Copyright © 2007 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 80, Issue 6, 1024-1036, 1 June 2007
doi:10.1086/518313
Article
A Genomewide Admixture Map for Latino Populations
Alkes L. Pricea, b, Nick Pattersonb, Fuli Yua, b, David R. Coxc, Alicja Waliszewskaa, b, Gavin J. McDonalda, b, Arti Tandona, b, Christine Schirmera, b, Julie Neubauera, b, Gabriel Bedoya, Constanza Duque, Alberto Villegas, Maria Catira Bortolinie, Francisco M. Salzanoe, Carla Gallof, Guido Mazzottif, Marcela Tello-Ruiz, Laura Riba, Carlos A. Aguilar-Salinas, Samuel Canizales-Quinteros, Marta Menjivari, William Klitzk, l, Brian Hendersonm, Christopher A. Haimanm, Cheryl Winklern, Teresa Tusie-Luna, Andrés Ruiz-Linares and David Reicha, b, 
, 
a Department of Genetics, Harvard Medical School, Boston
b Medical and Population Genetics Group, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
c Perlegen Sciences, Mountain View, CA
d Laboratorio de Genética Molecular, Universidad de Antioquia, Medellín, Colombia
e Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
f Laboratorios de Investigación y Desarrollo, Falcultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima
g Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
h Unit of Molecular Biology and Genomic Medicine, Instituto de Investigaciones Biomedicas
i Biology Department, Facultad de Química
j Universidad Nacional Autónoma de México, and Departament de Endocrinology y Metabolism, Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran
k Mexico City; School of Public Health, University of California, Berkeley
l Public Health Institute, Oakland
m Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles
n Laboratory of Genomic Diversity, SAIC-Frederick, National Cancer Institute, Frederick, MD
o and The Galton Laboratory, Department of Biology, University College London, London
Address for correspondence and reprints: Dr. David Reich, Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115.Abstract
Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.
Article Information
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