4 1738063 rs2703134 78171011 78.171011 0.691 B B A A A A A B A A
SNP_A- A A B B B B B A B B
4 1654306 rs10518188 79483184 79.483184 0.405 B B B B B B B B B B

Database 82 Iieterozygosity of phESC (Abbreviated as "pC") Lines ~ ^p, ,. ., a ~ ^ d ~ ~ o tn ~ v> > o o ~
c w ~ vZi v ~ a Q v o o ro o. c a 3 a. n, V a n a SNP A- A A A A A A A A B B
4 1661108 rs2119421 80807501 80.807501 0.714 A A A A A A A A B B
SNP A- A A A A A A A A A A
4 1703940 rs9307787 83047673 83.047673 0.75 A A A A A A A A A A
SNP A- A A A A B A B B A A
4 1650367 rs6813014 84235884 84.235884 0.548 B B A A B B B B A A
SNP A- A A A A A A A A A A
4 1752998 rs10516708 85194717 85.194717 0.643 A A A A A A A A B B
SNP A- A A B B A A A A A A
4 1669642 rs10516739 86522131 86.522131 0.655 B B B, B A B A A B B
SNP A- B B B B B B A A A A
4 1725569 rs10516760 87083328 87.083328 0.25 B B B B B B A A A A
SNP-A- A A A A B A A A A A
4 1732366' rs4693803 88425710 88.42571 0.5 A A A A B B A A B B
SNP A- A A A A A A B A B B
4 1657663 re10516796 89213912 89.213912 0.634 A A A A A A B B B B
SNP A- B B A A B A A A A A
4 1718322 rs1903002 90098072 90.098072 0.464 B B A A B B A A B B
SNP A- A A A A A A A A B B
4 1659867 rs7693500 90643667 90.643667 0.691 A A A A A A A B B B
SNP A- A A B B B B A A A A
4 1705800 rs4694023 91613152 91.613152 0.393 B B B B B B A A B B
SNP A- A A B B A A A A A A
4 1757446 rs7696847 92155216 92.155216 0.714 A A B B A B A B B B
SNP A- B B B B B B A A A A
4 1749382 rs6827937 94157783 94.157783 0.452 B B B B B B A B B B
SNP A- A A A A A A A A A A
4 1727842 rs10516919 94713877 94.713877 0.667 B B A A A A A A A A
SNP A- A A A A B A A A A A
4 1745861 rs1048627 95944765 95.944765 0.595 A A A A B B A A A A
SNP A- B B A A A A B A B B
4 1683945 rs1384869 96613355 96.613355 0.274 B B A A A A B B B B
SNP A- B B B B B B B B A A
4 1756011 rs6853079 99800789 99.800789 0.286 B B B B B B B B A A
SNP A- A A B B A A B A B B
4 1703546 rs1230164 100343201 100.343201 0.274 B B B B A B B B B B
SNP A- A A A A B A A A B B
4 1740940 rs238486 103377982 103.377982 0.595 A A A A B B A A B B
SNP A- A A A A B A B B A A
4 1684917 rs227284 103964838 103.964838 0.655 A A A A B B B B B B
SNP A- A A A A A A A A A A
4 1753948 rs445761 104804695 104.804695 0.679 B B A A A A A A A A
SNP A- B B A A B A A A A A
4 1747884 rs2866685 105649408 105.649408 0.5 B B A A B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines pqp i" L G ~ C ^ C C
V
a a a SNP A- B B A A A A B B B B
4 1720092 rs1873361 106282703 106.282703 0.345 B B A A A A B B B B
SNP_A- B B B B B B B B A A
4 1721929 rs715706 106873632 106.873632 0.286 B B B B B B B B A A
SNP_A- A A B B B B A A B B
4 1662125 rs1468221 108745388 108.745388 0.31 A A B B B B B B B B
SNP_A- A A B B A A A A A A
4 1642856 rs7654940 110143969 110.143969 0.524 B B B B A B B B B B
SNP_A- B B B B B B B B A A
4 1686749 rs6841595 113711446 113.711446 0.317 B B B B B B B B B B
SNP A- B B B B A A A A A A
4 1736814 r910516593 114436416 114.436416 0.524 B B B B B B A A A A
SNP A- B B B B B B B B A A
4 1732667 rs998359 116228635 116.228635 0.441 B B B B B B B B B B
SNP_A- A A A A A A A A A A
4 1671469 rs292910 117406405 117.406405 0.607 A A A A A A A A B B
SNP-A- B B B B B B B B A A
4 1696003 rs2125710 118964366 118.964366 0.25 B B B B B B B B B B
SNP A- A A B B B B A A A A
4 1695754 rs10518293 119688966 119.688966 0.691 A A B B B B A A B B
SNP_A- A A B B A A B B A A
4 1745189 rs10518336 120880537 120.880537 0.536 A A B B B B B B B B
SNP_A- A A B B B B B B A A
4 1648947 rs2036696 121573324 121.573324 0.667 A A B B B B B B B B
SNP_A- A A A A A A A A A A
4 1702984 rs998327 122441717 122.441717 0.726 A A A A B B A A A A
SNP-A- B B B B B B A A B B
4 1733111 rs4833836 123858274 123.858274 0.381 B B B B B B B B B B
SNP_A- A A A A A A B B A A
4 1643743 rs444646 124370464 124.370464 0.548 B B A A B B B B A A
SNP A- A A B B B B B B B B
4 1746251 rs10518307 125084153 125.084153 0:262 B B B B B B B B B B
SNP_A- A A A A A A A A B B
4 1648121 rs7682791 125875709 125.875709 0.631 A A A A A A A A B B
SNP_A- A A A A A A A A A A
4 1699868 rs953211 126708654 126.708654 0.488 B B A A A A B B A A.
SNP_A- A A B B A A A A A A
4 1706772 rs4834083 127331109 127.331109 0.726 A A B B B B A A B B
SNP_A- A A B B B B A A A A
4 1653649 rs318510 130173248 130.173248 0.571 A A B B B B A A A A
SNP_A- A A A A A A A A A A
4 1655974 rs2969001 131140397 131.140397 0.643 A A A A A A B B A A
SNP_A- B B B B B B A A B A
4 1694056 rs6846560 131988611 131.988611 0.357 B B B 13 B B B B B B

Database S2 fIeterozygosity of phESC (Abbreviated as "pC") Lines } L L
z ca ca A ~ =~ ., ~ m ~t v1 7 ~o ~ t~ ~
u P~+ u d~ d ~ n =, a a c o ~o c r v] 'o y .G rfy V a ~ , ~

SNP-A- A A B B B B A A A A
4 1719820 rs10518609 133609659 133.609659 0.658 A A B B B B A A A A
SNP-A- B B A A A A A A B A
4 1721507 rs9307688 134441091 134.441091 0.726 B B A A A A A A B B
SNP A- B B B B B B A A B B
4 1716218 rs9307703 135374277 135.374277 0.321 B B B B B B B B B B
SNP_A- A A A A A A A A A A
4 1719154 rs6535037 135968531 135.968531 0.691 B B A A A A B B A B
SNP_A- A A A A A A A A A A
4 1718316 rs10519369 137048788 137.048788 0.619 B B A B B B B B A B
SNP_A- A A B B B B A A A A
4 1643751 rs7692053 138020209 138.020209 0.631 B B B B B B A A A A
SNP-A- B B B B B B A A B B
4 1712218 rs1376088 139852726 139.852726 0.357 B B B B B B B B B B
SNP-A- A A B B B B A A A A 4 1688437 rs10519540 141950175 141.950175 0.429 B B
B B B B A B A B
SNP_A- A A A A A A B B A A
4 1669152 rs2062597 143153292 143.153292 0.61 A A A A A A B B A A
SNP A- A A A A A A A A B A
4 1651007 rs331963 144031456 144.031456 0.369 A A B B B B A A B B
SNP_A- B B A A A A A A A A
4 1705078 rs789351 146225975 146.225975 0.679 B B A A A A A A A A
SNP_A- A A A A A A A A A A
4 1700284 rs10519824 148107681 148.107681 0.658 A A A A A A A A A A
SNP_A- B B A A A A B A B B
4 1655082 rs6810951 149441717 149.441717 0.333 B B B B B B B B B B
SNP_A- A A A A A A A A A A
4 1650743 rs10489053 150276232 150.276232 0.643 B B A A A A A A AB
SNP_A- B B B B B B A A A A
4 1695870 rs991529 151852936 151.852936 0.485 B B B B B B A A A A
SNP_A- B B A A A A A A B A
4 1750768 rs361101 153131731 153.131731 0.631 B B B B A B A A B B
SNP_A- A A A A A A B A A A
4 1694614 rs7662116 154375569 154.375569 0.691 A A A A A A B B A A
SNP-A- A A B B B B B B B B
4 1651497 rs1125228 155126657 155.126657 0.738 A A B B B B B B B B
SNP_A- A A B B B B A A B A
4 1732214 rs6536240 158751762 158.751762 0.381 B B B B B B B B B B
SNP-A- B B B B B B B B A A
4 1721547 rs7678486 159498426 159.498426 0.25 B B B B B B B B A~B
SNP_A- A A B B B B A A B A
4 1695472 rs7665879 160305968 160.305968 0.31 B B B B B B B B B B
SNP_A- B B A A A A A A A A
4 1653797 rs6856295 160845965 160.845965 0.595 B B B B A B B B A A

Database S2 Heterozygosity of pbESC (Abbreviated as "pC") Lines a 'a A ~ =R ~, ,oo en er ~n 7 ~o ~ r` ~o " a ~ a 'i o c ~ ac. n. ti c ~c aa r ~ ~ W tj U ~ U U
a .. a. c SNP A- A A A A A JA A A A A
4 1705238 rs9308000 161359479 161.359479 0.655 A A A A A A A A A A
SNP A- B B A A B A B B B B
4 1679349 rs195894 163885040 163.88504 0.366 B B B B B B B B B B
SNP A- B B A A A A B B B A
4 1719176 rs4057797 164602658 164.602658 0.381 B B A A A A B B B B
SNP A- A A A A A A A A A A
4 1657975 rs4404502 165513434 165.513434 0.738 A A A A A A B B A B
SNP A- B B A A A A A A B B
4 1669824 rs4691246 167437606 167.437606 0.402 B B B B A B B B B B
SNP A- B B A A B A A A A A
4 1701924 rs7435411 169800826 169.800826 0.524 B B B B B B B B A B
SNP A- B B B B B B B B B B
4 1673825 rs13212 170689681 170.689681 0.274 B B B B B B B B B B
SNP A- A A A A A A A A A A
4 1736222 rs449424 171884933 171.884933 0.631 A A B B A B A A A A
SNP A- B A A A A A A A A A
4 1745583 rs1485870 173125585 173.125585 0.744 B B A A A A A A A A
SNP A- A A A A A A A A A A
4 1717120 rs10520252 174445689 174.445689 0.619 A A B B A B B B A A
SNP A- A A A A A A A A A A
4 1714548 rs10520282 175752491 175.752491 0.738 A A B B A B A A A A
SNP A- A A B B B B B B B A
4 1662283 rs393279 177816548 177.816548 0.488 A A B B B B B B B B
SNP A- B B B B B B A A B A
4 1675843 rs10520383 178915654 178.915654 0.357 B B B B B B B B B B
SNP A- A A A A A A A A B A
4 1737632 rs2706012 179727204 179.727204 0.718 A A A A A A A A B B
SNP A- A A A A A A A A B B
4 1720252 rs10520430 180911694 180.911694 0.679 A A B B A B A A B B
SNP A- A A A A B A A A A A
4 1644751 rs7667245 181665445 181.665445 0.695 A B B B B B A A A A
SNP A- A A A A A A B B A A
4 1649573 rs10520479 182667862 182.667862 0.702 A A A A A A B B A A
SNP A- B A A A B A A A B B
4 1689263 rs10520518 183365702 183.365702 0.369 B B B B B B A A B B
SNP A- B A B A A A B B A A
4 1738928 rs830838 187288258 187.288258 0.333 B B B B B 13 B B B B
SNP A- A A A A A A A A B B
4 1713082 rs1280100 187913282 187.913282 0.345 A B A A A A B B B B
SNP_A- A A B B B B A A B B
4 1654608 rs1505509 188945352 188.945352 0.345 A B B B B B A A B B
SNP A- A A A A A A A A A A
4 1680395 rs2376743 189829781 189.829781 0.679 A A A A A A B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ,,7õ C9 W'N ~-l O M d' ~!1 ~ ~D O l~ O
rA
~ ~~ a ~ fs ~j U ? U V
a . a a SNP A- B B A A B A A A A A
5 1689409 rs10512651 1816661 1.816661 0.405 B B B B B B A A B B
SNP A- B B A A B A B A B B
5 1642488 rs1445862 3675257 3.675257 0.25 B B B B B B B B B B
SNP A- A A A A A A A A B B
5 1651781 rs272190 5103830 5.10383 0.25 B B A A A A B B B B
SNP A- A A A A A A A A A A
5 1663379 rs2560294 5619114 5.619114 0.726 A A A A A A B B B B
SNP A- B B A A A A A A A A
5 1643560 rs10512858 6486915 6.486915 0.613 B B B B B B A A B B
SNP A- A A A A A A A A A A
5 1651637 rs4629562 7847326 7.847326 0.619 B B B B B B A A B B
SNP A- B B B B B B B B B B
5 1693207 rs9313236 8348429 8.348429 0.25 B B B B B B B B B B
SNP A- A A B B B B B B A A
5 1744546 rs12515692 9883408 9.883408 0.357 B B B B B B B B B B
SNP A- A A B B B B A A B B
5 1721268 rs2937513 11007551 11.007551 0.619 B B B B B B B B B B
SNP A- A A A B A A A A A A
5 1702624 rs173671 12217918 12.217918 0.476 B B B B B B B B A A
SNP A- B B A A A A A A A A
5 1695478 rs1476154 13000353 13.000353 0.691 B B A A A A A A A A
SNP A- A A A B A A A A A A
5 1757294 rs3734108 13806984 13.806984 0.56 A A B B B B B B B B
SNP A- A A B B B B A A A A
5 1696687 rs2938832 15817866 15.817866 0.25 B B B B B B B B B B
SNP A- B B A A A A B B B B
5 1713461 rs585991 17246633 17.246633 0.274 B B A A A A B B B B
SNP A- B B A A A A B B A A
5 1661473 rs1394215 18359538 18.359538 0.548 B B A A A A B B A A
SNP A- B B A A A A A A A A
5 1646961 rs2942296 19421031 19.421031 0.429 B B B A B B B B A A
SNP A- B B B B B B A A A A
5 1698916 rs248202 21159137 21.159137 0.274 B B B B B B B B B B
SNP A- A A A B A A A A A A
5 1757332 rs7705523 23659025 23.659025 0.714 A A B B B B A A B B
SNP A- A A A B A A B B A A
5 1672683 rs1995599 24552793 24.552793 0.548 B B B B B B B B B B
SNP A- A A A A A A A A A A
5 1660984 rs9293241 26606178 26.606178 0.56 B B A A A A B B B B
SNP A- A A A A A A A A A A
5 1704664 rs921469 29989233 29.989233 0.583 B B A A A A A A B B
SNP A- B B B B B B A A A A
5 1644843 rs1921111 30906615 30.906615 0.40 B B B B B B A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines _ ~.
~ ~ p h. ~ p eCa ~ o oz c3 CE r~ m '^"~ O M '~P ~A 7 D O l~ O
V cL V1 ~ ~ m~ O D U U U U y U U ~
COD EYj ,ti R R i ~ C. "'G G G Rb G C'~
A ,C
w V a a.
SNP_A- A A A A A A A A A A
1678791 rs893551 33493407 33.493407 0.607 A A A A A A A A A A
SNP_A- A A A A A A A A B B
5 1724049 rs716302 35846025 35.846025 0.357 B B A A A A A B B B
SNP_A- A A B B B B B B A A
5 1703432 rs159751 37035755 37.035755 0.464 A A B B B B B B A A
SNP_A- A A B B B B B B B A
5 1645375 rs4072686 38003109 38.003109 0.405 B B B B B B B B B B
SNP_A- A A B B A A A A A A
5 1719252 rs675502 39878266 39.878266 0.679 B B B B A B A A A A
SNP_A- A A A A A A B B A A
5 1685613 rs1697938 40890439 40.890439 0.441 A A A A A A B B A A
SNP_A- B B B B B B B B B A
5 1731232 rs276278 42016012 42.016012 0.298 B B B B B B B B B B
SNP A- A A B B B B B A A A
5 1694450 rs1072746 43646445 43.646445 0.441 A B B B B B B B A B
SNP_A- A A A A B A A A A A
5 1675759 rs2404958 50098792 50.098792 0.619 A B A A B B A A A A
SNP_A- B A B B A A A A B B
5 1723309 rs9283709 51510492 51.510492 0.595 B B B B B B A A B B
SNP-A- B A A A A A B A A A
5 1728968 rs10512988 52085030 52.08503 0.357 B B A A A A B B A A
SNP_A- B B B B B B A A B A
5 1746984 rs9292039 53454075 53.454075 0.268 B B B B B B A B B B
SNP_A- A A A A A A B A A A
5 1697874 rs6450270 54287290 54.28729 0.714 A A A A A A B B A A
SNP_A- B B A A A A B A A A
5 1684501 rs889310 56000924 56.000924 0.476 B B B A B B B B A B
SNP A- B B B B B B A A B B
5 1673657 rs2539731 57109292 57.109292 0.475 B B B B B B B B B B
SNP_A- B B B B B B B B B B
5 1716782 rs9292159 57677129 57.677129 0.31 B B B B B B B B B B
SNP_A- B B A A A A B B A A
5 1724117 rs9292180 58192447 58.192447 0.25 B B B A B B B B A B
SNP_A- A A A A A A A A A A
5 1755537 rs10514860 58859777 58.859777 0.726 A A A A A A A A A A
SNP_A- A A B B B B A A B B
5 1653871 rs6859376 59471964 59.471964 0.56 A B B B B B B B B B
SNP A- A A A A A A B B B A
5 1653455 rs159375 60469024 60.469024 0.691 A A A A A A B B B B
SNP_A- B B A A A A B , B B A
5 1682537 rs356598 63380121 63.380121 0.631 B B A A A A B B B B
SNP_A- A A B B B B B B A A
5 1755307 rs7704890 66151331 66.151331 0.357 A B B B B B B B A B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ ~ y ~ p a o o 0 r-~ F cC ~ ~ y wt O M 'd' N b O r O
u Z a=~ c~ R~ v ~ p ~ U U U 7 CU ro U
~ o a a a ~ c, t V C) c c SNP A- B B A B A A B B B B
1671457 rs6858907 67817289 67.817289 0.417 B B B B B B B B B B
SNP A- B B A B A A A A A A
5 1654744 rs1600073 74472493 74.472493 0.61 B B B B B B B B A A
SNP A- A A A A A A A A B B
5 1653531 rs10514059 75460983 75.460983 0.658 A A A A A A A A B B
SNP A- A A A A A A A A A A
5 1720510 rs2972341 76504599 76.504599 0.536 B B A A A A B B A B
SNP A- A A A B A A B B A A
5 1682839 rs949645 78478278 78.478278 0.564 A A B B B B B B A B
SNP A- B B B B B B B B B B
5 1747624 rs264986 79206180 79.20618 0.31 B B B B B B B B B B
SNP A- A A A A A A A A B B
5 1730614 rs964102 80843469 80.843469 0.679 B B A A A A B B B B
SNP A- A A A A A A B A B B
5 1732246 rs10514249 82540612 82.540612 0.56 A A A A A A B B B B
SNP A- B B B B B B B B B B
5 1729977 rs4639197 83381853 83.381853 0.25 B B B B B B B B B B
SNP A- B B A A A A B A A A
5 1742238 rs323744 86861304 86.861304 0.5 B B A A A A B B A B
SNP A- A A A B A A B A B B
5 1751644 rs819344 89093506 89.093506 0.463 A A B B A B B B B B
SNP A- A A B B B B A A A A
5 1690642 rs2935499 89626568 89.626568 0.548 A A B B B B A B B B
SNP A- B B A A A A B B A A
5 1744488 rs52308 90817903 90.817903 0.512 B B A A A A B B A A
SNP A- A A B B B B B A A A
5 1670907 rs248339 95229134 95.229134 0.643 A A B B B B B B B B
SNP A- B B A B A A A A B B
5 1729028 rs31248 96040439 96.040439 0:275 B B B B A B A B B B
SNY A- A A A A A A A A A A
5 1657092 rs10515273 97821155 97.821155 0.75 A A A A A A A A A A
SNP A- A A A A A A A A A A
5 1643346 rs2887526 98552712 98.552712 0.667 B B A A A A A A A A
SNP A- A A A B A A A A B B
5 1722905 rs2369754 99184261 99.184261 0.488 A A B B A B A B B B
SNP A- B B B B B B B B B B
5 1664073 rs1477625 101358141 101.358141 0.271 B B B B B B B B B B
SNP A- B B A A A A B A A A
5 1742802 rs9327861 101895776 101.895776 0.655 B B A A A A B B A A
SNP A- A A B B B B A A B B
5 1745283 rs39984 102625191 102.625191 0.31 A A B B B B A A B B
SNP A- A A A A A A B B A A
5 1734843 rs10515355 103975436 103.975436 0.738 B B A A A A B B A A

