Another way to simultaneously examine both sample identity and pedigree integrity is by reconciling genomic data with self-reported relationships between individuals (if available). Although this has consequences that impact which analytical approaches are appropriate for the downstream association study, having related samples in the dataset makes it possible to further investigate potential DNA sample mix-ups. Using dense marker data obtained in GWAS, it is easy to compute pairwise kinship estimates between every individual in the study using the -- genome option in PLINK. This procedure need not be performed on the entire GWAS using – dataset only 100,000 markers will also yield stable estimates of kinship coefficients. In addition to reporting the relationship type as reported using pedigree data (e.g. siblings, parent-child, unrelated), this procedure will also calculate the proportion of loci where two individuals share zero, one, or two alleles identical by descent (IBD). Individuals sharing two alleles IBD at every locus are either monozygotic twins, or the pair is actually a single sample processed twice. Individuals sharing zero alleles IBD at every locus are unrelated. Individuals sharing one
