Table 1. Summary of SNP Genotyping, Karyotyping, STR Analysis, and CNV qPCR Validation for the PGD-Derived hESC Lines.
| hESC Line | Chr | Position | Early | High | Detection | Validation | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP Genotyping | Karyotyping | Short Tandem Repeat Testing | qPCR CNV assay | ||||||||||||
| CNV | Interpretation | Inh | No. of SNPs in Region | No. of Markers | STR Results | Probe Used | Ratio (versus Diploid Control) | CNV qPCR Results | Conclusion | ||||||
| Lis04_ Twist | 2 | 114925151–119741942 | + | + | 2 | ROH | UTD | 1,372 | ND | None | NA | None | NA | NA | ROH |
| 2 | 134033864–137339476 | + | + | 2 | ROH | UTD | 1,062 | ND | None | NA | None | NA | NA | ROH | |
| 7 | 98674852–158812247 | + | + | 2 | Large ROH | Pat | 19,577 | ND | 4 | Homz, Pat | None | NA | NA | Large LOH, Pat, gam-early pass | |
| 8 | 111210397–112355790 | + | + | 2 | ROH | UTD | 180 | ND | None | NA | None | NA | NA | ROH | |
| 10 | 9044003–10289903 | + | + | 2 | ROH | UTD | 425 | ND | None | NA | None | NA | NA | ROH | |
| Lis12_ DM | 3 | 177373492–177393468 | + | + | 1 | 1-copy | Mat | 15 | ND | None | NA | Hs03228327 | 0.55 | 1 -copy | 1 -copy del, Mat, gam -early pass |
| 4 | 9820707–9843332 | + | + | 0 | 0-copy | Loss of both parental copies | 96 | ND | None | NA | Hs03239014 | Undetectable | 0-copy | 0-copy del, gam - early pass | |
| 7 | p13-q11.2 | - | + | 2 | ND | ND | Peri-inv | None | NA | None | NA | NA | Peri, long-term | ||
| 8 | 85878049–86910517 | + | + | 2 | ROH | UTD | 181 | ND | None | NA | None | NA | NA | ROH. | |
| 8 | 100005461–101295619 | + | + | 2 | ROH | UTD | 191 | ND | 6 | Homz, nl inh | None | NA | NA | ROH, nl inh | |
| 14 | 39412328–40455980 | + | + | 2 | ROH | UTD | 259 | ND | None | NA | None | NA | NA | ROH | |
| 17 | Whole chromosome | - | + | 3 | Dup | Pat | 29,097 | Tri17 | None | NA | None | NA | NA | Dup, long-term | |
| 22 | 26529417–27788788 | + | + | 2 | ROH | UTD | 262 | ND | None | NA | None | NA | NA | ROH | |
| Lis25_FAP | 1 | 51610325–52868170 | + | + | 2 | ROH | UTD | 301 | ND | None | NA | Not done | NA | NA | ROH |
| 3 | 121951424–123356123 | + | + | 2 | ROH | UTD | 344 | ND | None | NA | Not done | NA | NA | ROH | |
| 3 | 133103999–133195707 | + | + | 1 | 1-copy | UTD | 45 | ND | None | NA | Hs04750306 Hs01541029 | 0.976, 1.019 | 2-copies | False-positive | |
| 12 | 86694771–87755618 | + | + | 2 | ROH | UTD | 229 | ND | 4 | Hetz, nl inh | Not done | NA | NA | ROH, nl inh | |
| 15 | 70195123–71415221 | + | + | 2 | ROH | UTD | 276 | ND | None | NA | not done | NA | NA | ROH | |
Early, early passage; High, high passage; Interp, interpretation of the SNP genotyping CNV call; Inh, inheritance pattern of regions of CNV inferred from the SNP genotyping data; ROH, region of homozygosity; CNV, CNV value; Inh, inheritance; One copy, single-copy deletion; Zero copy, zero copy deletion; ND, not detected; Dup, duplication; UTD, unable to determine parent of origin; Mat, both alleles are of maternal origin (ROH); Pat, both alleles are of paternal origin (ROH) or duplicated allele is of paternal origin; loss of both, loss of both parental alleles; NA, not applicable; Peri-inv, pericentromeric inversion; Tri17, trisomy 17; Homz, homozygous; Hetz, heterozygous; nl inh, normal inheritance; gam-early pass, occurred during the period from gametogenesis to early passage, long-term, occurred during long-term culture; Probe used, catalog number of the CNV qPCR assay obtained from Life Technologies; Undet, undetectable. See also Figures S4, S5, and Tables S3 and S4.