Database S2 Heterozygosity of p1rESC (Abbreviated as "pC") Lines r..
a p p~.i 'r ~ p e~o¾ q 3 0 0 q, ~,^p ym r+ o cn 7 ~n ~c o ~ o C4+ V ~ U U U U U
~ P' b e~a e.. y ~ a * a w o o a o a r SNP_A- A A A A A A A A A A
1730932 rs4957531 106511277 106.511277 0.463 A A A A A A A B B B
SNP_A- A A A A B A A A A A
5 1757418 rs245243 109258634 109.258634 0.714 B B B A B B A B A A
SNP A- B B A A B A A A A A
5 1646761 rs10491424 110481705 110.481705 0.56 B B B B B B A A A A
SNP_A- B B B B B B B A B B
5 1691719 rs1213404 111130917 111.130917 0.35 B B B B B B B B B B
SNP_A- A A A A A A A A A A
5 1747768 rs971517 112050154 112.050154 0.476 A A A A A A A A A A
SNP A- A A A A A A A A A A
5 1726679 rs10519378 113555966 113.555966 0.738 A A A A A A A A A A
SNP_A- A A B B B B B B A A
5 1738592 rs2546480 114841054 114.841054 0.452 B B B B B B B B B B
SNP A- A A A A B A A A A A
5 1708792 rs2662458 115402242 115.402242 0.655 B B B B B B A A B B
SNP-A- B B A A A A A A A A
5 1720512 rs1027292 116078486 116.078486 0.548 B B A A A A A A B B
SNP_A- A A A A A A A A A A
5 1701708 rs1504978 118638459 118.638459 0.655 B B B B A B A A A A
SNPA- B B B B B B A A A A
5 1689317 rs10519615 119189176 119,189176 0.643 B B B B B B B B B B
SNP_A- A A A A A A B B A A
5 1751260 rs6897147 119692229 119.692229 0.691 A A A A A A B B A A
SNP-A- A A A A A A B B B B
5 1654688 rs161011 123703275 123.703275 0.286 A A B B B B B B B B
SNP_A- A A A A A A A A A A
5 1699578 rs7716491 124265772 124.265772 0.738 B B A A A A B B B B
SNP_A- B B A A A A A A A A
5 1703238 rs1826263 124839517 124.839517 0.571 B B A A A A B B B B
SNPA- A A A A A A B B A A
5 1715428 rs964185 125631547 125.631547 0.345 A A B B B B B B B B
SNPA- B A A A A A A A A A
5 1751090 rs1345663 126678081 126.678081 0.31 B B A A A A A A A A
SNP A- A A A A A A A A B B
5 1694738 rs9327460 127338947 127.338947 0.524 A A A A A A B B B B
SNP_A- B B A A A A A A B B
5 1658519 rs1181962 128414700 128.4147 0.333 B B A A A A B B B B
SNP_A- A A A A A A A A A A
5 1677377 rs25810 129015788 129.015788 0.595 A A A A A A A A B B
SNP_A- A A A A A A A A A A
5 1673843 rs10520083 129967905 129.967905 0.345 A A B B B B B B B B
SNP_A- B B B B B B A A A A
5 1705560 rs9327673 133230970 133.23097 0.286 B B B B B B B B B B

Database S2 Heterozpgosity of pbESC (Abbreviated as "pC") Lines ~, 'a '~ ~ ~=N .~ o cn er in 5 ~o o t~ o rA ~ y y~" ~ u U U U U U U

s A w U a a c SNP-A- B A A A A A A A A A
1662391 rs10515473 134961986 134.961986 0.714 B B A A A A A A B B
SNP-A- B A A A A A A A B B
5 1707797 rs10515481 136007946 136.007946 0.536 B B A A A A A A B B
SNP-A- B B A A A A A A A A
5 1720076 rs1560930 136590879 136.590879 0.537 B B A A A A A A B B
SNP-A- B B A A A A B A B B
5 1697724 rs288019 138219292 138.219292 0.39 B B B B B B B B B B
SNP-A- A A A A A A B A A A
5 1707038 rs2336977 139130436 139.130436 0.61 A B B B B B B B A A
SNP_A- B A B B B B B B A A
5 1703312 rs6860077 139725338 139.725338 0.31 B B B B B B B B B B
SNP_A- B B A A A A A A A A
5 1742086 rs246002 140321288 140.321288 0.5 B B B B B B A B A A
SNP-A- A A B B B- B B A A A
5 1730974 rs32927 141102251 141.102251 0,298 A B B B B B B B B B
SNP A- A A A A A A B B B B
5 1736416 rs997833 141815738 141.815738 0.286 A B B B B B B B B B
SNP A- A A A A A A A A B B
5 1722681 rs325227 143131067 143.131067 0.31 A B A A A A A A B B
SNP-A- A A A A A A A A B B
5 1749482 rs10515600 147316068 147.316068 0.548 B B B B B B A A B B
SNP-A- A A A A A A B B A A
5 1716760 rs185021 148147283 148.147283 0.524 B B B B B B B B A A
SNP A- B B A A A A B A A A
5 1642124 rs10515632 149082624 149.082624 0.333 B B B B B B B B A A
SNP_A- B B A A A A A A B B
5 1737743 rs1277464 150234035 150.234035 0.354 B B B B B B B B B B
SNP_A- A A A A A A B B A A
5 1678329 rs2304054 150923278 150.923278 0.548 B B A A A A B B B B
SNP_A- A A A A A A B A A A
5 1649583 rs10515686 152529312 152.529312 0.619 A A B B B B B B B B
SNP-A- A A A A A A B A B B
5 1652471 rs4129128 153102070 153.10207 0.321 B B A A A A B B B B
SNP A- A A A A A A A A A A
5 1700286 rs991314 154438135 154.438135 0.744 A A A A A A A A A A
SNP-A- A A A A A A A A A A
5 1752802 rs2569031 155177249 155.177249 0.488 B B B B B B A A B B
SNP_A- A A A A A A A A B B
5 1706578 rs873343 157106698 157.106698 0.25 B B B B B B A A B B
SNP-A- A A A A A A A A A A
5 1757398 rs9313777 157878177 157.878177 0.75 A A A A A A A A B B
SNP-A- A A A A A A B B B B
5 1736540 rs10515781 158633942 158.633942 0.321 B B B B B B B B B B

Database S2 Heterozygosity of pbESC (Abbreviated as "pC") Lines y s, L
~ a ^ ^ d ~ Z a ca ~ ~ =~ ~ o ~n ~ , ~n ~ ~o o t~ o a c v o ~ a ro `i' In w U U ; U
w a a SNP A- A A A A A A B B A A
5 1647073 rs411005 160517741 160.517741 0.476 B B A A A A B B A A
SNP A- B B A A A A B B A A
5 1724235 rs2170901 161840216 161.840216 0.429 B B B B B B B B A A
SNP A- A A A A A A A A A A
5 1754048 rs300238 162682948 162.682948 0.452 B B B B B B A A B B
SNP A- B B B B B B A A B B
5 1745987 rs158295 163217790 163.21779 0.25 B B B B B B A B B B
SNP A- A A A A A A A A A A
5 1720394 rs6869856 166017651 166.017651 0.412 A A A A A A A A A A
SNP A- B B B B B B A A A A
5 1687531 rs1911557 169681232 169.681232 0.25 B B B B B B B B B B
SNP A- A A A A A A A A A A
5 1749300 rs10516089 171083836 171.083836 0.726 B B A A A A B B A A
SNP A- A A A A A A A A A A
5 1665975 rs1909706 173644330 173.64433 0.707 A A A A A A A A A A
SNP A- A A A A B A A A A A
5 1724885 rs965017 174509108 174.509108 0.548 B B B B B B A A A A
SNP A- A A A A A A A A A A
5 1644515 rs1071882 178068646 178.068646 0.702 A A B B A B A A A A
SNP A- A A B B B B B B A A
5 1748220 rs2892344 180297919 180.297919 0.536 B B B B B B B B B B
SNP A- A A B B B B B B A A
6 1732501 rs3765437 508013 0.508013 0.536 A A B B B B B 13 A A
SNP-A- A A B B B B A A A A
6 1728682 rs238073 1192930 1.19293 0.381 A A B B B B A A B B
SNP A- A A A A A A A A A A
6 1747718 rs6919059 1729095 1.729095 0.691 A B A A A A B B A A
SNP A- B A A A A A B B A A
6 1723553 rs2326366 3923256 3.923256 0.417 B B A B A B B B B B
SNP A- B B B B B B B B A A
6 1747058 rs10484314 5593086 5.593086 0.333 B B B B B B B B B B
SNP A- B B B A B A A A A A
6 1673883 rs3851514 6219569 6.219569 0.75 B B B B B B B B A A
SNP A- A A A A A A A A A A
6 1737825 rs267202 7799235 7.799235 0.619 B B A B A B A A A A
SNP A- A A A A A A B B B B
6 1680945 rs1543731 8355978 8.355978 0.346 A A A B A B B B B B
SNP A- A A B B B B B B A A
6 1702006 rs9296701 9687981 9.687981 0.536 B B B B B B B B B B
SNP A- B B A A A A B B B B
6 1715186 rs4512212 10379387 10.379387 0.464 B B A B A B B B B B
SNP A- A A A A A A B B A A
6 1680453 rs2182335 11324963 11.324963 0.714 A A A B A B B B A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ^ y ~ v1 a, d ~ c u U U U U V
~ p. U
z c ~ ~ , a~ o a r+ a a n ~ n o w r`
U U ~ U U
ia c, a SNP-A- A A A A A A A A A A
6 1690060 rs2841555 13574809 13.574809 0.655 A A A A A A B B B B
SNP_A- A A A A B A B B A A
6 1646375 rs2237166 16755137 16.755137 0.536 B B B B B B B B A A
SNP_A- A A A A A A A A A A
6 1744270 rs2147211 17898170 17.89817 0.714 A A A A A A B B B B
SNP_A- A A A A A A A A A A
6 1679405 rs9297090 18873893 18.873893 0,571 B B A A A A A A B B
SNP_A- A A B B B B A A B B
6 1717924 rs971623 20437442 20.437442 0.405 B B B B B B B B B B
SNP_A- A A A A A A B B A A
6 1749068 rs10485012 22715005 22.715005 0.595 B B B B B B B B A A
SNP_A- A A A A A A A A A A
6 1754953 rs2022330 23554534 23.554534 0.667 B B B B B B B B B B
SNP_A- A A B B B B A A A A
6 1698352 rs499466 24069410 24.06941 0.5 B B B B B B B B A A
SNPA- B B B B B B A A B B
6 1682833 rs9295755 28141153 28.141153 0.25 B B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1656688 rs2747430 29756485 29.756485 0.702 B B A A A A A A A A
SNPA- A A A A A A A A A A
6 1715492 rs2395173 32512837 32.512837 0.691 B B A A A A B B A A
SNP_A- A A A A A A A A A A
6 1722893 rs9296266 38990614 38.990614 0.573 A A B B B B A A A B
SNP_A- B A B B B B B B B A
6 1724965 rs2395743 40400147 40.400147 0.488 B B B B B B B B B B
SNP_A- B B A A A A A A B B
6 1757782 rs3804281 41853967 41.853967 0.429 B B B B B B A B B B
SNP_A- A A B B B B B B B A
6 1700088 rs3763234 42725939 42.725939 0:298 A B B B B B B B B B
SNP_A- B B B B B B B B B A
6 1748380 rs525043 44511878 44.511878 0.25 B B B B B B B B B B
SNP_A- A A B B B B A A A A
6 1685295 rs9296453 45335410 45.33541 0.429 A B B B B B A A A A
SNP_A- A A A A A A A A A A
6 1708722 rs9296468 45876662 45.876662 0.726 A A B B B B A A A A
SNP_A- B A B B B B B B B A
6 1736458 rs10498767 46471516 46.471516 0.441 B B B B B B B B B B
SNP_A- A A B B B B B A A A
6 1642956 rs9296547 47474339 47.474339 0.643 A A B B B B B B A A
SNP_A- A A B B B B B B A A
6 1742558 rs2089505 48229201 48.229201 0.643 A A B B B B B B A A
SNP_A- A A A A A A A A B A
6 1738582 rs504213 49411897 49.411897 0.607 A A A A A A A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ca et ui D \0 W ~ vl a~i a~ u V ~ U U C~ 7 U ~ V b W
c SNP_A- B B B B B B B B B A
6 1658085 rs10484664 51124482 51.124482 0,256 B B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1723157 rs913098 51750772 51.750772 0.667 A B A A A A A A A A
SNP_A- B B A B A A B A B B
6 1726221 rs509946 52411949 52.411949 0.369 B B A B A B B B B B
SNP_A- B A B B B B A A B B
6 1717116 rs10484785 53457958 53.457958 0.476 B B B B B B A B B B
SNP_A- A A A A A A B B B B
6 1717814 rs1393779 54808762 54.808762 0.464 A B A A A A B B B B
SNP_A- A A A A A A A A A A
6 1693069 rs1925179 56129171 56.129171 0.655 A A A A A A A A A B
SNP_A- B A A A A A B A A A
6 1664153 rs6934928 58422082 58.422082 0.714 B B A A A A B B A A
SNP_A- A A A A A A B B A A
6 1682123 rs565795 62597708 62.597708 0.61 A A A A A A B B A B
SNP_A- B B B A B A A A B A
6 1692597 rs9293849 63255396 63.255396 0.333 B B B A B B A B B B
SNP_A- A A A A A A A A A A
6 1729072 rs9294630 65677619 65.677619 0.702 A B A A A A A A A B
SNP_A- A A A A A A A A A A
6 1685655 rs2502270 67886666 67.886666 0.488 A A A A A A B B A A
SNP_A- A A B B B B B B B A
6 1744006 rs4707479 68787830 68.78783 0.286 A A B B B B B B B B
SNP_A- A A B A B A A A B A
6 1683273 rs579588 69639537 69.639537 0.714 A A B A B B B B B B
SNPA- B B B B B B B B A A
6 1659091 rs591809 72270133 72.270133 0.524 B B B B B B B B A B
SNP_A- A A A A A A A A A A
6 1660794 rs959369 74620278 74.620278 0.607 A A A A A A A A A B
SNP_A- B B B B B B B B B A
6 1656648 rs1575856 76774483 76.774483 0.262 B B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1675424 rs1457947 77533004 77.533004 0.619 A A A A A A B B A A
SNP_A- A A A A A A A A A A
6 1657250 rs236225 79172654 79.172654 0.744 A A A A A A B B A A
SNPA- A A A A A A A A B B
6 1646741 rs239500 80761863 80.761863 0.595 B B A A A A B B B B
SNP_A- A A A A A A A A B A
6 1733643 rs310387 81832380 81.83238 0.56 A A A A A A A A B B
SNP_A- B B B B B B B B B B
6 1684117 rs2323435 82365338 82.365338 0.417 B B B B B B B B B B
SNP_A- B B B B B B A A B A
6 1749278 rs958568 83211843 83.211843 0.417 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
py C. C. A 'Q~ ""'i ,OO t? ef N D ~o t`b v Z, R cn G c. o. O. ~o O. r cp ~ F+ U
~ o a L G a c a SNP A- A A B B B B A A B B
6 1737476 rs6938512 85412591 85.412591 0.476 B B B B B B A A B B
SNP A- B B B A A JA A A B B
6 1658179 rs3966882 85938190 85.93819 0.46 B B B A B B B B B B
SNP A- A A B B B B A A A A
6 1704672 rs3857488 88057783 88.057783 0.548 B B B B B B A A A B
SNP_A- A A B B B B A A A A
6 1750678 ss942115 90274825 90.274825 0.691 A A B B B B A A A A
SNP A- B B B B B B B B B B
6 1641794 rs1753826 91283465 91.283465 0.274 B B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1747902 rs427118 92400922 92.400922 0.622 B B A A A A A A B B
SNP A- A A A A A A A A A A
6 1699604 rs609590 93182864 93.182864 0.595 B B A A A A B B B B
SNP A- A A A A A A A A A A
6 1671865 rs1906966 94362973 94.362973 0.571 A A A A A A B B B B
SNP_A- A A B A A A A A A A
6 1672477 rs2380218 95947837 95.947837 0.643 B B B B B B B B A A
SNP A- A A A A A A B B A A
6 1727169 rs6925466 96483564 96.483564 0.476 B B A B B B B B B B
SNP A- A A A A A A A A A A
6 1669372 rs2206094 97681917 97.681917 0.595 B B A A A A B B B B
SNP A- A A A A A A B B A A
6 1754567 rs10484477 103889951 103.889951 0.738 A A A A A A B B B B
SNP A- B B B B B B B B A A
6 1687147 rs1341123 104971433 104.971433 0.274 B B B B B B B B B B
SNP A- A A A A A A A A A A
6 1696467 rs1325421 105998201 105.998201 0.643 B B A B B B A A A A
SNP A- A A B B B B B B B B
6 1733167 rs1462145 107068713 107.068713 0.357 B B B B B B B B B B
SNP A- A A B B B B A A B B
6 1650105 rs7740028 110825873 110.825873 0.393 A A B B B B A A B B
SNP A- A A A A A A A A A A
6 1680493 rs2010315 112529340 112.52934 0.679 A A A A A A A A A A
SNP A- A A B B B B A A A A
6 1735595 rs1378682 113188320 113.18832 0.405 A A B B B B A A B B
SNP A- A A B B B B A A A A
6 1712634 rs2810160 114329403 114.329403 0.548 A B B B B B B B B B
SNP A- B A A A A A A A B B
6 1687581 rs1748168 114955404 114.955404 0.56 B B A A A A B B B B
SNP A- A A A A A A A A B B
6 1738139 rs2250263 116940700 116.9407 0.679 A B A A A A A A B B
SNP A- A A A A A A A A A A
6 1729937 rs929122 117712442 117.712442 0.726 A A A A A A A A B B

