and Puerto Ricans, the two largest Hispanic/Latino ethnic groups in the United States. This allows comparison of patterns of population structure and ancestry across multiple U.S. Hispanic/Latino populations. Our dense SNP marker panel is formed by the intersection of two of the most commonly used genotyping platforms, allowing for the inclusion of dozens of Native American, African, and European populations for ancestry inference. Our work expands on high-density population-wide genotype data from the International HapMap Project (HapMap) (International HapMap Consortium, 2005; Frazer et al., 2007), the Human Genome Diversity Panel (HGDP) (Rosenberg et al., 2002), and the Population Reference Sample (POPRES) (Nelson et al., 2008) that have representation of Mexicans but not other Hispanic/Latino groups either from the Caribbean or from South America, with a resulting gap for analyzing admixture in those populations. This project, therefore, represents an important step toward comprehensive panels for U.S.-based studies that can more accurately reflect the diversity within various Hispanic/Latino populations.
We applied the clustering algorithm FRAPPE to investigate genetic structure among Hispanic/Latino individuals using a merged data set with over 5,000 individuals with European, African, and Native American ancestry genotyped across 73,901 SNPs common to the Affymetrix 500K array and the Illumina 610-Quad panel (Materials and Methods). FRAPPE implements a maximum likelihood method to infer the genetic ancestry of each individual, where the individuals are assumed to have originated from K ancestral clusters (Tang et al., 2005). The plots for K = 3 and K = 7 are shown in Fig. 8.1 and for all other values of K in Fig. S1 (available online at www.pnas.org/cgi/content/full/0914618107/DCSupplemental) K = 3. We observed clustering largely by Native American, African, and European ancestry, with the Hispanic/Latino populations showing genetic similarity with all of these populations. However, significant population differences exist, with the Dominicans and Puerto Ricans showing the highest levels of African ancestry (41.8% and 23.6% African, SDs 16% and 12%), whereas Mexicans and Ecuadorians show the lowest levels of African ancestry (5.6% and 7.3% African, SDs 2% and 5%) and the highest Native American ancestries (50.1% and 38.8% Native American, SDs 13% and 10%). We also found extensive variation in European, Native American, and African ancestry among individuals within each population. A clear example could be observed in the Mexican sample, in which ancestry proportions ranged from predominantly Native American to predomi-