Chunk #35 — ONLINE METHODS — Association Analysis — Genomic Quality Control: Principal Component Analysis (PCA) and Relatedness Checking in the core PGC dataset
Supplementary Table 22 lists detailed per cohort exclusion numbers for individuals in the non-Asian samples. The Asian cohorts were sufficiently homogeneous as they did not show marked population structure in principal component analyses. The exclusion numbers for individuals during technical QC are in most cohorts low. For six cohorts (marked in yellow in Supplementary Table 22) it was necessary to exclude more than 100 cases during genomic QC so that Lambda GC fell within the window mentioned above. Supplementary Figure 4 gives details about this process and explains why the excluded cases could not be used with the presently available control cohorts for this manuscript.