Database S2 Heterozygosity of p1rESC (Abbreviated as "pC") Lines z c c SNP A- A A A A A A A A B B
6 1661803 rs9285429 118811259 118.811259 0.619 A A B B B B A A B B
SNP A- B B B B B B A A A A
6 1665123 rs1873553 120164641 120.164641 0.429 B B B B B B B B A A
SNP A- B B B B B B B B B B
6 1679087 rs6906196 122713901 122.713901 0.369 B B B B B B B B B B
SNP A- B B A A A A B B B B
6 1707510 rs6924068 124232587 124.232587 0.345 B B B B B B B B B B
SNP A- A A A A A A A A A A
6 1745119 rs484510 125528599 125.528599 0.691 A A A A A A A A B B
SNP A- A A B B B B A A A A
6 1685381 rs9321057 126198636 126.198636 0.405 A B B B B B B B B B
SNP A- A A B B B B B B A A
6 1751986 rs270044 128228176 128.228176 0.405 A B B B B B B B B B
SNP A- A A A A A A A A A A
6 1721422 rs1508439 129073191 129.073191 0.655 A B A A A A B B A A
SNP A- B A B B B B A A B B
6 1707720 rs10484282 130107771 130.107771 0.321 B B B B B B B B B B
SNP A- A A A A A A A A B B
6 1652817 rs766967 130912718 130.912718 0.488 A A B B B B B B B B
SNP A- A A B B B B A A B B
6 1653251 rs170881 132358254 132.358254 0.655 A A B B B B B B B B
SNP A- B B B B B B B B B B
6 1723663 rs2745426 133045037 133.045037 0.287 B B B B B B B B B B
SNP A- A A A A A A A A B B
6 1751418 rs509904 133558775 133.558775 0.713 A B A A A A A A B B
SNP A- B B A A A A B B A A
6 1735812 rs6570091 137092589 137.092589 0.464 B B A A A A B B B B
SNP A- A A A A A A B A A A
6 1669540 rs662100 137931606 137.931606 0.512 A A A A A A B B A A
SNP A- B B A A A A A A B B
6 1692831 rs2473522 139472945 139.472945 0.274 B B B B B B A A B B
SNP A- A A A A A A A A A A
6 1729139 rs9321743 140005650 140.00565 0.655 A A A A A A A A B B
SNP A- A A B B B B B A A A
6 1668519 rs225710 142582952 142.582952 0.548 B B B B B B B B A A
SNP A- A A B B B B B B B B
6 1741850 rs10484804 143972461 143.972461 0.262 B B B B B B B B B B
SNP A- A A A A A A A A A A
6 1699598 rs4243477 145767511 145.767511 0.655 A A A A A A A B B B
SNP A- A A B B B B B A A A
6 1714061 rs6923545 146286436 146.286436 0.417 B B B B B B B B B B
SNP A- A A A A A A A A B B
6 1643757 rs2025157 146851348 146.851348 0.607 A A A A A A A B B B

Database S2 Heterozygosity of pIiESC (Abbreviated as "pC") Lines L ~. ~.
p .L, i' C cC~S C C C
F7 ~ ~ CC Cd 'y .-1 O M `C V) IO f- ~ ..
U ~ ~ly ~ R cc v i~. c~t O. ~ G GL G d ~D C, SNPA- A A A A A A A A A A
6 1746680 rs10484677 148334072 148.334072 0.702 A A A A A A A A B B
SNP_A- B B A A A A B A B B
6 1674099 rs997682 149708313 149.708313 0.293 B B B B B B B B B B
SNP_A- A A B B B B A A B B
6 1742378 rs1933079 151696424 151.696424 0.464 A A B B B B A B B B
SNP_A- A A B B B B A A A A
6 1664463 rs872371= 153469676 153.469676 0.732 A A B B B B A B A A
SNP_A- A A A A A A A A A A
6 1706738 rs612450 154306471 154.306471 0.56 B B A B B B A A A A
SNP_A- A A A A A A B A A A
6 1661002 rs1980602 155248334 155.248334 0.429 B B A A A A B B B B
SL1P_A- B A B B B B B A B B
6 1700465 rs1391655 156092837 156.092837 0.298 B B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1660620 rs7770496 156806897 156.806897 0.372 A B A B B B A B B B
SNP_A- B A B A A A A A A A 6 1712976 rs4709298 157885415 157.885415 0.262 B B
B B B B A B A A
SNPA- B A A A A A B B B B
6 1676117 rs7753885 158892133 158.892133 0.488 B B A B B B B B B B
SNP A- B A A A A A B B A A
6 1669774 rs923459 159532261 159.532261 0.513 B B A A A A B B B B
SNP A- A A A A A A B A A A
6 1659978 rs927450 160152507 160.152507 0.583 A A A A A A B B B B
SNP_A- B A A A A A B B B B
6 1670969 rs598969 160664317 160.664317 0.425 B B A A 'A A B B B B
SNP A- A A B A A A B B A A
6 1697554 rs6910079 164339862 164.339862 0.441 A B B B B B B B B B
SNP_A- A A A A A A A A A A
6 1641972 rs907223 165179009 165.179009 0.702 A A A A A A A A B B
SNP A- A A A A A A A A A A
6 1698488 rs162293 167420582 167.420582 0.75 A A A A A A A A A A
SNP A- A A A A A A A A A A
7 1647507 rs1637750 2001052 2,001052 0.655 A A A A A A B B A A
SNP_A- A A A A A A B B A A
7 1710599 rs10257982 3107838 3.107838 0.452 A B A A A A B B B B
SNP_A- B B B B B B B B B B
7 1675597 rs10488360 4184450 4.18445 0.317 B B B B B B B B B B
SNP_A- A A B B B B B B A A
7 1712104 rs719423 7128355 7.128355 0.667 A A B B B B B B B B
SNPA- A A A A B A A A A A
7 1649251 rs38012 7815795 7.815795 0.464 B B B B B B B B B B
SNP A- A A A A A A A A A A
7 1714013 rs10253058 10364900 10.3649 0.738 A A A A A A A A B B

Database S2 Heterozygosity of phESC (Abbreviated as ` pC") Lines Q y ~ p ~ o ~ o 0 G ~~ a p a d y ~ o cn 'I t9 3 c o r o U U
~C b e ca , J, ~ a ~ a cw a o ¾ a a r U a ' a a SNP A- A A B B B B A A A A
7 1656052 rs7785008 10921568 10.921568 0.452 B B B B B B A A B B
SNP_A- B B A A B A A A A A
7 1678735 rs10270630 11629477 11.629477 0.738 B B B B B B A A B B
SNP A- B B A A A A A A A A
7 1672885 rs1036667 12197823 12.197823 0.488 B B B B A B A A A A
SNP_A- A A A A A A B B A A
7 1707354 rs2214867 13507965 13.507965 0.417 A A A A A A B B B B
SNP A- B B B B B B A A A A
7 1724539 rs7793372 14320689 14.320689 0.619 B B B B B B A A B B
SNP A- A A A A A A A A A A
7 1756798 rs1527203 15931001 15,931001 0.643 A A B B B B A A A A
SNP_A- A A A A A A A A A A
7 1755023 rs706057 16577230 16.57723 0.56 B B B B B B B B B B
SNP A- A A A A A A A A A A
7 1647845 rs4721619 17291814 17.291814 0.667 B B A A A A B B A A
SNP A- B B A A A A B B B B
7 1693824 rs2731551 18050825 18.050825 0.25 B B B B B B B B B B
SNP_A- B B A A A A B B A A
7 1724213 rs10486334 18974842 18.974842 0.726 B B B B B B B B A A
SNP A- B B B B B B A A B B
7 1716746 rs2248634 21065118 21.065118 0.262 B B B B B B B B B B
SNP A- A A A A A A A A A A
7 1706218 rs7781044 21636203 21.636203 0.61 A A A A A A B B B B
SNP A- B B A A A A A A A A
7 1718088 rs2286497 22701238 22.701238 0.305 B B B B B B B B B B
SNP A- B B B B B B A A B B
7 1755947 rs2521642 24200036 24.200036 0.31 B B B B B B B B B B
SNP A A A A A A A A A A A
7 1751950 rs4275130 26366016 26.366016 0.75 B B A A A A A A A A
SNP A- A A A B A A A A A A
7 1725907 rs6953785 27237607 27.237607 0.536 B B B B B B B B A A
SNP A- B B A B A A B B A A
7 1729503 rs4498447 28177012 28.177012 0.524 B B B B B B B B B B
SNP A- B B B B B B B B B B
7 1663287 rs1859681 28699408 28.699408 0.275 B B B B B B B B B B
SNP A- A A A A A A A A A A
7 1728544 rs1476991 29293282 29.293282 0.571 A A A A A A A A B B
SNP A- B B B B B B B B B B
7 1718026 rs997349 29955684 29.955684 0.357 B B B B B B B B B B
SNP A- A A A A A A A A B B
7 1695134 rs10487729 31345524 31.345524 0.726 A A A A A A B B B B
SNP A- A A B B B B B B A A
7 1694740 rs215675 32156237 32.156237 0.286 A B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines . y y .C ~ y --1 O M !t V7 7 ~D O n O
rA~ u U U U U U
p~ R ~ C.. a~ ~ c ~ a a a ~ a c p r cn o. .. a a"
SNP A- B A A A A A A A A A
7 1717858 rs10254116 33010729 33.010729 0.631 B B A A A A A A A A
SNP A- B B B B B B B B A A
7 1678175 rs10486619 33600838 33.600838 0.262 B B B B B B B B B B
SNP A- B B B B A A B B A A
7 1749566 rs741202 35093154 35.093154 0.262 B B B B B B B B A A
SNP A- B A B B B B B B B B
7 1731924 rs4720228 36725169 36.725169 0.476 B B B B B B B B B B
SNP A- A A A A A A B B A A
7 1671783 rs2893552 37928803 37.928803 0.679 A A A A A A B B A A
SNP A- B A A A A A A A A A
7 1730217 rs4723791 38613746 38.613746 0.56 B B A A A A A A A A
SNP A- A A B B B B A A A A
7 1669882 rs10486802 39497008 39.497008 0.571 A A B B B B A A A A
SNP A- A A B B A A A A A A
7 1721388 rs7807596 40599281 40.599281 0.417 A A B B B B B B A A
SNP A- A A A A A A A A A A
7 1750290 rs384469 41099793 41.099793 0.702 A B A A A A B B A A
SNP A- A A B B A A A A A A
7 1695614 rs721273 42867596 42.867596 0.702 A A B B B B A A A A
SNP A- A A A A A A A A A A
7 1736506 rs2330918 43444472 43.444472 0.75 A B A A A A A A A A
SNP A- A A A A A A A A B A
7 1732094 rs10253161 46769632 46.769632 0.714 A A A A A A A A B B
SNP A- A A A A A A B B B B
7 1710294 rs7357251 47841498 47.841498 0.417 A A A A A B B B B B
SNP A- A A A A A A A A B A
7 1669906 rs3923511 48463293 48.463293 0.688 A A A A A A B B B B
SNP A- A A B B B B B B B B
7 1748806 rs716719 50102978 50.102978 0,262 A A B B B B B B B B
SNP A- A A B B B B B B B B
7 1646085 rs2159809 52287324 52.287324 0.39 A B B B B B B B B B
SNP A- B A A A A A A A B B
7 1655668 rs6955211 63316490 63.31649 0.464 B B A A A A A B B B
SNP A- A A A A A A A A A A
7 1695272 rs9638255 67214110 67.21411 0.655 A A A A A A A B A A
SNP A- A A A A A A A A B A
7 1673105 rs1699443 68224124 68.224124 0.583 A B A A A A A A B B
SNP A- A A B B B B B B B B
7 1667673 rs10499812 69098641 69.098641 0.333 A B B B B B B B B B
SNP A- A A B B B B A A A A
7 1757146 rs6976144 77019455 77.019455 0.5 A B B B B B B B A B
SNP A- A A A A A A B B A A
7 1741890 rs10485887 77712706 77.712706 0.548 A A A B A B B B A B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines , '~' =L, C e~~C ~ - G ' G
~p. 'G O, .G _ ~ =R -1 0 M C' tn 1O O r~ 0 cc n = a c c o c c c ~
V Cj U U
c cn c SNP_A- A A B A A A A A B A
7 1663217 rs984312 78285441 78.285441 0.631 A A B B B B A A B B
SNP_A- B B B B B B A A B B
7 1676663 rs3211816 79922641 79.922641 0.39 B B B B B B B B B B
SNP_A- A A B A A A A A B A
7 1724625 rs3801720 81447606 81.447606 0.595 A B B B B B B B B B
SNP_A- A A A A A A A A A A
7 1701440 rs1693380 82818863 82.818863 0.738 A A A A A A B B A A
SNP_A- B B B B B B A A A A
7 1690947 rs10499889 84765715 84.765715 0.369 B B B B B B B B A A 11 SNP_A- A
A A JA A A A A B JA

