Another way to detect batch effects is to assess differences in allelic frequency between each batch and a pool of all other batches in a study, using a homogeneity test (see Supporting Information). This allelic frequency test can be affected not only by laboratory processing, but also by the biological characteristics of the samples in a batch, such as continental ancestry, other ethnic variation and relatedness. After taking continental ancestry into consideration, no batch outliers were found in any of the four projects, except for the batch with only three passing samples noted above (see Figure S2 and text in Supporting Information).
