Chen et al. [2013] found that LAMP-LD and MULTIMIX software programs, both of which use dense SNP genotype data and incorporate LD when estimating local ancestry, perform better than the LAMP software, which relies on a pre-defined set of AIMs that are in low LD. When averaging local ancestry based on LAMP, LAMP-LD, and MULTIMIX across chromosome 3, LAMP-LD estimates showed the highest correlation (0.989) with global ancestry estimates on chromosome 3 from a supervised ADMIXTURE analysis. LAMP-LD and MULTIMIX resulted in discordant ancestry inferences for 18% of the SNPs with unphased genotype data for the sample individuals. The two methods inferred a similar number of generations since admixture for the Mexican American sample individuals, between 10 and 12, based on the number of inferred ancestry blocks, for which the authors found to be consistent with previous reports on Hispanic populations. However, when using phased genotype data for the GAW18 individuals with MULTIMIX, the number of generations since admixture was overestimated, which may be an artifact attributable to the uncertainty introduced by the genotype phasing of admixed samples.