7 1722683 rs1063964 87480120 87.48012 0.607 A A A A A A A A B B
SNP_A- B B A A A A A A A A
7 1697794 rs7799830 88761617 88.761617 0.429 B B A A A A B B A A
SNP_A- A A A A A A B B B A
7 1692549 rs3802029 90126750 90.12675 0.595 B B A B B B B B B B
SNP_A- B B A A A A A A A A
7 1721485 rs1468180 92759526 92.759526 0.441 B B A A A A A A A B
SNP_A- A A B B B B A A B A
7 1705566 rs6465448 94217939 94,217939 0.548 B B B B B B A A B B
SNP_A- A A A A A A A A A A
7 1644895 rs1403179 96113755 96.113755 0.75 B B A A A A B B A A
SNPA- B B B B B B A A B A
7 1698924 rs7779090 96790254 96.790254 0.345 B B B B B B B B B B
SNP_A- A A B A A A A A A A
7 1755481 rs2572009 99133656 99.133656 0.524 A A B B B B A A A A
SNP_A- A A A A A A A A A A
7 1669180 rs10487284 102064226 102.064226 0.667 A A A A A A A A A B
SNP_A- A A B A A A B B B A
7 1730488 rs10487162 102860400 102.8604 0.256 B B B B B B B B B B
SNP_A- A A A A A A A A A A
7 1715320 rs2519681 105578447 105.578447 0.369 B B A B B B B B A B
SNP A- A A B B B B A A B B
7 1657867 rs997381 106280867 106.280867 0.524 B B B B B B A A B B
SNP_A- A A B A A A A A B A
7 1703262 rs3801948 106832398 106.832398 0.643 A A B B B B A A B B
SNP_A- B A A A A A A A B A
7 1687475 rs1015422 107930809 107.930809 0.298 B B A B B B B B B B
SNP_A- A A B B B B A A A A
7 1643849 rs2106442 108493824 108.493824 0.476 A A B B B B B B A A
SNP_A- B A B B B B A A A A
7 1688527 rs10487320 109537858 109.537858 0.619 B B B B B B A B A A
SNP_A- A A A A A A A A A A
7 1641802 rs10500003 110076704 110.076704 0.702 A B A A A A A A A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines p ~ , ,~'. ~ cC C " ^ C
A~ ~ ~ =~ ,~ ~,ar d' 'rn ti ~ M b' N 7 ~O ~o r c. c o c. ~o p. t;
c-n ~ a a k V c ' c c SNP A- A A A A A A B A A A
7 1740412 rs10487331 110945463 110.945463 0.726 A A A B B B B B A B
SNP A - A A A A A A A A A A
7 1745955 rs2529588 111697006 111.697006 0.726 A A A A A A A B A B
SNP A- B B B B B B B A A A
7 1724315 rs1548395 112947523 112.947523 0.298 B B B B B B B B A B
SNP A- B B A A A A B B B B
7 1719538 rs6973150 114297804 114.297804 0.45 B B B B B B B B B B
SNP A- B B B, B B B A A B B
7 1736164 rs10500054 115247129 115.247129 0.5 B B B B B B A B B B
SNP A- B B A A A A B A B A
7 1733815 rs7783832 116468422 116.468422 0.298 B B B B B B B B B B
SNP A- B B A A A A A A A A
7 1676935 rs10487392 117466579 117.466579 0.488 B B B B B B A A A B
SNP A- A A B B B B A A B B
7 1647647 rs10488301 119761267 119.761267 0.262 A B B B B B A B B B
SNP A- B B B B B B A A B B
7 1655036 rs1206486 121146345 121.146345 0.441 B B B B B B A B B B
SNP A- A A A A A A B B B B
7 1643783 rs10487974 122442567 122.442567 0.381 A B B B B B B B B B
SNP A- A A A A A A A A B A
7 1690238 rs6948425 123386447 123.386447 0.476 A A B B B B A B B B
SNP A- B B A A A A B B B B
7 1745008 rs723444 124253175 124.253175 0.417 B B B B B B B B B B
SNP A- B A A A A A B A B A-7 1675675 rs2107098 124969695 124.969695 0.488 B B A A A A B B B B
SNP A- A A A A A A A A A A
7 1678693 rs2299447 125743520 125.74352 0.738 A A A A A A A A A A
SNP A- A A A A A A A A B B
7 1670675 rs6467115 126530478 126.530478 0.643 A A A A A A A A B B
SNP A- B B A A A A B B B A
7 1708033 rs10487505 127454114 127.454114 0.464 B B B B B B B B B B
SNP A- A A A A A A A A A A
7 1656498 rs10488628 127961843 127.961843 0.405 A B B B B B A A A B
SNP A- A A B B B B B A A A
7 1742598 rs7803075 130199321 130.199321 0.726 A A B B B B B B A A
SNP A- A A A A A A B B B B
7 1695048 rs1790998 133595635 133.595635 0.476 A A B B B B B B B B
SNP A- A A A A A A A A A A
7 1721434 rs2551778 134556904 134.556904 0.548 A A A A A A A A A A
SNP A- B A A A A A A A A A
7 1669022 rs10253975 135674764 135.674764 0.662 B B A A A A A A A A
SNP A- A A B B B B A A B B
7 1715624 rs2253729 139396073 139.396073 0.583 A B B B B B A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ , W W -1 O M et Ii D O C- ~ .
~ a a~ ~ ca ro o 0 aa 0~ R a ~ n c c' a o n r rn U
c SNP_A- A A B B B B A A A A
7 1652925 rs1527304 141162389 141.162389 0.571 A A B B B B A A A B
SNP_A- A A A A A A A A A A
7 1715016 rs6949653 143162918 143.162918 0.691 A' B B B B B A A A A
SNP_A- A A B B B B A A A A
7 1666637 rs4725680 144870787 144.870787 0.369 A B B B B B A A A A
SNP_A- A A A A A A A A B A
7 1681703 rs10487936 145527849 145.527849, 0.732 A A A A A A A A B B
SNP_A- A A A A A A A A A A
7 1680321 rs10278315 146403556 146.403556 0.726 A A A A A A A A A A
SNP_A- A A A A A A A A B B
7 1720798 rs1177946 147495250 147.49525 0.643 A A A A A A A A B B
SNP_A- A A A A A A B B A A
7 1713513 rs1403222 149691561 149.691561 0.536 B B A A A A B B A B
SNP_A- A A B B B B A A A A
7 1736364 rs306293 154243700 154.2437 0.643 A A B B B B A A B B
SNP_A- A A A A B A B B A A
7 1691199 rs2301916 156473603 156.473603 0.369 B B B B B B B B B B
SNPA- A A A A A A A A A A
8 1659972 rs747351 228574 0.228574 0.369 B B B B A B B B A B
SNP_A- B B A A A A A A A A
8 1725579 rs4876153 2291741 2.291741 0.691 B B A A A A A A A B
SNP_A- A A B B B B B B B A
8 1651465 rs9314492 3332437 3.332437 0.476 A A B B B B B B B B
SNPA- A A A A A A B A B A
8 1695486 rs10503246 4117771 4.117771 0.714 B B A A A A B, B B B
SNPA- A A A A A A B A B B
8 1650643 rs4146469 5253259 5.253259 0.441 B B B B B B B B B B
SNP_A- A A A A A A B B A A
8 1714359 rs6559072 5839489 5.839489 0.679 B B A A A A B B A A
SNP_A- A A B B B B A A B A
8 1660050 rs3020252 6450411 6.450411 0.634 B B B B B B A A B B
SNP_A- A A A A A A A A A A
8 1757262 rs2409113 8849712 8.849712 0.72 B B A A A A A A A A
SNP_A- A A A A A A A A A A
8 1680667 rs1588198 9929939 9.929939 0.655 B B B B B B A B A A
SNP_A- A A A A A A A A A A
8 1679891 rs2278335 10740863 10.740863 0.702 B B A A A A A A A B
SNP A- A A A A A A A A B B
8 1715348 rs10503478 13876453 13,876453 0.607 A A B B B B A B B B
SNPA- A A A A A A B B A A
8 1659353 rs2410193 14445035 14.445035 0.738 A A A A A A B B A B
SNPA- A A A A A A A A B A
8 1756484 rs351572 16065839 16.065839 0.595 A A A A A A A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
~-. 'a R e~V L 7 W ~"~ G O. f3. tL `D CL
U U U
vr ~" . . Q Q fx u A a, a SNP_A- B B A A A A B B B A
8 1750990 rs7003503 17226143 17.226143 0.25 B B B A B B B B B B
SNP_A- A A A B A A B B B A
8 1688509 rs7006702 19316813 19.316813 0.333 A B B B B B B B B B
SNP_A- A A A B A A A A A A
8 1747706 rs2083637 19909455 19.909455 0.738 A B B B B B B B A A
SNPA- B A B B B B B B A A
8 1646595 rs2306518 22526253 22.526253 0.357 B, B B B B B B B A A
SNP A- A A A A A A A A A A
8 1699334 rs10503733 23589963 23.589963 0.714 A B A A A A B B A A
SNP_A- B A A A A A A A B B
8 1752532 rs2976457 24923988 24.923988 0.548 B B A A A A B B B B
SNPA- B B A A A A A A A A
8 1746191 rs10503776 25765786 25.765786 0.671 B B A A A A B B A A
SNP_A- A A B A A A A A B B
8 1742962 rs10503872 30556573 30.556573 0.476 A B B A A B A A' B B
SNP_A- A A A B B A A A A A
8 1710298 rs10503907 32291552 32.291552 0.607 A A A B B B B B A B
SNP_A- A A B A A A B B A A
8 1646333 rs1551652 34443033 34.443033 0.662 A A B A A B B B A A
SNP_A- B B B A A A A A B B
8 1679337 rs10503970 34985910 34.98591 0.262 B B B A A B B B B B
SNPA- B B A A A A B B B A
8 1701068 rs581187 37119893 37.119893 0.286 B B A A A A B B B B
SNPA- A A B B B B B B B B
8 1747018 rs3935233 39307991 39.307991 0.31 A B B B B B B B B B
SNP_A- A A B A A A B B B B
8 1730295 rs9298596 40431722 40.431722 0.333 A A B A A B B B B B
SNPA- A A A B B A A A B A
8 1664173 rs341817 50186153 50.186153 0.56 A A A B B B A B B B
SNP_A- B B B B B B B B B B
8 1712754 rs318913 51075845 51.075845 0.262 B B B B B B B B B B
SNP_A- A A A A A A A A A A
8- 1716236 rs10504120 52554998 52.554998 0.726 A A A A A A A A A A
SNP_A- A A A B A A A A B B
8 1645251 rs2249236 53110767 53.110767 0.286 A B A B B B A B B B
SNP_A- B B B A A A A A B 13 8 1674928 rs360956 54063839 54.063839 0.61 B B B A B B A A B B
SNP_A- A A B A A A A A A A
8 1661925 rs7824078 55966296 55.966296 0.631 A A B A B B A A A B
SNP_A- A A A B A A A A A A
8 1734483 rs2670052 57666163 57.666163 0.583 A B A B B B A A A A
SNPA- A A A B A A A A A A
8 1649879 rs9297980 58641477 58.641477 0.476 A A B B B B A B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ C c~~e q ' p p "t'v o t7 o ry) cl) d d~ ~r u U U U U U U
C. R. G f3, r`
Cj k a c a SNP_A- B B B B B B B B A A
8 1689109 rs7012230 62449232 62.449232 0.31 B B B B B B B B B B
SNP_A- B B B B B B A A A A
8 1729837 rs874777 65147501 65.147501 0.583 B B B B B B A A A A
SNP_A- B A A A A A A A A A
8 1688563 rs977467 67469418 67.469418 0.56 B B A A A A A B B B
SNP_A- A A A A A A A A A A
8 1656454 rs900896 68690751 68.690751 0.702 A A B A B B A A A A
SNP_A- B A A A A A B B A A
8 1673083 rs1404605 69369253 69.369253 0.585 B B A A A A B B A A
SNP_A- A A B B B B A A A A
8 1673921 rs10504451 70626182 70.626182 0.524 A B B B B B A A B B
SNP_A- B A A A A A B A A A
8 1660240 rs10504477 71500739 71.500739 0.487 B B B A B B B B B B
SNP_A- A A A A A A A A A A
8 1698932 rs2732090 72080811 72.080811 0.5 A B A A A A A B B B
SNP_A- A A A A A A B A A A
8 1710462 rs10504526 73129106 73.129106 0.548 A A A A A A B B A A
SNP_A- B B A A A A A A A A
8 1684163 rs10504552 75038119 75.038119 0.286 B B A A A A A A A A
SNP_A- B B B B B B B B A A
8 1673775 rs1375646 76679672 76.679672 0.321 B B B B B B B B B B
SNP_A- B B A A A A A A A A
8 1753574 rs1993196 78213269 78.213269 0.583 B B A A A A B B A A
SNP_A- A A A B A A A A A A
8 1713893 rs2461063 80781668 80.781668 0.631 A A B B B B B B B B
SNP_A- B B A A A A B B B B
8 1650035 rs1199030 81917969 81.917969 0.357 B B A A A A B B B B
SNPA- A A A A A A B B A A
8 1709456 rs1525339 83916405 83.916405 0.738 A A A A A A B B A A
SNP_A- B B B B B B B B A A
8 1747972 rs1465809 85243012 85.243012 0.25 B B B B B B B B B B
SNPA- A A B B B B A A A A
8 1690861 rs3808538 86308563 86.308563 0.738 A A B B B B A A B B
SNPA- B B A A A A A A B B
8 1642120 rs10504819 87183400 87.1834 0.369 B B A A A A A A B B
SNPA- B B B B B B B B B B
8 1704458 rs997597 88259667 88.259667 0.274 B B B B B B B B B B
SNP_A- B B B B B B A A A A
8 1731702 rs10504855 88844371 88.844371 0.345 B B B B B B B B B B
SNPA- A A B B B B A A A A
8 1669078 rs160410 90717844 90.717844 0.658 A A B B B B A A A A
SNP_A- A A A A A A A A A A
8 1713264 rs1818193 91886818 91.886818 0.631 A A A A A A A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
p CC a! y ti O M '7 ~ ~D o r O
V C.) u 7 U "O U 'O ~y ~ CQ Ctl -~i= ~ ~ II. ~l LL CL C3. p~D ry l~
wu a SNP A- B B B B B B A A A A
8 1679699 rs2245797 95329376 95.329376 0.31 B B B B B B B B B B
SNP A- A A A A A A A A B B
8 1738642 rs962451 101400186 101.400186 0.583 A A A A A A A A B B
SNP A- B B A A A A B B B B
8 1677965 rs4495397 103476369 103.476369 0.268 B B A A A A B B B B
SNP A- A A B B B B A A A A
8 1718730 rs543736 104082125 104.082125 0.619 B B B B B B A B A A
SNP A- A A B B B B B A B B
8 1724051 rs10505064 105831730 105.83173 0.345 B B B B B B B B B B
SNP A- A A A B A A A A B B
8 1691919 rs2930485 107881851 107.881851 0.607 B B B B B B A B B B
SNP A- A A A A A A A A A A
8 1652191 rs10505107 108392560 108.39256 0.619 A A B A B B A A A A
SNP_A- B B B B B B B B A A
8 1756952 rs1353298 108959098 108.959098 0.321 B B B B B B B B B B
SNP A- A A A B A A A A A A
8 1695466 rs5772 110167808 110.167808 0.571 B B B B B B A B B B
SNP A- A A B B B B A A A A
8 1747370 rs10505135 111120579 111.120579 0.345 A A B B B B A B B B
SNP A- A A B B B B B B B B
8 1745327 rs10505156 112369457 112.369457 0.25 B B B B B B B B B B
SNP A- A A A A A A A A A A
8 1681911 rs10505180 113392265 113.392265 0.726 B B A A A A A A A A
SNP A- B B A B A A B A B B
8 1694542 rs2125552 113984509 113.984509 0.274 B B B B B B B B B B
SNP A- B B B B B B B B A A
8 1713409 rs9297496 114629527 114.629527 0.321 B B B B B B B B B B
SNP A- B B B B B B B B B B
8 1725803 rs7828185 116438576 116.438576 0.286 B B B B B B B B B B
SNP A- A A B B B B B B B B
8 1698988 rs10505328 119219639 119.219639 0,441 B B B B B B B B B B
SNP A- A A A A A A B A A A
8 1753414 rs3924784 121618858 121.618858 0.667 A A A A A A B B B B
SNP A- A A A A A A B A A A
8 1735413 rs17478 122793072 122.793072 0.595 A A B A B B B B B B
SNP A- B B B B B B B A A A
8 1655430 rs6470143 124219594 124.219594 0.345 B B B B B B B B A A
SNP A- A A A A A A B B A A
8 1754805 rs3909562 124803864 124.803864 0.405 A B A A A A B B B B
SNP A- B A B B B B B A B B
8 1696789 rs2382993 125770106 125.770106 0.345 B B B B B B B B B B
SNP A- B A A B A A A A A A
8 1686811 rs897153 126747483 126.747483 0.643 B B B B B B A B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~ p,, = 8 - ' ~ c = e c CQ cd tn ~ ~D O [ i 0 ~ cp ~ v a~ a~i R G ~ G G LL 7 G ~C p. l~
~ a ~ ~ w v a o d SNP A- A A B B B B A A A A
8 1753008 rs2091933 127485749 127.485749 0.679 A B B B B B A A B B
SNP A- B B B B B B B A A A
8 1651085 rs10505486 128074016 128.074016 0.441 B B B B B B B B B B
SNP A- B B A A A A A A A A
8 1682761 rs4123791 129288419 129.288419 0.417 B B A A A A A A A A
SNP A- B A B B B B B B B B
8 1692841 rs9297775 129805894 129.805894 0.333 B B B B B B B B B B
SNP A- A A A A A A B B B B
8 1653731 rs10505545 130646449 130.646449 0.538 A A B B B B B B B B
SNP A- A A A A A A A A A A
8 1655374 rs7460225 131408555 131.408555 0.464 A B B B B B A B A A
SNP A- B A A A A A B B A A
8 1672735 rs7008202 132143592 132.143592 0.357 B B A A A A B B B B
SNP A- B B B B -B B A A B B
8 1725115 rs4736424 133782292 133.782292 0.31 B B B B B B A B B B
SNP A- A A B B B B B B A A
8 1647079 rs10505607 134527931 134.527931 0.441 A B B B B B B B B B
SNP A- A A B B B B A A A A
8 1700220 rs4909801 135948341 135.948341 0.702 A B B B B B A B A A
SNP A- A A B A A A B B A A
8 1675316 rs4909582 137288153 137.288153 0.488 A A B B B B B B A A
SNP A- B A B B B B B B A A
8 1661056 rs9324439 138086052 138.086052 0.452 B B B B B B B B B B
SNP A- A A A A A A B B A A
8 1689603 rs1325053 139156386 139.156386 0.732 A A A B B B B B A A
SNP A- A A B A A A A A A A
8 1710354 rs2468705 140618265 140.618265 0.75 B B B B B B A A A A
SNP A- A A A A A A A A B B
9 1643050 rs10491691 336963 0.336963 0.655 B B A A A A B B B B
SNP A- A A A A A A A A A A
9 1704718 rs2370220 907667 0.907667 0.726 A A B B B B A A A A
SNP A- B B A A A A A A A A
9 1681445 rs7040916 2645520 2.64552 0.726 B B A A A A A A A A
SNP A- A A B B B B B B A A
9 1734535 rs1358908 3162093 3.162093 0.524 A A B B B B B B A A
SNP A- B B B B B B A A A A
9 1685961 rs1455177 3782613 3.782613 0.488 B B B B B B B B B B
SNP A- B B B B B B B B B B
9 1642494 rs10491650 5193054 5.193054 0.354 B B B B B B B B B B
SNP A- B B B B B B B B B B
9 1696419 rs1407473 7989681 7.989681 0.31 B B B B B B B B B B
SNP A- A A A A A A B B B B
9 1709516 rs1433548 8927116 8.927116 0.31 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines !t m VtA ; b 0 r 0 G. 'D G
-7=~ ~ ~ L .C ( y V G ~ G C7.

