We obtained prephased reference haplotypes from the February 2012 release of the 1000 Genomes project (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521/, accessed March 7, 2012). We created three reference haplotype panels based on different combinations of 1000 Genomes populations. The first 1000 Genomes reference panel was created by combining YRI (N = 88), CEU (N = 85), and ASW (N = 61) populations, which were specifically chosen to provide a close match to African American study populations. We previously evaluated several different combinations of HapMap phase III reference populations for our African American study population and found that the combined YRI+CEU+ASW panel had optimal imputation performance [22]. The YRI+CEU+ASW panel has also been shown elsewhere to outperform other combined HapMap phase III panels [8].
