Three additional quality measures are used in the QA process to detect mixed (contaminated) DNA samples. First, we identify outliers in autosomal heterozygosity within each ethnic group (for example, as points more than 1.5 inter-quartile ranges from the upper/lower quartile value). Second, we screen for samples with a high variance of BAF for non-homozygous SNPs, as described in Supporting Information. Third, we look for unusual patterns of relatedness, such as samples that appear to be related to many other samples. Samples with one or more of these characteristics may be mixtures of multiple DNA samples, which can be identified by examination of BAF/LRR plots. Figure S1 in Supporting Information shows examples of normal and low quality samples. The “Relatedness” section below describes an example of mixed sample detection.