SNP A- A A A A A JA B B A A
9 1682679 rs1613507 9791755 9.791755 0.563 B B A A A A B B A A
SNP A- A A A A A JA A A A A
9 1673445 rs10511545 10341048 10.341048 0.726 A A A A A A A A A A
SNP A- A A A A A A B B B B
9 1679185 rs4740473 11080005 11.080005 0.369 B B A A A A B B B B
SNP A- B B B B B B A A A A
9 1744452 rs 1825739 11777410 11.77741 0.429 B B B B B B B B A B
SNP A- A A B B B B A A 'A A
9 1714556 rs1086377 12824688 12.824688 0.702 A A B B B B'B B A A
SNP A- A A A A A A B B B A
9 1672461 rs7038474 13355816 13.355816 0.702 B B A A A A B B B B
SNP A- A A A A A A A A A A
9 1704214 rs10511587 13970584 13.970584 0.738 B B A A A A B B A A
SNP A- A A A A A A A A A A
9 1714243 rs4615688 14495861 14.495861 0.714 A A A A A A A A A A
SNP A- B B B B B B A A A A
9 1741448 rs10511603 15006475 15.006475 0.536 B B B B B B B B A A
SNP_A- B B A A A A A A A A
9 1742240 rs1001265 17618726 17.618726 0.726 B B A A A A A A A A
SNP A- B B A A A A A A B B
9 1675206 rs7862683 18257947 18.257947 0.427 B B A A B B B B B B
SNP A- A A B B A A A A B A
9 1706426 rs7859334 20660966 20.660966 0.56 A A B B B B B B B B
SNP A- A A A A A A A A B A
9 1669996 rs871024 21793880 21.79388 0.441 A A A A A A B B B B
SNP A- B B B B A A A A B A
9 1662201 rs10511705 22537789 22.537789 0.512 B B B B B B B B B B
SNP A- A A A A A A A A A A
9 1673761 rs9298846 23216243 23.216243 0.655 B B A A A A A A A B
SNP A- B B B B B B A A A A
9 1752066 rs10511761 25602704 25.602704 0.441 B B B B B B A A A A
SNP A- A A B B B B B B B B
9 1690106 rs4978049 26131011 26.131011 0.381 B B B B B B B B B B
SNP A- B B B B A A A A A A
9 1700687 rs983863 26681668 26.681668 0.345 B B B B B B A A A A
SNP A- B B B B A A A A A A
9 1690672 rs1452357 28090846 28.090846 0.707 B B B B B B A A A A
SNP A- A A A A A A A A B B
9 1693514 rs824257 28765262 28.765262 0.655 A A A A A A A A B B
SNP A- A A B B A A B B A A
9 1665553 rs10511842 30009704 30.009704 0.25 A B B B B B B B A B
SNP A- B A B B A A A A B B
9 1724125 rs10511886 31826555 31.826555 0.607 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines .. ' ~ - C c~rC q ~ C C
z '~ 'a ~ Q =~ ti ~ M d' V7 7 ~O ~ r ~ ..
cn c c o o c c ~
~ a b n a ~`~ ~j d ; U U
a ~ a a SNP_A- A A B B B B A A A A
9 1648177 rs20583 33016572 33.016572 0.452 A B B B B B A A A B
SNP_A- A A A A A A A A A A
9 1717742 rs6476493 35884737 35.884737 0.691 A A A A A A A A A A
SNP_A- A A B B B B B B B B
9 1671263 rs4880042 36940301 36.940301 0.393 A A B B B B B B B B
SNP_A- B A A A A A A A B A
9 1681599 rs2181139 38364977 38.364977 0.25 B B A A A A B B B B
SNP_A- B B B B B B B B B B
9 1666811 rs4111409 40345280 40.34528 0.262 B B B B B B B B B B
SNP_A- B B B B B B B B A A
9 1727790 rs7864775 69030853 69.030853 0.548 B B B B B B B B A B
SNP_A- B B A A A A B A B B
9 1699350 rs10511972 69672094 69.672094 0.619 B B A A A B B -B B B
SNP_A- A A A A A A A A A A
9 1753754 rs10511984 70399849 70.399849 0.75 A A A A A A A B A A
SNP_A- A A A A A A A A B A
9 1748876 rs10511999 71526051 71.526051 0.595 A A A A A A A A B B
SNP A- B B B B B A B B B B
9 1750024 rs1998372 72123726 72.123726 0.369 B B B B B B B B B B
SNP_A- B B B B B B B B B A
9 1733975 rs2377524 76002013 76.002013 0.321 B B B B B B B B B B
SNPA- A A A A A A A A B B
9 1707951 rs10512079 78602073 78.602073 0.25 A A A A B B A B B B
SNP_A- A A A A A A A A A A
9 1655498 rs1316823 79531349 79.531349 0.643 B B A A A A A A A A
SNP_A- A A A A A A A A B A
9 1721234 rs1572147 80160841 80.160841 0.634 A A B A B B A A B B
SNPA- B B B B B B A A A A
B
9 1757764 rs7873639 80780459 80.780459 0.286 B B B B B B A A A
A
SNP_A- B B B B B B B B A
9 1685995 rs2774635 82184146 82.184146 0.286 B BB B B B B B A B
SNPA- A A A A A A A A A A
9 1698246 rs1436932 83903397 83.903397 0.476 B B A A A A A A A B
SNPA- A A A B A A B B A A
9 1743644 rs7030902 85064645 85.064645 0.548 A A B B B B B B A B
SNP_A- B B A A A A A A A A
9 1642838 rs1475524 87362117 87.362117 0.357 B B B A B B A B A A
SNP_A- B B A A A A B B A A
9 1683979 rs4744114 91732136 91.732136 0.452 B B B A B B B B A A
SNPA- A A B B B B A A A A
9 1645449 rs1547201 95896039 95.896039 0.548 A A B B B B B B B B
SNP_A- B B A A A A A A A A
9 1751508 rs1924001 102134812 102.134812 0.643 B B A A A A B B A A

Database S2 Heferozygosity of phESC (Abbreviated as "pC") Lines Q w ~ c ~ ~ o 0 ,C ~ FI z O. B. ~.Gr Qi vv'~I ' O M V' N ~D O h O
cnr~ .G ~ v~i v CS' V U ~ V U U (J ro ~ ~
~ y.y ~ CQ CC V ,~ CL "a a G Qi ~D G 1~
v .Q .O ~Ty ~ ~ ! d. Rn SNP_A- B B A A A A B B A A
9 1724479 rs1463983 105506339 105.506339 0.429 B B B A B B B B B B
SNP_A- B B A A A A B B B B
9 1653563 rs2418076 110092906 110.092906 0.298 B B A A A A B B B B
SNP_A- A A B B B B A A B B
9 1744924 rs1813202 111767658 111.767658 0.286 B B B B B B B B B B
SNP A- B B A B A A A A B B
9 1731818 rs10513222 113757379 113.757379 0.321 B B B B B B A A B B
SNP_A- A A A A A A A A A A
9 1733479 rs10513267 115067920 115.06792 0.75 A B A A A A A A A A
SNP-A- A A A A A A A A A A
9 1643236 rs4112759 117313823 117.313823 0.75 A A A A A A A A A A
SNP_A- A A A B A A A A B B
9 1750306 rs7849366 118191918 118.191918 0.286 A A B B B B B B B B
SNP_A- B B B B B B B B B B
9 1686447 rs10514837 118919482 118.919482 0.321 B B B B B B B B B B
SNP_A- B A A A A A B B B B
9 1656426 rs10491529 120012279 120.012279 0.25 B B B B B B B B B B
SNP-A- A A A A A A A A A A
9 1677789 rs306796 121206889 121.206889 0.631 A A A A A A A A B B
SNP-A- A A A A A A A A A A
9 1705544 rs7043602 126285054 126.285054 0.738 A A A A A A B B A A
SNP_A- B B A A A A A A A A
9 1653355 rs883335 129165519 129.165519 0.595 B B B B B B A A B B
SNP_A- B A A A A A A A A A
9 1699424 rs2269337 130602238 130.602238 0.742 B B A A A A A A A A
SNP_A- B B A A A A A A A A
9 1747024 rs2809243 132799854 132.799854 0.298 B B A A A A B B A A
1 SNP_A- A A A A A A A A A A
0 1659685 rs1392827 1234414 1.234414 0.667 A A B B B B B B A A
1 SNP A- B B B B B B B B B B 0 1753764 rs4880915 1747289 1.747289 0.293 B B B
B B B B B B B
I SNP-A- A A A A A A A A A A
0 1727231 rs9329289 2532389 2.532389 0.405 A A B B B B B B B B
I SNP-A- B B B B B B A A B B
0 1732637 rs2388557 3181527 3.181527 0.321 B B B B B B B B B B
I SNP A- B B B B B B B B B B
0 1679829 rs1679440 4468715 4.468715 0.286 B B B B B B B B B B
1 SNP_A- A A A A A A B B A A
0 1713889 rs946785 7041660 7.04166 0.595 A A B B B B B B B B
1 SNP_A- B B B B B B B B A A
0 1717612 rs4385796 8539643 8.539643 0.286 B B B B B B B B A B
1 SNP_A- A A A A A A $ B A A
0 1740604 rs1762757 9449776 9.449776 0.726 A A A A A A B B A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ^ c 2 0 0 ~, ~ z a a p ~ ~ o rP er v~ 5 ~o o c~ o p., e v o v v c c c ~ c o ¾ r ~ p" c s k u a : a a 0 1686911 rs10508380 10003736 10.003736 0.738 A A B B A B B B A A
1 SNP_A- B B A A B A A A B B
0 1739848 rs1041044 10644387 10.644387 0.5 B B B B B B B B B B
1 SNP_A- B B B B B B B B B B
0 1721418 rs4750093 11829643 11.829643 0.429 B B B B B B B B B B

0 1739768 rs1108131 12537753 12.537753 0.75 B B B B A B B B A A
1 SNP_A- A A A A A A A A A A
0 1737160 rs564166 13110955 13.110955 0.738 B B A A A A A A A A
I SNP-A- A A A A B A A A A A
0 1678303 rs10508465 13725194 13.725194 0.429 A A B B B B B B A A
I SNP_A- B B B B B B A A A A
0 1669628 rs10508473 14241057 14.241057 0.417 B B B B B B B B A A
I SNP-A- B B B B B B B B B A
0 1714770 rs1361588 16119457 16.119457 0.298 B B B B B B B B B B
I SNP_A- A A B B B B A A B B
0 1700268 rs10490962 17240369 17.240369 0.56 B B B B B B B B B B
I SNP A- A A A A B A B B B B
0 1744374 rs10508555 18316688 18.316688 0.441 B B B B B B B B B B
I SNP_A- B B A A A A B B A A
0 1748644 rs984292 19028813 19.028813 0.393 B B B B A B B B A B
I S1VP_A- A A B B B B A A A A
0 1686549 rs2358348 19533421 19.533421 0.643 A A B B B B A A A A
I SNP A- B B A A B A B B B B
0 1678189 rs788977 21229153 21.229153 0.262 B B B B B B B B B B

0 1672001 rs1417374 23168481 23.168481 0.298 B B A A A A A A A B
1 SNP_A- B B B B B B B B B B
0 1726471 rs2150651 24829491 24.829491 0.321 B B B B B B B B B B
1 SNP_A- A A A A A A A A A A
0 1751938 rs10508686 25367068 25.367068 0.714 A A B B A B A A A A
I SNP A- A A A A B A A A A A
0 1713661 rs4747530 25876455 25.876455 0.56 B B B B B B B B A A
I SNP A- A A A A A A B B B B
0 1706402 rs10508717 26712334 26.712334 0.524 A A B B A B B B B B

0 1713649 rs1970631 28271741 28.271741 0.452 A A B B B B A A A B
1 SNP_A- B B A A B A B B B A
0 1907064 rs703041 29265782 29.265782 0.25 B B B B B B B B B B
1 SNP_A- A A A A B A B A B B
0 1755663 rs2776644 30294654 30.294654 0.488 B B B B B B B B B B
1 SNP_A- B A A B B A A A A A
0 1679427 rs2490527 32711123 32.711123 0.631 B B B B B B A B A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L 4 1.
p p.~ ~ ~ b c~~e p q C
F~ R R A Q y r-i O M 'V' N ~O O r o u ~ ~~ C~J C~i ~ Q u V ~ V V V V V
Vj ~i ''~U C~7 c~ ~ I~.R G ''! G G G G D O+ l~
k V a 3 o n 0 1678169 rs2269101 33546185 33.546185 0.286 A B B A A B B B B B
I SNP A- A A A A A JA B A A A
0 1674978 rs224750 34271036 34.271036 0.619 A A A A A A B B A A

0 1722205 rs1032408 43808849 43.808849 0.738 A A B B B B A A A A

0 1700828 rs1583421 45099157 45.099157 0.583 B B A A A A A A A A
I SNP A- B B A B B A A A A A
0 1718604 rs10508908 49643864 49.643864 0.5 B B A B B B A B B B

0 1741518 rs10508929 51841987 51.841987 0.423 A B A B B B B B A A
I SNP A- A A B B B B B B A A
0 1674358 rs2339628 52548976 52.548976 0.679 A B B B B B B B B B

0 1665161 rs1937666 53326630 53.32663 0.464 B B A B B B A B B B
I SNP A- B B B A A A A A B B
0 1648887 rs10508976 54302305 54.302305 0.56 B B B A B B B B B B
I SNP A- A A B A A A A A A A
0 1660432 rs422296 54965065 54.965065 0.714 A A B A B B A A B B

0 1642640 rs6481257 58608558 58.608558 0.274 B B B B B B B B B B

0 1697033 rs10509093 60193775 60.193775 0.452 A A B B B B A A A A

0 1723683 rs4245585 61596196 61.596196 0.286 B B B A B B B B B B
I SNP A- A A A A A A A A A A
0 1653973 rs10509139 62150158 62.150158 0.691 B B A A A A A A A A
I SNP A- B B B B B B B B B B
0 1713014 rs2787720 63018471 63.018471 0.488 B B B B B B B B B B
I SNP A- B B B B B B A A A A
0 1667099 rs1255484 65108003 65.108003 0.488 B B B B B B B B A A
I SNP A- A A B B B B B B B B
0 1658163 rs7073489 67452445 67.452445 0.274 B B B B B B B B B B

0 1642112 rs4746654 68476694 68.476694 0.441 B B B B B B B B B B

0 1720304 rs7918860 70340702 70.340702 0.583 B B A B B B A A B B
I SNP A- A A A A A A B B A A
0 1729287 rs10509321 71655739 71.655739 0.298 B B A A A A B B B B
I SNP A- B B B B B B A A A A
0 1707688 rs10509334 73110058 73.110058 0.427 B B B B B B B B A A
I SNP A- A A B A A A B B B B
0 1654508 rs1865636 77473753 77.473753 0.5 A A B A B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as' pC") Lines L L L
=~ cv 'i.' ' =' C O
=cCh Fl ~ =cd ~ ~ 'y r1 O M <1' ~ b O [~ O
u u u ca a a a a e ,a ~j V U
a a a I SNP A- A A A A A JA A A A A
0 1697249 rs10509384 78693188 78.693188 0.726 B B A A A A B B B B

0 1679101 rs1344967 79197624 79.197624 0.262 A A B B B B B B B B

0 1748530 rs10509397 79905374 79.905374 0.476 B B A B B B B B A A
I SNP A- A A A B A A A A A A
0 1736610 rs7914988 80540330 80.54033 0.441 B B A B B B A A B B

0 1665139 rs342372 84579316 84:579316 0.536 B B B A B B A A B B

0 1715818 rs2067731 86973180 86.97318 0.381 B B B A B B B B A A
I SNP A A A A A A A B B A A
0 1689101 rs2949392 87497414 87.497414 0.5 A A B A B B B B B B
I SNP A- B B A A A A A A A A
0 1657815 rs391683 90510663 90.510663 0.679 B B B A B B B B A A

0 1706118 rs303212 91151335 91.151335 0.298 B B B B B B B B B B

0 1703070 rs747334 92734724 92.734724 0.476 A A B B B B B B A A

0 1717632 rs716361 93308518 93.308518 0.321 B B B B B B B B B B

0 1713435 rs2490739 94587885 94.587885 0.631 A A A A A A A A A A
I SNP A- A A A A A A B B A A
0 1642080 rs3781270 95520148 95.520148 0.607 A A A A A A B B B B
I SNP_A- A A A A A A A A A A
0 1680183 rs10509692 97226588 97.226588 0.583 B B B B B B A A B B

0 1705694 rs10509700 97884521 97.884521 0.5 A A B B B B A A B B

0 1753314 rs793515 98978459 98.978459 0.345 B B B B B B B B B B

0 1742188 rs10509754 103711687 103.711687 0.262 B B B B B B B B B B
I SNP A- A A A A A A A A B B
0 1716744 rs2451500 106622867 106.622867 0.707 A A A A A A B B B B

0 1684935 rs10509832 109070424 109.070424 0.667 A A B B B B B B B B
I SNP A- A A A A A A B B B B
0 1676403 rs4113 111223756 111.223756 0.369 A A B B B B B B B B
1 SNP A- A A~ A A A A A A A A
0 1726183 rs7099088 114343455 114.343455 0.631 B B B B B B B B A A
I SNP A- B B B B B B B B A A
0 1732939 rs10509976 115170888 115.170888 0.286 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines Fl L L ~ R p ~ p p ..
'~ Pa cp ai d N ~ 'C 7 R7 o cn ~~ R ~~ v ~ c =~ a a a o a o Va ~
I SNP A- A A B B B B B B B B
0 1675599 rs2420070 116671318 116.671318 0.548 B B B B B B B B B B
I SNP A- B B B B B B A A A A
0 1700278 rs4447088 117536799 117.536799 0.274 B B B B B B B B B B

0 1660760 rs880977 118409221 118.409221 0.452 B B A A A A B B B B

0 1747698 rs2619111 118956986 118.956986 0.702 A A B B B B A A A A

0 1682085 rs10490913 120144426 120.144426 0.537 B B B B B B B B B B
I SNP A- A A B B B B A A B B
0 1731688 rs1980030 120960017 120.960017 0.393 B B B B B B B B B B

0 1641760 rs1326654 122305416 122.305416 0.405 B B B B B B B B B B

0 1741090 rs2420995 123842994 123.842994 0.393 B B B B B B B B B B
I SNP A- A A A A A A A A A A
0 1751948 rs845101 125180422 125.180422 0.631 B B A A A A A A A A
I SNP A- B B B B B B A A B B
0 1711689 rs1278305 127801415 127.801415 0.524 B B B B B B B B B B
I SNP A- A A A A A A A A A A
0 1715610 rs10510154 128412532 128.412532 0.738 A A A A A A A A A A

0 1706112 rs2251104 130003906 130.003906 0.333 A A B B B B B B B B

0 1712012 rs1886380 130596834 130.596834 0.702 A A B B A B A A B B
1 SNP A- A A B B B B B B A. A
0 1652639 rs4077516 133237947 133.237947 0.369 A B B B B B B B B B

1 1727870 rs2499935 5066470 5.06647 0.417 B B A B B B B B B B

1 1656094 rs2001778 5575584 5.575584 0.452 B B B B B B B B B B

1 1680969 rs10500667 6284499 6.284499 0.274 B B A B B B B B B B

1 1656388 rs2595456 6841339 6.841339 0.524 B B B B B B B B B B
I SNP A- A A B B B B A A A A
1 1649885 rs3884596 7488751 7.488751 0.571 B B B B B B A B B B
I SNP A- B B A A A A B B B B
1 1663461 rs3993279 10627568 10.627568 0.321 B B B B A B B B B B

1 1723239 rs10500740 11167698 11.167698 0.274 B B B B B B B B B B
1 SNP A- A A B f13 B B A A B B
1 1712474 rs1344613 12408280 12.40828 0.31 B B B B B B B B B B

