COPDGene has both array and WGS genotype data on the same samples available through TOPMed. Genotypes derived from array and whole-genome sequencing data for the same samples should be consistent but are often not18,25. To evaluate the consistency of genotyping, we performed a technical comparison of array and WGS data using the same set of samples from COPDGene (n = 3235 with African-American ancestry). The array data were phased independently and integrated with the WGS phased data available in TOPMed, followed by imputation and association testing using genotyping platform as the outcome. If the array- and WGS-derived genotypes for the same set of samples were equivalent, one would expect to observe no significant associations, but in fact we observed many false positives (Supplementary Fig. 3).
