Ancestry outliers were identified by multidimensional scaling, combining the iCOGS data with genotypes from the HapMap 2 populations, on the basis of a subset of 37,000 uncorrelated markers that passed quality control (including ~1,000 that were selected as ancestry-informative markers). Most studies were predominantly of a single ancestry (European or East Asian), and individuals with >15% minority ancestry, as determined on the basis of the first two principal components, were excluded. Two studies from Singapore (SGBCC) and Malaysia (MYBRCA) contained a substantial fraction of individuals of mixed European and Asian ancestry (likely of South Asian ancestry). For these studies, no exclusions for ancestry outliers were made, but principal-components analysis adequately corrected for inflation in these studies. Similarly, for the two African-American studies (NBHS and SCCS), no exclusions for ancestry outliers were made.