Database S2 Heterozygosity of PhESC (Abbreviated as "pC") Lines s. s. ~.
~ = y p q o o 0 p, ca c~ ~ ~'v, =~ o cn er tn 5 \o o c~ o `' o cc U
a a c' C. c I SNP A- A A A A A A A A B B
1 1705810 rs1894131 15104916 15.104916 0.441 A B A A A A B B B B
I SNP_A- A A B B B B B B A A
1 1674594 rs2190454 17490211 17.490211 0.333 A B B B B B B B B B
I SNP A- B B A A A A B B A A
1 1701156 rs211102 18003069 18.003069 0.25 B B B B A B B B B B
1 SNP_A- B B A A A A A A A A
1 1685951 rs894556 19822510 19.82251 0.56 B B B B B B A A B B
1 SNP_A- B A A A A A A A A A
1 1685201 rs10500886 20976742 20.976742 0.607 B B A A A A A A A A
1 SNP_A- B B A A A A B B A A
1 1668135 rs6483807 21873219 21.873219 0.5 B B A B B B B B A A
1 SNP_A- B A B B B B A A A A
1 1713403 rs10500927 22398998 22.398998 0.262 B B B B B B B B B B
1 SNP_A- B B B A A A A A A A
1 1697826 rs1600958 23180524 23.180524 0.388 B B B B B B A A A A
I SNP_A- A A B B B B A A A A
1 1753516 rs975980 24515539 24.515539 0.441 A B B B B B A A B B

1 1652525 rs10501011 25497059 25.497059 0.417 A B B B B B A A B B
I SNP_A- A A A A A A A A A A
1 1665219 rs980562 30413393 30.413393 0.726 A B A B B B B B A A
i SNP_A- B B B A A A B B B B
1 1720570 rs1848394 30965654 30.965654 0.619 B B B B B B B B B B
I SNP_A- B B A A A A B B A A
1 1749112 rs10488689 31659092 31.659092 0.286 B B A A A A B B B B
1 SNP_A- B B B B B B B B B B
1 1701102 rs1033717 33023147 33.023147 0.342 B B B B B B B B B B
1 SNP_A- B B B A A A A A A A
1 1752850 rs2136509 34753380 34.75338 0.537 B B B B B B A A B B
I SNP_A- A A A A A A A A B B
1 1691121 rs10501163 36830990 36.83099 0.286 A A A A A A A A B B
1 SNP_A B A A A A A A A B B
1 1725595 rs992118 40016469 40.016469 0.286 B B A B B B A B B B
1 SNP_A- A A A A A A B A B A
1 1667717 rs7102885 40922404 40.922404 0.655 A A A B B B B B B B
1 SNP_A- A A B A A A A A A A
1 1717738 rs1531932 41781058 41.781058 0.643 A A B B A B A A A A
I SNP_A- A A B B B B B A B B
1 1709380 rs692726 50396846 50.396846 0.321 A A B B B B B B B B
I SNP_A- A A A B B A A A A A
1 1752494 rs629948 55113024 55.113024 0.643 A A A B B B A A A A
I SNP_A- A A B A A A B A B B
1 1697650 rs1080800 56067666 56.067666 0.381 A B B A A B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L L
p .. .. ~ t¾ C 'C Ci Fl ~ ~ R RI ~ ' Q 'rn -i O M 'd' ln D ID O N
u a a z ~
U u w a a a I SNP A- A A B B B B B A B A
1 1658985 rs540505 56621831 56.621831 0.536 A B B B B B B B B B

1 1749414 rs612688 57333672 57.333672 0.25 B B B B B B A A B B

1 1698180 rs10501369 57870148 57.870148 0.512 A A A A A A B B A A
I SNP A- B B A B B A A A A A
1 1729269 rs1941030 59982334 59.982334 0.56 B B A B B B B B A A

1 1656934 rs528736 65461684 65.461684 0.393 B B B B B B A A B B
1 SNP_A- A A A A A A A A A A
1 1738462 rs624765 69826722 69.826722 0.714 A B A A A A A A A A

1 1645461 rs527529 74298448 74.298448 0.573 A A B B B B B B A A

1 1711405 rs1793483 76653115 76.653115 0.583 A A A A A A A A A B

1 1739334 rs3819256 77379509 77.379509 0.571 B B B B B B B B A B

1 1712184 rs7128417 77883622 77.883622 0.25 B B B B B B B B B B
I SNP A- A A A B A A A A A A
1 1734963 rs483089 78543310 78.54331 0.655 A A B B B B A A A B

1 1695384 rs1569168 79525377 79.525377 0.441 B B B A B B A A B B
1 SNP A- A A A A A A A A A A .
1 1695760 rs10501496 80598450 80.59845 0.298 B B A A A A B B A B

1 1679629 rs666649 81460553 81.460553 0.56 B B B B B B B B B B
I SNP A- A A A A A A A A A A
1 1674894 rs2000922 82720260 82.72026 0.619 A A A A A A B B A A
I SNP A- A A A A A A A A A A
1 1645839 rs7924334 83853909 83.853909 0.714 A A A A A A A A A A

1 1654894 rs10501586 84433725 84.433725 0.726 A A A A A A B B A B

1 1756404 rs10501612 85594787 85.594787 0.342 B B B B B B B B B B
i SNP A- A A B B B B B B A A
1 1722491 rs503952 86520236 86.520236 0.268 B B B B B B B B A B

1 1740548 rs10501723 89922680 89.92268 0.5 B B B A B B A A A B

1 1741388 rs1528760 90459676 90.459676 0.738 A A A A A A A A A B
I SNP A- B B B B B B A A A A
1 1755135 rs10501759 91082163 91.082163 0.537 B B B B B B A A A A

Database S2 Heterozygosity of pIiESC (Abbreviated as "pC") Lines s. w ~.
~ A z c a. a ¾ N ~; . o r~ v in y ~o ~o r ~
" z ~.`~a ~ ' ~ a , ~ c. =~ o. o. c. o c, ~o c, r I SNP A- A A A A A JA B B A A
1 1656446 rs554735 91994827 91.994827 0.524 B B A A A A B B A B

1 1720756 rs2605592 92842667 92.842667 0.702 A A A A A A B B B B

1 1672903 rs609493 93708735 93.708735 0.286 B B B B B B A B B B

1 1659851 rs12627 94442268 94.442268 0.607 A A B A B B B B A B
I SNP-A- A A A A A A B B A A
1 1649021 rs1940201 95387950 95.38795 0.31 B B B A B B B B B B

1 1706350 rs10501859 95973889 95.973889 0.298 B B B B B B B B B B

1 1670058 rs1939713 99567868 99.567868 0.631 A A B A B B B B A A
I SNP A- A A A A A A A A A A
1 1712712 rs667504 100221671 100.221671 0.738 A A A A A A A A B B

1 1729283 rs313403 102697742 102.697742 0.524 A A B B B B A B A A

1 1643334 rs260818 103425315 103.425315 0.417 B B B B B B B B B B

1 1690312 rs10502051 104808805 104.808805 0.286 B B B B B B B B B B

1 1746850 rs10502080 106341710 106.34171 0.346 B B B B B B B B B B
I SNP A- A A B B B B B B B B
1 1718590 rs2640757 107936868 107.936868 0.31 A A B B B B B B B B

1 1739572 rs2298501 109571744 109.571744 0.56 A A B B B B B B B B

1 1742110 rs170486 110202174 110.202174 0.452 B B A A A A A A A A
I SNP A- B B B B B B A A B B
1 1720008 rs10502152 111296905 111.296905 0.321 B B B B B B A B B B

1 1658493 rs7118530 113395335 113.395335 0.357 A B B B B B A A A A

1 1689389 rs2247060 114257194 114.257194 0.536 B B B B B B B B B B
I SNP A- A A B B B B A A A A
1 1652091 rs572619 115738853 115.738853 0.619 A A B B B B A B A A

1 1737192 rs660443 116265903 116.265903 0.362 A A B B B B A A A A

1 1643985 rs1219410 121294459 121.294459 0.691 B B A A A A A A B B

1 1728568 rs872414 122170647 122.170647 0.452 A A A B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines i. L L
.= y p C. O ^ O O
A C¾,, f at y rl O M 'd' V7 ~ D O P O
~ ^ ~ ~ ~ =L ~ c7 'O 7 "O 'II
a o. o a. ~o aa r;
U o ' o 0 1 1696469 rs2078158 122950070 122.95007 0.333 B B A B B B B B B B
I SNP A- A A A A A A A A B B
1 1748196 rs1940751 127447038 127.447038 0.683 A A A A A A A A B B

1 1741458 rs1368850 130433518 130.433518 0.598 A B A B B B B B A A

1 1732434 rs748807 131232636 131.232636 0.452 A B B B B B B B B B
I SNP A- A A A A A A A A A A
2 1644365 rs7973282 1095178 1.095178 0.738 A A A A A A A B A A

2 1716332 rs215994 2587421 2.587421 0.274 B B B B B B A B B B

2 1708039 rs4625554 4286565 4.286565 0.298 B B B B B B B B B B

2 1727428 rs1861584 5578079 5.578079 0.702 A A B B B B A B B B

2 1708085 rs4883241 9384549 9.384549 0.369 A A B B B B A A B B
1 SNP A- . B A B B B B B B B B
2 1709352 rs560444 9940542 9.940542 0.321 B B B B B B B B B B

2 1667917 rs1009954 11789366 11.789366 0.333 B B B B B B B B B B

2 1749536 rs10505774 13327672 13.327672 0.714 A B A A A A B B A A

2 1696855 rs10492150 14935164 14.935164 0.333 B B B B B B B B B B

2 1680095 rs4366546 18267461 18.267461 0.75 A A A A A A A A A A
I SNP A- A A A A A A B B B A
2 1714486 rs10505845 19976927 19.976927 0.714 A A A A A A B B B B

2 1729086 rs4131935 20632200 20.6322 0.738 B B A A A A B B B B

2 1673313 rs2417981 21483114 21.483114 0.5 B B B B B B A A A A

2 1645425 rs3884510 24249990 24.24999 0.512 A A B B B B B B A A
I SNP A- B A B B B B B B B B
2 1672243 rs10505945 24803300 24.8033 0.381 B B B B B B B B B B
I SNP A- B A A A A A A A B A
2 1692085 rs10505972 25379461 25.379461 0.393 B B B A B B B B B B

2 1674778 rs9300175 27617467 27.617467 0.417 B B B B B B B B A B

2 1649795 rs148898 29606383 29.606383 0.691 A A A A A A A B A B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines , = y = eC^C q , p , q ..
U p. I-~1 ~ u GJ ~ pu V U U U U U
cn C~ ti a a W Cj a I SNP A- B A B B B B B B B B
2 1658781 rs10506065 30342307 30.342307 0.417 B B B B B B B B B B
1 SNP_A- A A A B B A A A A A
2 1722521 rs7979386 30966129 30.966129 0.464 A B A B B B A B A A

2 1705996 rs2593998 32333520 32.33352 0.714 A A A A A A A B A B
1 SNP_A- A A A A A A B A B A
2 1644085 rs1905428 33450742 33.450742 0.512 A A A A A A B B B B
I SNP_A- A A B A A A B A B A
2 1711331 rs2389276 33989158 33.989158 0.595 A B B A A B B B B B
1 SNP_A- B A A B B A A A A A
2 1692149 rs10506124 37305503 37.305503 0.571 B B A B B B A B A A
1 SNP_A- A A B B B B B B B A
2 1720482 rs7969928 39561348 39.561348 0.393 A A B B B B B B B B
1 SNP_A- B B A A A A A A A A
2 1659791 rs7309345 40585255 40.585255 0.75 B B A A A A A A A A
1 SNP_A- A A A B A A B A A A
2 1754513 rs1369610 41755818 41.755818 0.369 A B A B B B B B A B
1 SNP_A- A A A A A A A A A A
2 1693494 rs1506678 43535759 43.535759 0.631 A B A A A A A A A A

2 1702318 rs7310869 44951653 44.951653 0.536 A B B B B B A A B B
I SNP_A- B B B B B B B B B B
2 1748898 rs10506292 49031020 49.03102 0.381 B B B B B B B B B B
I SNP_A- A A A A A A A A A A
2 1733843 rs7968810 52445260 52.44526 0.738 A A A A A A A A A A
I SNP A- A A B A A A B B B A
2 1712318 rs10506393 56672989 56.672989 0.691 A B B A A B B B B B
I SNP_A- A A A B B A A A A A
2 1657234 rs3913094 57197682 57.197682 0.655 A A A B B B A A A B
I SNP_A- A A A A A A B A A A
2 1662747 rs10506408 58834234 58.834234 0.512 A B A A A A B B A B
1 SNP_A- B A A B B A A A B B
2 1688045 rs7308021 61145687 61.145687 0.571 B B A B B B A A B B
1 SNP_A- B B B A A A A A A A
2 1749010 rs513203 62226007 62.226007 0.56 B B B A A B B B B B
1 SNP_A- A A A A A A B B A A
2 1730271 rs1596727 63609374 63.609374 0.583 A A A A A A B B A A
1 SNP_A- A A B B B B B B A A
2 1716970 rs8756 64646019 64.646019 0.595 A A B B B B B B B B

2 1721334 rs10506514 65583191 65.583191 0.298 B B B B B B B B A A

2 1646303 rs7313431 66378203 66.378203 0.631 A A A A A A A A A A

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines ~. ~ ~.
= =
z a, a ~ ~ o c a a a o n ~ c r U
a .. o. c.

2 1695666 rs710779 68249633 68.249633 0.476 B B B A A B B B B B
i SNP_A- B B B B B B A A B B
2 1700862 rs2567134 69233806 69.233806 0.31 B B B B B B B B B B

2 1757570 rs7960254 70109323 70.109323 0.405 B B B A A B B B B B

2 1676631 rs10506645 70671767 70.671767 0.31 B B B A A B B B B B
I SNP_A- A A B A A A A A B B
2 1743470 rs7964705 72103027 72.103027 0.31 A A B A A B B B B B

2 1660536 rs1396226 73586112 73.586112 0.429 B B A B B B B B B B
1 SNP_A- A A B A A A A A A A
2 1662713 rs1275643 74439702 74.439702 0.393 B B B A A B B B A A

2 1667227 rs310877 75889008 75.889008 0.274 B B B B B B B B B B
I SNP_A- A A A A A A A A A A
2 1732426 rs7315131 76389953 76.389953 0.381 B B A A A A A B A A

2 1667491 rs1796135 77491016 77.491016 0.524 B B B A A B A B B B

2 1643877 rs1244908 79104469 79.104469 0.631 A A B B B B A B B B
I SNP A- A A B B B B A A A A
2 1737202 rs10506839 79948071 79.948071 0.31 A A B B B B A A B B
I SNP A- A A A B B A A A A A
2 1700433 rs10506846 80609736 80.609736 0.655 A A A B B B A B B B
1 SNP A- A A B A A A, A A A A
2 1738317 rs892540 81919943 81.919943 0.667 B B B A A B A A A A

2 1688895 rs7960510 82715458 82.715458 0.274 B B B B B B B B B B
I SNP A- A A B B B B A A A A
2 1675076 rs839159 85096176 85.096176 0.726 B B B B B B A A B B

2 1663055 rs2635067 85762474 85.762474 0.571 B B B A A B A A B B
I SNP A- B B B B B B B B B B
2 1727255 rs1019206 87893500 87.8935 0.333 B B B B B B B B B B
1 SNP_A- B B B B B B A A A A
2 1657981 rs2731240 89061896 89.061896 0.31 B B B B B B A B A A

2 1696519 rs924328 91753976 91.753976 0.31 B B B B B B A A B B
I SNP A- B B A A A A B A A A
2 1747554 rs4761590 93076279 93.076279 0.655 B B A A A A B B B 13, 2 1701918 rs759572 95985503 95.985503 0.524 B B B A B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines Fl Cd L7 ~ QI r~ ~1 O M 'ct N ~ ~O O r O
~ z Q~ v d~ a u u u u I+j 'S R C`nC 4~i C~tl G *'~~ O+ GL CL ~ ¾i \O G l~
V o I SNP_A- A A A A A JA A A A A
2 1734475 rs1394380 97055132 97.055132 0.75 A A A A A, A B B A A

2 1690482 rs10492276 97699500 97.6995 0.691 A A B B B B A A B B
I SNP A- B B B B B B B B B B
2 1704900 rs1718312 101743655 101.743655 0.393 B B B B B B B B B B

2 1698694 rs10507166 102367680 102.36768 0.369 B B B B B B B B B B
I SNP A- 'B B A A A A A A A A
2 1731482 rs7954946 103966503 103.966503 0.333 B B A A A A A A A A
I SNP A- A A A A A A B B A A
2 1689283 rs10507197 104564170 104.56417 0.583 A A A A A A B B B B
I SNP A- B B A A A A A A B B
2 1723539 rs1444581 105816718 105.816718 0.488 B B A A A A A A B B

2 1676727 rs715447 107449185 107.449185 0.464 B B B B B B B B B B
I SNP A- A A A A A A A A A A
2 1742456 rs10507234 108519202 108.519202 0.714 B B A A A A B B A A

2 1655216 rs4767550 116413870 116.41387 0.595 A A B B B B A A B B
I SNP A- B A A A A A B B B B
2 1673501 rs1726392 117061645 117.061645 0.321 B B B B B B B B B B

2 1748666 rs3858710 118701913 118.701913 0.573 A B A A A A A A B B

2 1708029 rs1558062 124778387 124.778387 0.524 A B B B B B A B A A
1 SNP_A- A A B B B B B A A A
2 1716508 rs345676 126581103 126.581103 0.643 A B B B B B B B A A
I SNP A- B A B B B B A A B B
2 1664795 rs1983314 129393207 129.393207 0.333 B B B B B B B B B B
I SNP A- B B A A A A B A A A
3 1652867 rs7985257 18787997 18.787997 0.524 B B A A A A B B A A
I SNP A- A A B B B B B B A A
3 1686943 rs535233 20445317 20.445317 0.321 B B B B B B B B A B
I SNP A- A A A A A A B A A A
3 1745741 rs2862901 23933239 23.933239 0.571 B B A A A A B B A A

3 1642868 rs10507349 25679528 25.679528 0.274 B B A A A B B B B B

3 1702806 rs1161470 28322644 28.322644 0.31 B B B B B B B B B B

3 1664657 rs213611 30348913 30.348913 0.705 A A A A A A B B B B

3 1658585 rs206079 31818618 31.818618 0.417 B B B B B B B B B B

Database S2 Heterozygosity of p1iESC (Abbreviated as "pC") Lines Ctf CS ~ QI vi '-1 O M 'V' ~ ~ ~D O [~ 0 cj) ~ CaJ ~ ty '~ U ~..~ ~ V V V V V
CC ~ R a~ ~ n a ~ c a cs ~ o, c-n ' . a a w U a ~ ~ a I SNP A- B B B B B B B B B B
3 1685897 rs4941700 32383381 32.383381 0.262 B B B B B B B B B B

