The analysis of whole genome sequence (WGS) data and genome-wide single nucleotide polymorphism (SNP) chip data from Mexican American pedigrees provided by the Genetic Analysis Workshop 18 (GAW18) presents a number of challenges due to both ancestry admixture as well as relatedness among individuals. Mexican Americans are known to be a multi-way admixed population who descend from a combination of European, Native American and West African progenitors [Johnson et al. 2011; Manichaikul et al. 2012]. The five contributions to the GAW18 Admixture group considered a wide variety of topics under the general theme of inferring, accounting for, and incorporating ancestry admixture in genetic analyses. The authors considered admixture not only as a potential confounder but also exploited differential ancestry for improved association mapping and more accurate genotype imputation. In this summary paper we describe methods and analyses conducted by the Admixture group, as well as the most relevant findings of the contributors, providing insight into their strengths and limitations.
