Table 1.
Summary and categorization of small genetic variants detected in iPSCs from neonatal and aged donors
| Variants |
|||||||
|---|---|---|---|---|---|---|---|
| Per donor |
Per iPSC clone |
||||||
| Donor | iPSC clone | Passage | Total number | Polymorphisms and common variants (categories A and B; %) | Donor-specific variants (category C) | Donor-specific variants (category C) | Potentially GAVs (category C GAVs) |
| iPSCs - Neonatal donors | |||||||
| D#1 hUVEC | C2 | P8 | 37106 | 98.7 | 481 | 471 | 249 |
| C5 | P9 | 475 | 252 | ||||
| C6 | P12 | 470 | 247 | ||||
| D#2 hUVEC | C2 | P7 | 36354 | 98.6 | 514 | 507 | 293 |
| C4 | P7 | 504 | 291 | ||||
| C5 | P7 | 503 | 288 | ||||
| D#3 hUVEC | C1 | P9 | 42815 | 98.2 | 762 | 754 | 368 |
| C2 | P10 | 749 | 361 | ||||
| C3 | P9 | 751 | 366 | ||||
| D#22 hCBEC | C15 | P9 | 41226 | 98.4 | 645 | 634 | 296 |
| C17 | P9 | 631 | 296 | ||||
| C21 | P10 | 631 | 295 | ||||
| D#23 hCBEC | C1 | P7 | 34512 | 98.4 | 539 | 533 | 302 |
| C5 | P7 | 530 | 299 | ||||
| C6 | P9 | 531 | 301 | ||||
| D#25 hCBEC | C11 | P8 | 37776 | 98.5 | 559 | 555 | 286 |
| C12 | P8 | 552 | 285 | ||||
| C13 | P8 | 555 | 286 | ||||
| Mean | 38298 | 98 | 583 | 574 | 298 | ||
| iPSCs - Aged donors | |||||||
| D#31 hSVEC (64 years) | C1 | P10 | 35509 | 98.7 | 465 | 454 | 251 |
| C3 | P9 | 452 | 250 | ||||
| C4 | P8 | 450 | 248 | ||||
| D#37 hSVEC (73 years) | C4 | P9 | 40296 | 98.4 | 626 | 594 | 292 |
| C8 | P9 | 600 | 292 | ||||
| C10 | P9 | 602 | 297 | ||||
| D#38 hSVEC (88 years) | C5 | P7+8 | 43292 | 97.8 | 946 | 920 | 291 |
| C6 | P9+10 | 920 | 290 | ||||
| C9 | P8 | 921 | 292 | ||||
| D#37 hPBEC (73 years) | C4 | P8 | 39588 | 98.4 | 620 | 613 | 301 |
| C14 | P9 | 616 | 304 | ||||
| C15 | P10 | 616 | 305 | ||||
| Mean | 39671 | 98 | 664 | 647 | 284 | ||
| iPSCs - All donors | |||||||
| Mean | 38847 | 98 | 616 | 603 | 292 | ||
Exomes from 30 early passage clonal iPSC lines of neonatal and aged donors were sequenced. Categories of variants are as follows: (A) polymorphisms described in any population of GnomAD and 1000 Genomes with minor allele frequency (MAF) ≥ 0.01; (B) potentially common variants not listed as polymorphisms, that were found in more than one donor; and C) donor-specific variants present in iPSCs of one donor only. Potential GAVs compromise all variants in substantial gene regions such as coding and non-coding transcript region, UTRs, and splice regions, after exclusion of intergenic and intron variants.