3 1664201 rs1538001 33683068 33.683068 0.274 B B B B B B B B B B

3 1742432 rs6563348 35588714 35.588714 0.397 A A B B B B B B B B
I SNP A- B B B B B B A A A A
3 1709846 rs2224655 36217500 36.2175 0.298 B B B B B B B B A A

3 1719156 rs1359214 36774982 36.774982 0.452 B B A A A A B B B B

3 1699940 rs10507466 37361657 37.361657 0.75 A A A A A A B B B B
I SNP A- A A B B B B B B A A
3 1757710 rs2197879 38143188 38.143188 0.286 B B B B B B B B A A
I SNP A- A A A A A A A A A A
3 1725889 rs4566029 39136387 39.136387 0.691 A A A A A A B B A A
I SNP A- B B B A A A B B B B
3 1648291 rs7322754 40220977 40.220977 0.31 B B B B B B B B B B

3 1644487 rs1409075 42143450 42.14345 0.5 B B B B B B A A A A

3 1692131 rs9316020 42892291 42.892291 0.274 B B B B B B B B B B

3 1683729 rs9285153 43710570 43.71057 0.536 B B B B B B B B B B

3 1675092 rs10507544 46298746 46.298746 0.286 B B B B B B B B B B
I SNPA- A A A A A' A B A A A
3 1706220 rs1983805 48609971 48.609971 0.655 A A A A A A B B A A

3 1656586 rs1359613 49664241 49.664241 0.381 A B A A A A B B B B
I SNP A- A A A A A A B A A A
3 1687875 rs9316513 50452286 50.452286 0,643 A B A A A A B B A A

3 1699260 rs1891948 52537146 52.537146 0.429 B B A A A A A B B B

3 1670827 rs9316642 53093973 53.093973 0.571 A B B B B B B B B B
I SNP A- A A A A A A A A A A
3 1664927 rs 1010947 53921670 53.92167 0.702 A B A A A A A A A A

3 1686045 rs10507599 54585799 54.585799 0.286 A B B B B B B B B B

3 1686285 rs2253408 55216697 55.216697 0.75 A A B B B B B B B B

3 1668215 rs959745 56718869 56.718869 0.274 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as r'pC") Lines ': ~ C C O, y C C
~ ~ z 'a 'a ~ ~ N .. o en v n S ~o o t~ o y U
v] w d U U U U
~6 {Y = G o, Ic rA W ? k U c c c 1 SNP_A- A A B B B B A A A A
3 1706400 rs10492603 57769822 57.769822 0.679 A A B B B B A A A A
1 SNP_A- B B B B B B B B A A
3 1695368 rs2786664 59574054 59.574054 0.417 B B B B B B B B A A
1 SNP_A- A A A A A A A A A A
3 1690895 rs3102221 60652316 60.652316 0.488 A B B B B B A B A A
1 SNP_A- A A A A A A A A A A
3 1731184 rs7323089 61693413 61.693413 0.56 A A A A A A A B A A
I SNP_A- B B A A A A B A B B
3 1697063 rs2134898 62767058 62.767058 0.25 B B A A A A B B B B
1 SNP_A- B A B B B B B B A A
3 1707522 r89317406 63717021 63.717021 0.417 B B B B B B B B B B
I SNP_A- B B A A A A A A A A
3 1645393 rs7321823 65570977 65.570977 0.679 B B A A A A A A A A
I SNP_A- A A A A A A A A A A
3 1726077 rs10492592 66385683 66.385683 0.714 A B B B B B A A B B
1 SNP_A- A A A A A A A A A A
3 1650731 rs 176343 68069259 68.069259 0.702 A B A A A A A A A A
I SNP A- A A A A A A A A A A
3 1705084 rs2782448 68801734 68.801734 0.643 A A A A A A A A A A

3 1715042 rs3909263 71753222 71.753222 0.321 B B B B B B A A B B

3 1732673 rs10507812 72886773 72.886773 0.75 A A B B B B B B A A

3 1713643 rs9318226 73391987 73.391987 0.419 B B A A A A A A B B
I SNP A- A A B B B B A A A A
3 1756880 rs9318324 74649787 74,649787 0.658 A A B B B B A A B B

3 1685215 rs10507835 75353682 75.353682 0.691 A A A A A A B B A A

3 1679595 rs1952548 76037205 76.037205 0.333 B B B B B B B B B B
I SNP A- A A A A A A B B A A
3 1687191 rs7326108 77781442 77.781442 0.393 B B A A A A B B B B

3 1680379 rs3903388 78802822 78.802822 0.393 B B B B B B A A B B

3 1664955 rs1215462 79594011 79.594011 0.536 B B B B B B B B B B

3 1727874 rs1744600 80158809 80.158809 0.631 B B B B B B B B A A
I SNP A- A A A A A A B B A A
3 1710116 r810507917 80741431 80.741431 0.488 A A A A A A B B B B
I SNP A A A A A A A A A A A
3 1663633 rs9318868 81947326 81.947326 0.643 B B A A A A A A B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines A p ~+ 5 5 ~ a ~
^ R C. C. C. õ~G ~ =~ ~o . M C U1 ~D 0 l 7Z
V ~ ~ V] u CJ '~" C" u V u V ~ V V
.C '~ ` u C3 f7. "fL G G R. b G r ~n ~" ti n a ~s` U U U
a w o I SNP_A- B B A A A A A A A A
3 1693530 rs9319022 83601961 83.601961 0.345 B B B B B B B B B B
1 SNP_A- A A A A A A A A A A
3 1706422 rs1331567 84793816 84.793816 0.56 A A A A A A A A A A
1 SNP_A- A A B B B B A A B B
3 1733077 rs995475 87558036 87.558036 0.357 B B B B B B B B B B
1 SNP_A- A A A A A A A A A A
3 1679861 rs1113478 88908389 88.908389 0.417 A A B A B B B B B B
I SNP_A- A A A A A A A A A A
3 1649205 rs665530 90571947 90.571947 0.726 A A A A A A B B A A
1 SNP_A- A A A A A A A A A A
3 1726887 rs1926489 91465990 91.46599 0.524 B B A A A A A A B B
I SNP_A- A A B B B B A A A A
3 1714183 rs913005 92275844 92.275844 0.607 B B B B B B A A A A
1 SNP_A- A A B B B B A A A A
3 1701716 rs9301876 92819688 92.819688 0.56 A A B B B B A A A A
I SNP_A- A A A A A A A A A A
3 1681625 rs1412938 93661657 93.661657 0.726 A A A A A A A A A A
1 SNP_A- A A B B B B A A B B
3 1648409 rs9302001 94261393 94.261393 0.274 A A B B B B B B B B
1 SNP_A- A A B B A A B B B B
3 1741482 rs7324781 95032754 95.032754 0.405 B B B B B B B B B B
1 SNP_A- A A A A A A A A A A
3 1661319 rs4603415 96610639 96.610639 0.631 B B A A A A B B A B
1 SNP_A- A A B B A A A A A A
3 1664929 rs285067 97536416 97.536416 0.691 A B B B B B A A A A
1 SNP_A- B B A A A A A A B A
3 1709292 rs1886553 98448739 98.448739 0.486 B B A A B B A A B B

3 1749428 rs2760306 99841672 99.841672 0.298 B B B B B B B B B B
I SNP_A- A A A A A A A A A A
3 1703098 rs10508075 101237184 101.237184 0.464 A B A A B B B B A A
1 SNP_A- A A B B B B A A B B
3 1680317 rs1015795 102023701 102.023701 0.488 A B B B B B A. A B B
I SNP_A- A A A A A A A A B A
3 1704124 rs279927 102539019 102.539019 0.643 A A A A A A A A B B
1 SNP_A- A A B B B B A A B B
3 1752530 rs1033147 103460337 103.460337 0.333 A A B B B B B B B B
1 SNP_A- B A B B B B A A B A
3 1654228 rs9300981 104440279 104.440279 0.286 B B B B B B B B B B
1 SNP_A- B B A A A A B B B B
3 1715354 rs7318881 105459909 105.459909 0.671 B B A A A A B B B B
I SNP_A- B A B B B B B A B B
3 1645715 rs7327250 106243682 106.243682 0.329 B B B B B B B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines U U U U U
Zs o~ a a*-~ n. atL sr U sy U
Ua c~ a 1 SNP_A- B B B B A JA B A A A
3 1756346 rs1320446 106965333 106.965333 0.679 B B B B B B B B A A
1 SNP_A- A A B B B B B B B B
3 1732084 rs231604 107524007 107.524007 0.381 A A B B B B B B B B
1 SNP_A- B B B B B B B B B B
3 1681321 rs4772985 108080882 108.080882 0.25 B B B B B B B B B B
I SNP_A- B B A A A A A A B B
3 1648777 rs10492480 108947427 108.947427 0.333 B B A A A A A A B B
I SNP_A- B B A A A A B B A A
3 1654860 rs2183850 110513987 110.513987 0.714 B B A A A A B B A A
1 SNP_A- B B B B B B B B A A
4 1733261 rs1952805 19586195 19.586195 0.345 B B B B B B B B B B
1 SNP_A- B A A A A A A A A A
4 1702470 rs1923 22511019 22.511019 0.429 B B A A A A B B A A
1 SNP_A- B A A A B A A A A A
4 1645139 rs4983041 24495978 24.495978 0.595 B B B A B B A A B B
1 SNP_A- A A B B B B A A A A
4 1676969 rs10483331 26546808 26.546808 0.417 B B B B B B B B A A
1 SNP_A- A AA A A A A A A A
4 1680111 rs4981658 27234585 27.234585 0.732 A A A A A A B B A A

4 1734437 rs2333423 28146939 28.146939 0.381 B B B B B B B B B B
I SNP_A- A A B B B B A A A A
4 1669916 rs10483350 28885906 28.885906 0.738 A A B B B B A A A A

4 1732697 rs225842 29622687 29.622687 0.441 B B B B B B B B B B

4 1656700 rs1278891 31464813 31.464813 0.595 A A B A B B B B B B
1 SNP_A- A A A B A A B B B B
4 1740154 rs9322929 33377471 33.377471 0.345 B B B B B B B B B B

4 1757044 rs799493 34621626 34.621626 0.691 B B B B B B A A A A
1 SNP_A- A A A A A A A A A A
4 1676887 rs847498 35546428 35.546428 0.607 A A A A A A A A A A
1 SNP_A- A A B B B B A A A A
4 1665507 rs1950361 36101975 36.101975 0.329 B B B B B B B B B B
1 SNP_A- A A A A A A A A B B
4 1705178 rs4901596 37659956 37.659956 0.667 B B A A A A B B B B
I SNP A- A A A A A A A A A A
4 1654996 rs6571869 38248210 38.24821 0.679 A A B B B B B B A A
1 SNP_A- ~ A A A A A A A A A A
4 1708854 rs10483511 39587714 39.587714 0.571 B B B B B B B B B B

4 1653001 rs10498360 40670723 40.670723 0.476 B B B B B B B B B B

Database S2 Heterozygosity of phE SC (Abbreviated as "pC") Lines s. s.
.~. h cC~a ' C ^ C q ~ . ~ Z d O. .G ~ =i 2yo M et' ~ 7 ~ '~D ~ ,O
p n u u u V U U U U
u z ~,a N ~ u ~ c. ~ a a a ~ a ~ a r n ~ a a ~a k~ ~j V j (~ V
c a a 1 SNP_A- A A A A A A B B A A
4 1753660 rs1951874 41387217 41.387217 0.345 A A B B B B B B A A
I SNP_A- A A B B B B A A A A
4 1653419 rs2010338 45895631 45.895631 0.655 A A B B B B A A A A
1 SNP_A- B B A A A A A A A A
4 1663303 rs10483573 46932227 46.932227 0.357 B B A A A A A A B B
1 SNP_A- A A A A A A A A B B
4 1664801 rs698340 47611853 47.611853 0.585 B B A A A A A A B B
1 SNP_A- B B B B B B B B A A
4 1722201 rs7146291 48172131 48.172131 0.274 B B B B B B B B B B
1 SNP_A- B B A A A A A A A A
4 1650017 rs8006972 48690753 48.690753 0.31 B B B B A B A A B B
1 SNP_A- A A A A B A A A B B
4 1720778 rs10498420 49483793 49.483793 0.476 B B B B B B B B B B
I SNP_A- A A A A A A A A A A
4 1743320 rs963626 50157439 50.157439 0.691 A A A A A A B B A A
I SNP_A- A A A A A A A A A A
4 1641756 rs1956574 51163026 51.163026 0.655 A A A A A A A A B B
1 SNP_A- A A B B B B A A A A
4 1669704 rs7151306 52273870 52.27387 0.607 B B B B B B A A B B
1 SNP_A- B B A A A A A A A A
4 1748272 rs877018 52892776 52.892776 0.451 B B B B A B B B B B
1 SNP_A- A A B B B B A A A A
4 1714357 rs1382978 55788938 55.788938 0.536 A A B B B B A B A A

4 1714205 rs10483679 56503799 56.503799 0.61 B B B B A B A A B B
1 SNP_A- A A B B B B A A A A
4 1654106 rs238376 57129665 57.129665 0.357 A B B B B B A B B B
1 SNP_A- B B A A B A A A A A
4 1690578 rs10498488 58658876 58.658876 0.451 B B B B B B A A A A
I SNPA- A A A A A A A A A A
4 1690058 rs9323353 59240800 59.2408 0.619 A A B B A B A A A A
1 SNP_A- B A A A A A A A A A
4 1671347 rs2296274 60986931 60.986931 0.75 B B A A A A A A B B

4 1755551 rs9285590 61521469 61.521469 0.417 A A A A A A B B B B

4 1707294 rs1271582 64634456 64.634456 0.441 B B A A A A B B B B

4 1648725 rs10483805 67325404 67.325404 0.329 B B B B B B B B B B

4 1699466 rs1956528 67858721 67.858721 0.631 B B A A A A B B B B
I SNP_A- B B A A A A B B B B
4 1682431 rs749397 69414068 69.414068 0.262 B B A A A A B B B B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines p,.I=. h C C~~a C " C F7 ~ Q y!~ R R ~ QI rq -i O f7' 'V' N 7 ~O O l~ 'RO
V IZi I-~- V] _ d C~J ~ QU V ~ u V V V ' ..
Z+ S R R y '~ CL ~ CL Oa G CL ~ LL , r U1 ~ b G L ~y V V 1 t.,) C> c, . G

1 SNP_A- A A B B B B A A A A
4 1674164 rs2215132 71545542 71.545542 0.262 A B B B B B A A B B
1 SNP_A- A A A A A JA A A A A
4 1672631 rs2803971 72182227 72.182227 0.713 A A A A A A A A B B
1 SNP_A- A A A A B A A A A A
4 1648423 rs1028258 75447775 75.447775 0.726 A A B B B B A A A A
I SNP_A- B B B B B B A A B B
4 1700204 rs7152153 76265708 76.265708 0.286 B B B B B B A A B B
1 SNP_A- A A A A B A A A B B
4 1701478 rs7156671 76991628 76.991628 0.7 A A B B B B A A B B
1 SNP_A- B B A A A A B B B B
4 1706776 rs10483905 78043978 78.043978 0.429 B B A A A A B B B B
1 SNP_A- A A A A A A A A A A
4 1667157 rs997842 78614233 78.614233 0.679 A A A A A A A B B B
I SNP_A- B B B B B B B B B B
4 1722889 rs2049826 79383063 79.383063 0.345 B B B B B B B B B B
I SNP_A- A A A A A A B A A A
4 1645339 rs2372083 81860288 81.860288 0.452 B B A A A A B B B B
I SNP_A- A A B B B B A A B B
4 1704748 rs2372424 83017248 83.017248 0.438 A A B B B B A A B B
1 SNP_A- B B A A A A A A A A
4 1757272 rs8003423 83533541 83.533541 0.643 B B B B A B A A A A
1 SNP_A- A A A A A A A A A A
4 1644835 rs1530325 84781909 84.781909 0.702 B B A A A A A B B B
1 SNP_A- B B B B B B B B A A
4 1680733 rs10498604 86238836 86.238836 0.298 B B B B B B B B B B
1 SNP_A- A A B B B B A A A A
4 1702796 rs8018273 86867956 86.867956 0.524 A P. B B B B A A A A
1 SNP_A- B B A A A A A A B B
4 1687761 rs429923 87481126 87.481126 0.405 B B A A A A A A B B
1 SNP_A- A A A A A A A A A A
4 1725723 rs1742083 90256423 90.256423 0.321 B B B B B B B B B B
1 SNP_A- A A B B B B A A A A
4 1661389 rs10498627 91041872 91.041872 0.583 A A B B B B A A B B
1 SNP_A- B B B B B B A A B B
4 1705392 rs2148567 93244403 93.244403 0.286 B B B B B B A A B B

4 1734665 rs1456988 97557760 97.55776 0.679 B B A A A A A A B B
1 SNP_A- A A A A A A A A A A
4 1684765 rs200331 98457298 98.457298 0.488 B B A A A A B B A A
1 SNP_A- B A A A A A A A A A
4 1682935 rs3918051 99023837 99.023837 0.61 B B A A A A B B A A
1 SNP_A- A A A A A A B B A A
4 1734911 rs10484072 102695759 102.695759 0.631 A A B B B B B B B B

Databasc S2 Aeterozygosity ot pS~ESC (Abbxeviated as "pC'} Lires R G G.C di ~ ti ~O M 7 /1 ~O ,a P' '~O
IS" a i n a a o a c o a ~
U U C' c I SNP_A- A A A A A A B B A A
4 1659209 rs1048257 104475429 104.475429 0.667 A A B B B B B B B B
I SNP_A- B A B B B B B B B B
1669336 rs1405186 21306806 21.306806 0.441 B B B B B B B B B B
I SNP A- B B A A A A B B B B
5 1690082 rs2169637 25517776 25.517776 0.262 B B A A A A B B B B
1 SNP A- B B A A A. A B A B A
5 1643639 rs10519635 27330404 27.330404 0.607 B B B B B B B B B B
I SNP_A- B B A A A A A A A A
5 1740804 rs4779462 28026287 28.026287 0.598 B B B B B B A A A A
I SNP_A- A A A A A A B A A A
5 1722463 rs2219507 29646927 29.646927 0.691 A A A A A A B B A A
I SNP_A- B B B B B B B B B B
5 1730684 rs10519737 30756749 30.756749 0.381 B B B B B B B B B B
1 SNP_A- A A A A A A A A B B
5 1648795 rs1343900 31431890 31.43189 0.667 A A B B B B A B B B
I SNP A- A A B B B B B B A A
5 1755583 rs10519956 32849133. 32.849133 0.345 B B B B B B B B A B
1 SNP_A- A A A A A A A A A A
5 1699406 rs1948650 33827340 33.82734 0.738 A A A A A A B B A B
I SNP_A- A A A A A A A A A A
5 1645977 rs10518868 34381353 34.381353 0.655 A A B B B B B B A A
1 SNP_A- A A B B B B B B A A
5 1665819 rs471122 41345866 41.345866 0.3 A A B B B B B B A B
1 SNP_A- B B A A A A B B B B
5 1673073 rs10519044 44169166 44.169166 0.381 B B B B B B B B B B

