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

被引:107
作者
Tian, Chao
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.
机构
[1] Univ Calif Davis, Dept Biochem, Rowe Program Human Genet, Davis, CA 95616 USA
[2] Univ Calif Davis, Dept Med, Rowe Program Human Genet, Davis, CA 95616 USA
[3] Perlegen Sci, Mountain View, CA USA
[4] Calif State Univ Los Angeles, David Geffen Sch Med, Los Angeles Biomed Res Inst Harbor, Div Nephrol & Hypertens, Torrance, CA 90032 USA
[5] Feinstein Inst Med Res, Robert S Boas Ctr Genom & Human Genet, N Shore Long Isl Jewish Hlth Syst, Manhasset, NY USA
[6] Univ Calif Irvine, Ctr Med, Div Nephrol & Hypertens, Orange, CA 92668 USA
[7] Obras Sociales Hermano Pedro, Antigua, Guatemala
[8] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA
[9] NIDDKD, NIH, Phoenix, AZ 85016 USA
关键词
D O I
10.1086/513522
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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 values F-ST > 0.30 (mean F-ST = 0.48) and Mayan/Pima values F-ST < 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.
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收藏
页码:1014 / 1023
页数:10
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