To identify which regions of the genome in African American cases and controls had African or European origin, we used a Hidden Markov Model with three hidden states corresponding to the number of chromosomes of European ancestry at a given locus. Given a polymorphic locus t in the genome, we indicate with pE(t) the frequency of the reference allele in the European population, p′E(t) the frequency of the reference allele in the Illumina European cohort, with pA(t) the frequency of reference allele in the African population, with p′B(t) the frequency of the reference allele in the Illumina African American cohort, and m=21% the expected European ancestry in African American samples. We approximated the ancestral frequencies of the two populations using the Illumina controls cohort in the following way: pE(t)∼p′E(t)pA(t)∼p′B(t)−mp′E(t)1−m