5 1740676 rs493728 48678247 48.678247 0.441 B B B B B B B B B B
1 SNP_A- B A B B B B A A B B
5 1709940 rs1478200 51948279 51.948279 0.357 B B B B B B B B B B
1 SNP_A- B B A A A A A A A A
5 1720532 rs2553222 52657040 52.65704 0.691 B 13 A A A A B B A B
I SNP_A- A A A A A A B B B A
5 1654466 rs4534776 55408068 55.408068 0.463 A A B B B B B B B B
I SNP_A- A A B B B B A A A A
5 1752856 rs1550574 56000660 56.00066 0.536 A A B B B B A A A B
1 SNP_A- A A A A A A A A A A
5 1735597 rs2033721 58609267 58.609267 0.714 A B B B B B A A A B
1 SNP_A- A A A A A A A A A A
5 1642536 rs3935962 59611593 59.611593 0.536 A B A A A A A A A B
1 SNP_A- B B B B B B B B B B
5 1726387 rs10519148 60507655 60.507655 0.25 B B B B B B B B B B

5 1750348 rs2652824 61207054 61.207054 0.286 B B B B B B B B 13 B

Database S2 Heterozygosity of phESC (Abbreviated as "pC") Lines L L y.
Q ~ õ^ i , L'.. ..r7 C^~C ^ '~' ^ ^
.^ R `/-C-'yi a a .C ~C uõ"O M e1' V7 ~ ~D O l~ O
z C4 b ca ca ~ d ~ a ~ Cw G a v o o p C
I SNP-A- A A A A A JA A A A A
1741266 rs10518707 65152676 65.152676 0.488 A B B B B B A A A A
I SNP_A- A A A A A A B B B B
5 1739192 rs305002 67928959 67.928959 0.595 A A A A A A B B B B

5 1677047 rs2128112 69973340 69.97334 0.262 B B B B B B B B B B
I SNP-A- B A A A A A B B A A
5 1698770 rs3898352 74308825 74.308825 0.631 B B B B A B B B A A

5 1654378 rs1446312 75199244 75.199244 0.738 A A A A A A B B A B
I SNP-A- A A A A A A A A B B
5 1657306 rs7163689 76352533 76.352533 0.488 A B B B A B B B B B

5 1701268 rs1001460 77291934 77.291934 0.56 A A B B B B B B A B
1 SNP_A- A A A A A A A A A A
5 1689635 rs1320323 79128502 79.128502 0.59 A A A A A A A A A A

5 1749864 rs1846911 80255705 80.255705 0.329 A A B B B B B B B B

5 1714319 rs10520585 83462510 83.46251 0.286 B B B B A B B B B B
I SNP A- B B A A A A B B B A
5 1654264 rs1961601 84030610 84.03061 0.31 B B B B A B B B B B

5 1650691 rs1122907 84708371 84.708371 0.691 A A B B B B A A A A
1 SNP_A- B A A A A A A A A A
5 1665669 rs10520655 85887415 85.887415 0.595 B B A A A A A A A B

5 1694944 rs3817428 87216251 87.216251 0.75 A A A A A A B B A A
1 SNP_A- A A A A A A B B B B
5 1683397 rs1079537 89675287 89.675287 0.452 B B B B A B B B B B
I SNP-A- B B B B B B B A B A
5 1752072 rs10520710 90688998 90.688998 0.287 B B B B B B B B B B

5 1731798 rs1989269 91611056 91.611056 0.305 B B B B B B B B B B

5 1728656 rs10520754 92760413 92.760413 0.548 A A A A A A A A A A

5 1700188 rs4321143 93957372 93.957372 0.262 B B B B B B B B B B
1 SNP_A- A A A A A A B B A A
5 1686439 rs1551466 99344619 99.344619 0.345 B B B B B B B B B B

5 1647533 rs352716 100155950 100.15595 0.31 A A B B B B B B A A
The results show heterozygosity of derived phESC lines and displays changes in genotype by comparison with the related donor genotype. Portions of heterozygous segments of the donor genome became homozygous in phESC. Chromosome-chromosome number; RS ID-RS number in dbSNP
database; Base pair-base pair distance as recorded by Affimetrix GeneChip; Freq A in Cauc-the frequency of A allele in Caucasian population.

[0329] In prior research, parthenogenetic activation of mouse oocytes has resulted in homozygous embryonic stem cell lines (Lin et al., Stem Cells (2003) 21:152).
In human oocytes, the suppression of the second meiotic division after oocyte parthenogenetic activation and the generation of diploid embryos does not lead to the derivation of wholly homozygous hES cells.

[0330] Based on the HLA-typing results, differentiated cells derived from all phESC lines should be wholly histocompatible with the_ oocyte donors, making this a method to create cells of therapeutic use (Table 19).

Table 19. HLA-typina for phESC cell lines MHC I MHC II

phESC-1 A*01 B*15(63) Cw*04 DRB1*12 DQB1*06 DQAI*O1 A*02 B*35 Cw*0708 DRBl*13 DQB1*03 DQAI*0505 phESC-1 A*O1 B*15(63) Cw*04 DRBI*12 DQB1*06 DQA1*O1 donor A*02 B*35 Cw*0708 DRBI*13 DQBI*03 DQAI*0505 phESC-3, 4, A*02 B*52 Cw*03 DRB1*Ol DQB1*05 DQAl*0101 A*03 B*22 Cw*04 DRB1*03 DQB1*02 DQAl*05 phESC-3, 4, A*02 B*52 Cw*03 DRB1*O1 DQBl*05 DQAl*0101 5 donor A*03 B*22 Cw*04 DRBI*03 DQB1*02 DQA1*05 phESC-6 A*02 B*07 Cw*04 DRB1*04 DQB1*06 DQA1*O1 A*03 B*27 Cw*07 DRBI*15 DQB1*03 DQA1*03 phESC-6 A*02 B*07 Cw*04 DRB1*04 DQBI*06 DQA1*O1 donor A*03 B*27 Cw*07 DRB1*15 DQBI*03 DQAI*03 phESC-7 A*O1 B*38 Cw*06 DRB1*13 DQB1*06 DQA1*0106 A*02 B*57 Cw*12 DRB1*14 DQBI*06 DQA1*0103 phESC-7 A*O1 B*38 Cw*06 DRB1*13 DQB1*06 DQA1*0106 donor A*02 B*57 Cw*12 DRB1*14 DQBI*06 DQA1*0103 NSF A*25 B*15(62) Cw*12 DRBI*04 DQB1*06 DQA1*O1 A*32 B*18 Cw*12 DRB1*15 DQBI*03 DQAI*03 [0331] DNA-profiling of the genetic material derived from the human fibroblasts used as feeder cells revealed no contamination of the phESC cell lines with material from the human fibroblasts (Table 19).

[0332] The phESC-l line remained undifferentiated during ten months of culture, spanning 35 passages. The other cell lines were successfully cultivated over at least 21 passages. The cells from all phESC lines formed cystic embryoid bodies in suspension culture and gave rise to derivatives of all three germ layers: ectoderm, mesoderm, and endoderm, after differentiation in vitro (FIG. 4). Approximately 5% of embryoid bodies from the phESC-1 line gave rise to beating cells five days following plating. The phESC-6 line produced pigmented epithelial-like cells (FIG. 41, K). Ectoderm differentiation is presented by positive innnunocytochemical staining for neuron specific markers neurofiliment 68 (FIG.
4A), NCAM (FIG. 4B), beta III-tubulin (FIG. 4C) and the glial cell marlcer GFAP (FIG. 4D, M). Differentiated cells were positive for mesoderm markers including alpha-actinin (FIG.
4G) and desmin (FIG. 4J), which are muscle specific markers, and the endothelial markers PECAM-1 (FIG. 4E) and VE-Cadherin (FIG. 4F). Endoderm differentiation is presented by positive staining of differentiated derivatives for alpha-fetoprotein. These data demonstrate that phESC can be differentiated into the three germ layers that lead to all cell types of a human body.

[0333] The altered karyotype of phESC-7 may be a reason to exclude it form clinical use.
Alterations of genomic inlprinting in human embryos can contribute to the development of disorders linked to maternally or paternally expressed genes (Gabriel et al., Proc Natl Acad Sci USA (1998) 95:14857). In'order to investigate other characteristics of the phESC lines, and to determine their suitability for use in cell therapy, imprinting analysis was performed.
[0334] Northern blots were made and screened with DNA probes SNRPN, Pegl_2, Pegl_A, H19, and GAPDH (as an internal control) as outlined above. Blotted nucleic acids were obtained from NSF, neonatal skin fibroblasts; hES, human embryonic stem cell line derived from fertilized oocytes; 1, p1hESC-1; 2, phESC-3, 3, phESC-4, 4, phESC-5; 5, phESC-6; 6 phESC-7. NSF RT-, hES RT-, 1 RT- are negative controls. FIG. 3 shows the results of the imprinting blot.

[0335] The matern.al imprinting gene, Pegl_A sllows strong binding in all of the cell lines tested. Weaker (relative to Pegl_A), but consistent binding was observed in all of the cell lines for the maternal imprinting gene H19. SNRPN shows binding predominantly in NSF, hES, phESC-4, and phESC-6. Pegl_2 shows binding predominantly in NSF, hES, phESC-1 (weaker signal), phESC-3, phESC-5, and p1iESC-6. GAPDH binding confirmed similar loading of RNA in all lanes.

[0336] Cornea formation and histoloQv [0337] The growing synthetic comeas were cultured by completely immersing the spheres in medium as described. Gross visual inspection of the spheres shows that they are relatively transparent balls of tissue, and grow to over 1 cm in diameter (FIG. 8).

[0338] Upon gross examination, it appears that the spheres are substantially hollow, comprising a wall of approximately 0.5 mm in thickness. Subsequent histological/microscopic examination reveals that the specimens consist of two strips of mainly fibrous tissue, with an occasional fibroblasts. Staining identifies the presence of a basement membrane which is PAS and Trichrome negative, which suggests the presence of Bowman's layer (i.e., the stroma of the cornea). Atop the fibrous tissue layer is a single cell layer which contains nucleoli suggesting epithelium rather than endothelium.
Based on this analysis, it was concluded that the tissue specim.ens are compatible with cornea.

[0339] Although the invention has been described with reference to the above examples, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims.

References 1. J. Cibelli et al., Methods for making and using reprogrammed human somatic cell nuclei and autologous and isogenic human stem cells. US Patent Application No.
20030232430, December 18, 2003.

2. H. Lin et al., Multilineage potential of homozygous stem cells derived from metaphase II oocytes. Stem Cells (2003) 21:153-161 3. K.E. Vrana et al., Nonhuman primate parthenogenetic stem cells. PNAS (2003) (Suppl l ):11911-11916.

4. J.P.M. Dumoulin et al., Effect of oxygen concentration on human in vitro fertilization and embryo culture. Human Reproduction. (1999) 14(2):465-469.

5. B.Fischer and B.D. Bavister, Oxygen tension in the oviduct and uterus of rhesus monkeys, hamsters and rabbits. J Reprod Fertil (1993) 99:673-679.

6. D.I. Kaufinan and J.A. Mitchell, Intauterine oxygen tension during oestrous cycle in the hamster: patterns of change. Comp Biochem Physiol Comp Physiol (1994) 107(4):
673-678.

7. F.D. Houghton ef al., Oxygen consumption and energy metabolism of the early mouse embryo. Mol Reprod Dev (1996) 44:476-485.

8. A. Van Soom et al., Prevalence of apoptosis and inner cell allocation in bovine embryos cultured under different oxygen tension with or without cysteine addition.
Theriogenology (2002) 57(5):1453-1465.

Claims (36)

1. An isolated retinal-stem cell derived synthetic cornea.

2. The isolated cornea of claim 1, wherein the retinal stem cell is differentiated from a parthenogenetically activated human oocyte.

3. The isolated cornea of claim 1, wherein the cornea is terminally differentiated.

4. The isolated cornea of claim 1, wherein the cornea comprises epithelial cells.

5. The isolated cornea of claim 4, wherein the cornea comprises stroma cells.

6. The isolated cornea of claim 1, wherein the cornea has the ability to change light phase velocity.

7. The isolated cornea of claim 1, wherein the cornea has a transverse diameter of about mm to 11.5 mm.

8. The isolated cornea of claim 1, wherein the cornea has a thickness of about 0.5 mm to 0.6 mm in the center and about 0.6 mm to 0.8 mm at the periphery.

9. The isolated cornea of claim 1, wherein the cornea is deposited as ATTC
accession No.

10. The isolated cornea of claim 2, wherein the cornea is histocompatible with the oocyte donor.

11. The isolated cornea of claim 2, wherein the cornea comprises homoplasmic mitochondrial DNA (mtDNA).

12. The cornea of claim 10, wherein the cornea is transplantable in humans.

13. A method of producing a synthetic cornea comprising:

a) parthenogenetically activating a human oocyte, wherein activating comprises: i) contacting the oocyte with an ionophore at high O2 tension and ii) contacting the oocyte with a serine-threonine kinase inhibitor at low O2 tension;
b) cultivating the activated oocyte of step (a) at low O2 tenison until blastocyst formation;
c) transferring the blastocyst to a layer of feeder cells, and culturing the transferred balstocyst under high O2 tension;
d) mechanically isolating an inner cell mass (ICM) from trophectoderm of the blastocyst of step (c);
e) culturing the cells of the ICM of step (d) on a layer of human feeder cells under high O2 tension, wherein retinal stem cells are identified in the culture by human embryonic stem cell markers (hES) and neuron specific markers, and wherein the identified retinal stem cells are subsequently isolated;
f) culturing the isolated stem cells of step (e) in media comprising serum replacement (M/SR), plasmonate, and at least one mitogen that activates the gp130/STAT
pathway and/or the MAP kinase pathway on a fibroblast feeder layer treated with a DNA
synthesis inhibitor;
g) culturing the mitogen treated cells of step (f) in M/SR comprising plasmonate (M/SRP), without added mitogen, to near confluence, wherein 1/2 volume of the M/SRP is replaced with M/SR periodically until the near confluent cells develop pigmentation and a domed appearance; and h) transferring the pigmented cells of step (g) in M/SR to a gelatin coated substrate, wherein 1/2 volume of the M/SR is replaced with M/SR periodically until a synthetic cornea develops.

14. The method of claim 13, wherein the cornea develops in the absence of a 3-D
scaffold.

15. The method of claim 13, wherein the mitogen is selected from leukemia inhibitory factor (LIF), bFGF, and a combination thereof.

16. The method of claim 13, wherein the DNA synthesis inhibitor is an alkylating agent.

17. The method of claim 16, wherein the DNA synthesis inhibitor is mitomycin C.

18. The method of claim 13, wherein the feeder cells are human.

19. The method of claim 13, wherein the hES markers are selected from the group consisting of SSEA-3, SSEA-4, TRA-1-60, TRA-1-91, OCT-4, and a combination thereof.

20. The method of claim 13, wherein the neuron specific markers are selected from the group consisting of neurofiliment 68, NCAM, beta III-tubulin, GFAP, and a combination thereof.

21. A retinal-stem cell derived synthetic cornea obtained by the method of claim 13.

22. A method of treating a subject in need thereof, comprising replacing a cornea of the subject with a synthetic cornea.

23. The method of claim 22, wherein the subject has an injured cornea.

24. The method of claim 22, wherein the subject has a disease which effects the cornea.

25. The method of claim 24, wherein the disease is selected from the group consisting of keratitis, corneal ulcer, corneal abrasion, snow blindness, arc eye, Thygeson's superficial puncate keratopathy, Fuchs' dystrophy, keratoconus, keratpconjunctivitis sicca, corneal infections, and corneal dystrophy.

26. A method of identifying an agent that affects the cornea of an eye comprising:
(a) contacting a retinal-stem cell derived synthetic cornea with an agent;
and (b) observing a change to the cornea in the presence and absence of the agent, wherein a change to the cornea is indicative of an agent that affects the cornea.

27. The method of claim 26, wherein the agent has a therapeutic effect on the cornea.

28. The method of claim 26, wherein the agent has an adverse effect on the cornea.

29. The method of claim 26, wherein change to the cornea is selected from the group consisting of modulation of gene expression, modulation of protein expression, change in opacity, change in plasticity, change in hardness, change in light phase velocity, and change in shape.

30. The method of claim 28, wherein the agent is an environmental chemical.

31. The method of claim 27, wherein the agent is a drug.

32. The method of claim 31, wherein the drug is a topical drug.

33. A method for replacement of a cornea of an eye with the synthetic cornea according to claim 1, comprising:
a) surgically excising the cornea from the eye;
b) inserting the synthetic cornea into the area of the removed cornea; and c) allowing the synthetic cornea to interface with tissue underlying the excision to anchor the synthetic cornea to the eye.

34. The method of claim 33, further comprising separating a portion of the outer surface of a cornea thereby forming a corneal flap and a corneal bed, the corneal flap having an anterior surface and a posterior surface, the corneal bed having a shaped anterior surface;
implanting the synthetic cornea on the corneal bed, the cornea having an anterior surface and a posterior surface; and replacing the portion of the cornea that was separated.

35. A method of delivering an effective amount of an agent to the eye of a subject comprising:
a) transforming at least a portion of the cells comprising the synthetic cornea of claim 1 with a nucleic acid vehicle, wherein the vehicle encodes the agent;
b) identifying a population of cells comprising the synthetic cornea of step (a) which express the agent encoded by the nucleic acid; and c) replacing cornea cells of the subject with transformed cells of the synthetic cornea of step (b), wherein the replaced cells deliver the agent to the eye of the subject.

36. The method of claim 35, wherein the replacing step comprises replacing the cornea of the subject with the synthetic cornea of step (b).