Table 2.
Summary Information for the Seven Waves of Genotyping and the Quality Control Undertaken
| Project 1: ALCO CIDR | Project 2: ALCO deCODE | Project 3: MIG deCODE | Project 4: EUTWIN | Project 5: ADOL deCODE | Project 6: GL_CIDR | Project 7: WH deCODE | |
|---|---|---|---|---|---|---|---|
| Primary phenotype | Alcohol use (population sample) | Alcohol use (population sample) | Migraine (case/control sample) | Lipid levels (population sample) | Melanoma risk factors (population sample) | Glaucoma (population sample) | Womens' health (case/control sample) |
| Genotyping lab | CIDR | deCODE | deCODE | University of Helsinki | deCODE | CIDR | deCODE |
| Illuminia SNP platform | HumanCNV370-Quadv3 | HumanCNV370-Quadv3 | Human610-Quad | Human 317K | Human610-Quad | Human610-Quad | Human610-Quad |
| No. of genotyped samples | 4241 | 2611 | 999 | 462 | 4391 | 657 | 2360 |
| No. of genotyped SNPs | 343,955 | 344,962 | 592,385 | 318,210 | 592,392 | 589,296 | 562,193 |
| BeadStudio GenCall score < 0.7 | 24,494 | 27,459 | 46,931 | NAa | 47,418 | 36,877 | 57,589 |
| SNPs with call rate < 0.95 | 11,584 | 7537 | 8038 | 5021 | 8447 | 12,455 | 33,459 |
| SNPs with HWE failure p < 10−6 | 4318 | 1194 | 1221 | 67 | 2841 | 15,474 | 1763 |
| SNPs with MAF < 0.01/ only 1 observed allele | 7874 | 8976 | 33,347 | 264 | 33,347 | 28,607 | 24,509 |
| No. of SNPs after QC | 323093 | 321,267 | 530,922 | 312,937 | 529,379 | 531,042 | 518,948 |
| Percentage of genotyped SNPs | 93.93% | 93.13% | 89.62% | 98.34% | 89.36% | 90.11% | 92.31% |
For each project, DNA was extracted in accordance with standard protocols. Across projects, participants were genotyped on the Illumina 317K, 370K, or 610K SNP platforms, and genotypes were called with the Illumina BeadStudio software. After the quality control (QC) of the individual projects, the data from the seven waves of genotyping were integrated. As shown in Figure S1, a number of samples were duplicated among the various genotyping projects, allowing for cross-project QC. After integration of the data sets, the data were screened for missingness within individuals (>5%, taking into account the number of SNPs that were genotyped for each individual), pedigree and sex errors, and Mendelian errors (genotypes for all family members for a given SNP were removed upon detection of errors). After QC, in cases where one individual from a monozygotic twin pair had been genotyped, duplicate genotypes were assigned to the ungenotyped cotwin, resulting in a sample of 16,507 individuals. After screening for non-European ancestry (Figure S2), this resulted in a final sample of 16,140 individuals. HWE denotes Hardy-Weinburg equilibrium.
GenCall data were not available for this sample.