In the T2D NHS project, the relatedness analysis revealed two samples that appeared to be related to nearly every other sample in the study with a kinship coefficient between the expected values of half sibs and first cousins (Figures S3 – S6). These samples have relatively high heterozygosity and their BAF plots indicate that they are mixed samples (Figure S1 d and e). Several other samples that appeared to have relatedness to a large number of other samples are not clearly mixed, but appear to be of low quality since they all have more than five chromosomes flagged for high variance of BAF (e.g. Figure S1 f). Similar samples were found in the T2D HPFS project and both projects are discussed further in Supporting Information.
