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PMID: 17557415 Published · ppublish English Comparative Study Journal Article Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural

A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping.

American journal of human genetics ·Vol. 80 ·No. 6 ·2007-06-00 ·Pages 1014-23

Tian C, Hinds DA, Shigeta R, Adler SG, Lee A, Pahl MV, Silva G, Belmont JW, Hanson RL, Knowler WC, Gregersen PK, Ballinger DG, Seldin MF

Abstract

For admixture mapping studies in Mexican Americans (MAM), we define a genomewide single-nucleotide-polymorphism (SNP) panel that can distinguish between chromosomal segments of Amerindian (AMI) or European (EUR) ancestry. These studies used genotypes for >400,000 SNPs, defined in EUR and both Pima and Mayan AMI, to define a set of ancestry-informative markers (AIMs). The use of two AMI populations was necessary to remove a subset of SNPs that distinguished genotypes of only one AMI subgroup from EUR genotypes. The AIMs set contained 8,144 SNPs separated by a minimum of 50 kb with only three intermarker intervals >1 Mb and had EUR/AMI FST values >0.30 (mean FST = 0.48) and Mayan/Pima FST values <0.05 (mean FST < 0.01). Analysis of a subset of these SNP AIMs suggested that this panel may also distinguish ancestry between EUR and other disparate AMI groups, including Quechuan from South America. We show, using realistic simulation parameters that are based on our analyses of MAM genotyping results, that this panel of SNP AIMs provides good power for detecting disease-associated chromosomal segments for genes with modest ethnicity risk ratios. A reduced set of 5,287 SNP AIMs captured almost the same admixture mapping information, but smaller SNP sets showed substantial drop-off in admixture mapping information and power. The results will enable studies of type 2 diabetes, rheumatoid arthritis, and other diseases among which epidemiological studies suggest differences in the distribution of ancestry-associated susceptibility.

MeSH Terms
Algorithms Chromosome Mapping Chromosomes, Human Genetic Markers Genetic Predisposition to Disease Genetic Testing Genetics, Population Genome, Human Genotype Humans Indians, North American/genetics Indians, South American/genetics Markov Chains Mexican Americans/genetics Monte Carlo Method Polymorphism, Single Nucleotide Whites
Chemicals
Genetic Markers
Authors & Affiliations
13 authors, click to expand affiliations / ORCID
Tian Chao
Rowe Program in Human Genetics, Department of Biochemistry, University of California Davis, Davis, CA 95616, USA.
Hinds David A
Shigeta Russell
Adler Sharon G
Lee Annette
Pahl Madeleine V
Silva Gabriel
Belmont John W
Hanson Robert L
Knowler William C
Gregersen Peter K
Ballinger Dennis G
Seldin Michael F
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Article Info
Journal
American journal of human genetics
Abbr.
Am J Hum Genet
ISSN
0002-9297
DOI
10.1086/513522
Published
2007-06-00
Pages
1014-23
Language
English
Region
United States
NLM ID
0370475
PMCID
PMC1867091
Subset
IM
Grants
NIDDK NIH HHS · R01 DK071185 · United States
NIDDK NIH HHS · U01 DK057249 · United States
NIDDK NIH HHS · U01 DK57249 · United States
Intramural NIH HHS · United States
External Links
PubMed source DOI: 10.1086/513522 PMC Full Text View journal details
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