Table 4.
Nature of Discordant Genotypes from 500K Arrays Between gDNA and wgaDNA
| Nature of discordance |
109023 |
109025 |
0270 |
0271 |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| gDNA genotype | wgaDNA genotype | NspI | StyI | Total % of discordant genotypes | NspI | StyI | Total % of discordant genotypes | NspI | StyI | Total % of discordant genotypes | NspI | StyI | Total % of discordant genotypes |
| AA | BB | 64 | 43 | 0.3 | 214 | 134 | 0.8 | 1 | 26 | 0.4 | 2 | 1 | 0.1 |
| BB | AA | 72 | 53 | 0.4 | 257 | 195 | 1.0 | 5 | 22 | 0.4 | 3 | 2 | 0.1 |
| AA | AB | 700 | 607 | 4.0 | 1389 | 990 | 5.2 | 375 | 447 | 11.3 | 278 | 278 | 17.2 |
| BB | AB | 735 | 558 | 4.0 | 1508 | 1068 | 5.6 | 452 | 445 | 12.4 | 361 | 371 | 22.7 |
| AB | AA | 8302 | 7365 | 47.9 | 11,330 | 9773 | 46.2 | 1279 | 1710 | 41.1 | 529 | 525 | 32.7 |
| AB | BB | 7503 | 6672 | 43.4 | 9965 | 8895 | 41.2 | 1069 | 1431 | 34.4 | 483 | 395 | 27.2 |
| Total | 17,376 | 15,298 | 24,663 | 21,055 | 3181 | 4081 | 1656 | 1572 | |||||
NspI arrays contain 262,264 SNPs; StyI arrays contain 238,304 SNPs. Total % of discordant genotypes includes discordant genotypes from both NspI and StyI chips for each sample.