Table 2.
Descriptive information of six GWA data sets
| GWA1_100K | GWA2_100K | GWA3_300K | GWA4_300K | GWA5_300K | GWA6_1.8m | |
|---|---|---|---|---|---|---|
| Sample information | ||||||
|
| ||||||
| Number of samples | 500 | 441 | 541 | 183 | 268 | 292 |
| Number of cases | 354 | 313 | 270 | 92 | 176 | 175 |
| Number of controls | 146 | 128 | 271 | 91 | 92 | 117 |
|
| ||||||
| SNP information | ||||||
|
| ||||||
| Number of SNPs | 105834 | 109924 | 317503 | 317503 | 317503 | 909622 |
| Number of SNPS on sex chromosome | 0 | 0 | 9173 | 9173 | 9173 | 37380 |
| SNPs with call rate less than 95% | 1584 | 1018 | 3101 | 7235 | 28124 | 131770 |
| SNPs with minor allele frequency (MAF) < 0.01 |
5005 | 10642 | 252 | 30970 | 45173 | 39408 |
| SNPs with no polymorphism observed | 1810 | 2150 | 91 | 20540 | 31852 | 66 |
| SNPs with only heterozygotes observed | 0 | 2 | 0 | 0 | 113 | 2046 |
| Polymorphic SNPs with no heterozygote observed |
25 | 94 | 5 | 139 | 358 | 130957 |
| SNPs with HWE χ2 > 50 in case group | 26 | 205 | 9126 | 396 | 10084 | 6511 |
| SNPs with HWE χ2 > 50 in control group | 330 | 666 | 7741 | 596 | 2117 | 4555 |
| SNPs with HWE χ2 > 50 in combined samples |
752 | 1112 | 9265 | 5443 | 12160 | 10023 |
|
| ||||||
| SNP QC Results Summary: | ||||||
|
| ||||||
| Number of autosomal chromosome Markers | 105834 | 109924 | 308330 | 308330 | 308330 | 872242 |
| Autosomal SNPs Passing Call Rate/MAF | 100610 | 96260 | 304342 | 269795 | 256811 | 606999 |
| Threshold (0.01 ≤ MAF < 0.05 and call rate ≥ 0.99) or (0.05 ≤ MAF < 0.10 and call rate 0.97) or (0.10 ≤ MAF and call rate ≥ 0.95) |
||||||
| Pass above, no polymorphism observed | 0 | 0 | 0 | 0 | 0 | 0 |
| Pass above, only heterozygotes observed | 0 | 2 | 0 | 0 | 0 | 6 |
| Pass above, no heterozygote observed | 0 | 0 | 0 | 2 | 100 | 0 |
| Pass above, fail HWE test (χ2 > 50 in case group or χ2 > 50 in control group) |
76 | 191 | 8 | 28 | 3443 | 1303 |
| Number of usable SNPs | 100534 | 96067 | 304334 | 269765 | 253268 | 605690 |