Local ancestry is defined as the genetic ancestry of an individual at a particular chromosomal location, where an individual can have 0, 1 or 2 copies of an allele derived from each ancestral population. Two group members [Chen et al., 2013; Yorgov et al., 2013] estimated local ancestry on chromosome 3 using the LAMP-LD software program [Baran et al., 2012]. Both Yorgov et al. [2013] and Chen et al. [2013] used the HGDP Native American samples and the HapMap CEU and YRI samples as the reference population panels for local ancestry estimation, and the SHAPEIT software was used for phasing the reference population samples. Yorgov et al. [2013] performed the analysis with 40,098 chromosome 3 markers to allow the LAMP-LD method to leverage the structure of linkage disequilibrium. Chen et al. [2013] additionally evaluated the LAMP [Sankararaman et al., 2008] and MULTIMIX [Churchhouse and Marchini, 2013] methods. Phased reference panel data was used with the MULTIMIX software, and local ancestry estimates when using phased and unphased genotype data for the GAW18 sample individuals were compared. For the local ancestry analysis
