A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations

Abstract

Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is ~1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as "f value") and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas.

Genome-wide screen for asthma in Puerto Ricans: evidence for association with 5q23 region

“…Here, we confirm our previous findings using a much larger set of AIMs (n = 2730) suggesting that any association study of asthma in Latino populations should be tested and corrected for population stratification. In addition, we have identified AIMs on the Affymetrix 100K arrays for Latino populations, which may be helpful for future investigators intending to perform admixture mapping or genome-wide association studies in Latino populations, complementing three recent reports of Latino Admixture Mapping panels (Mao et al 2007;Price et al 2007;Tian et al 2007). …”

Analysis of admixture proportions in seven geographical regions of the state of Guerrero, Mexico

“…Multiple different panels of AIMs to infer ancestry proportions in recently admixed populations from the Americas have been used (Galanter et al, 2012; Mao et al, 2007; Price et al 2007; Watkins et al, 2012; Yaeger et al, 2008). …”

“…Studying this genetic information can contribute to the reconstruction of Mexican population history. Admixture studies are also relevant from the biomedical point of view, as admixture‐based approaches, such as admixture mapping, can identify genetic factors associated with diseases and complex traits (Mao et al, 2007; Shriner et al, 2011). In genetic association studies in admixed populations, individual admixture proportions are routinely incorporated into the statistical models to minimize potential false positives due to population stratification (Flores‐Alfaro, Burguete‐García, & Salazar‐Martínez, 2012).…”

Ancestry informative markers and admixture proportions in northeastern Mexico

“…3,4 Panels of AIMs for Latin American populations have been proposed. [5][6][7] These maps will allow the application of admixture mapping studies as an approach for the identification of genetic risk factors for complex diseases in populations of mixed ancestry. 6 In Mexico, the current population is constituted predominantly by Mestizo, resulting from the admixture of Native Americans and Spaniards who arrived in the country during the conquest, and in smaller proportion by Africans brought to the country as slaves.…”