Table 1. Quality control details of genotyping in both cohorts.
| Cohort | Raine | BATS/TEST | BATS/TEST |
|---|---|---|---|
| Genotyping Centre |
Centre for Applied Genomics (Toronto, Ontario, Canada) |
deCODE (Iceland) |
CIDR (USA) |
| Chip |
Illumina 660 K |
Illumina 610 K |
Illumina 610 K |
| # genotyped SNPs (as supplied) |
657,366 |
592,392 |
589,296 |
| mean GenCall <0.7 |
95,876 |
47,418 |
36,877 |
| >5% missing |
1843 (97,719) |
8447 (47,950) |
12,455 (37,499) |
| p(HWE) <10-6 |
919 (98,449) |
2841 (49,616) |
15,474 (51,646) |
| MAF<0.01 (or monomorphic) |
23,370 (121,734) |
33,347 (69,632) |
28,607 (67,969) |
| # SNPs left |
535,632 |
529,379 |
531,042 |
| % genotyped SNPs |
81.48% |
89.36% |
90.11% |
| Dropout rate due to QIMR SNP QC | 18.52% | 10.64% | 9.89% |