A Genomewide Single-nucleotide-polymorphism Panel with High Ancestry Information for African American Admixture Mapping

Overview

Journal Am J Hum Genet

Publisher Cell Press

Specialty Genetics

Date 2006 Sep 9

PMID 16960800

Citations 113

Authors

Chao Tian

David A Hinds

Russell Shigeta

Rick Kittles

Dennis G Ballinger

Michael F Seldin

Affiliations

Soon will be listed here.

Abstract

Admixture mapping requires a genomewide panel of relatively evenly spaced markers that can distinguish the ancestral origins of chromosomal segments in admixed individuals. Through use of the results of the International HapMap Project and specific selection criteria, the current study has examined the ability of selected single-nucleotide polymorphisms (SNPs) to extract continental ancestry information in African American subjects and to explore parameters for admixture mapping. Genotyping of two linguistically diverse West African populations (Bini and Kanuri Nigerians, who are Niger-Congo [Bantu] and Nilo-Saharan speakers, respectively), European Americans, and African Americans validated a genomewide set of >4,000 SNP ancestry-informative markers with mean and median F(ST) values >0.59 and mean and median Fisher's information content >2.5. This set of SNPs extracted a larger amount of ancestry information in African Americans than previously reported SNP panels and provides nearly uniform coverage of the genome. Moreover, in the current study, simulations show that this more informative panel improves power for admixture mapping in African Americans when ethnicity risk ratios are modest. This is particularly important in the application of admixture mapping in complex genetic diseases for which only modest ethnicity risk ratios of relevant susceptibility genes are expected.

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References

Lautenberger J, Stephens J, OBrien S, Smith M . Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet. 2000; 66(3):969-78. PMC: 1288177. DOI: 10.1086/302820. View

Pritchard J, Stephens M, Donnelly P . Inference of population structure using multilocus genotype data. Genetics. 2000; 155(2):945-59. PMC: 1461096. DOI: 10.1093/genetics/155.2.945. View

Pfaff C, Parra E, Bonilla C, Hiester K, McKeigue P, Kamboh M . Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet. 2000; 68(1):198-207. PMC: 1234913. DOI: 10.1086/316935. View

Smith M, Lautenberger J, Shin H, Chretien J, Shrestha S, Gilbert D . Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet. 2001; 69(5):1080-94. PMC: 1274377. DOI: 10.1086/323922. View

Collins-Schramm H, Phillips C, Operario D, Lee J, Weber J, Hanson R . Ethnic-difference markers for use in mapping by admixture linkage disequilibrium. Am J Hum Genet. 2002; 70(3):737-50. PMC: 384950. DOI: 10.1086/339368. View

Kong A, Gudbjartsson D, Sainz J, Jonsdottir G, Gudjonsson S, Richardsson B . A high-resolution recombination map of the human genome. Nat Genet. 2002; 31(3):241-7. DOI: 10.1038/ng917. View

Collins-Schramm H, Kittles R, Operario D, Weber J, Criswell L, Cooper R . Markers that discriminate between European and African ancestry show limited variation within Africa. Hum Genet. 2002; 111(6):566-9. DOI: 10.1007/s00439-002-0818-z. View

Collins-Schramm H, Chima B, Operario D, Criswell L, Seldin M . Markers informative for ancestry demonstrate consistent megabase-length linkage disequilibrium in the African American population. Hum Genet. 2003; 113(3):211-9. DOI: 10.1007/s00439-003-0961-1. View

Falush D, Stephens M, Pritchard J . Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003; 164(4):1567-87. PMC: 1462648. DOI: 10.1093/genetics/164.4.1567. View

10.

Collins-Schramm H, Chima B, Morii T, Wah K, Figueroa Y, Criswell L . Mexican American ancestry-informative markers: examination of population structure and marker characteristics in European Americans, Mexican Americans, Amerindians and Asians. Hum Genet. 2003; 114(3):263-71. DOI: 10.1007/s00439-003-1058-6. View

11.

Rosenberg N, Li L, Ward R, Pritchard J . Informativeness of genetic markers for inference of ancestry. Am J Hum Genet. 2003; 73(6):1402-22. PMC: 1180403. DOI: 10.1086/380416. View

12.

Hoggart C, Shriver M, Kittles R, Clayton D, McKeigue P . Design and analysis of admixture mapping studies. Am J Hum Genet. 2004; 74(5):965-78. PMC: 1181989. DOI: 10.1086/420855. View

13.

Patterson N, Hattangadi N, Lane B, Lohmueller K, Hafler D, Oksenberg J . Methods for high-density admixture mapping of disease genes. Am J Hum Genet. 2004; 74(5):979-1000. PMC: 1181990. DOI: 10.1086/420871. View

14.

Smith M, Patterson N, Lautenberger J, Truelove A, McDonald G, Waliszewska A . A high-density admixture map for disease gene discovery in african americans. Am J Hum Genet. 2004; 74(5):1001-13. PMC: 1181963. DOI: 10.1086/420856. View

15.

Pfaff C, Barnholtz-Sloan J, Wagner J, Long J . Information on ancestry from genetic markers. Genet Epidemiol. 2004; 26(4):305-15. DOI: 10.1002/gepi.10319. View

16.

Zhu X, Cooper R, Elston R . Linkage analysis of a complex disease through use of admixed populations. Am J Hum Genet. 2004; 74(6):1136-53. PMC: 1182078. DOI: 10.1086/421329. View

17.

Seldin M, Morii T, Collins-Schramm H, Chima B, Kittles R, Criswell L . Putative ancestral origins of chromosomal segments in individual african americans: implications for admixture mapping. Genome Res. 2004; 14(6):1076-84. PMC: 419786. DOI: 10.1101/gr.2165904. View

18.

Montana G, Pritchard J . Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet. 2004; 75(5):771-89. PMC: 1182107. DOI: 10.1086/425281. View

19.

Zhang C, Chen K, Seldin M, Li H . A hidden Markov modeling approach for admixture mapping based on case-control data. Genet Epidemiol. 2004; 27(3):225-39. DOI: 10.1002/gepi.20021. View

20.

Kong X, Murphy K, Raj T, He C, White P, Matise T . A combined linkage-physical map of the human genome. Am J Hum Genet. 2004; 75(6):1143-8. PMC: 1182151. DOI: 10.1086/426405. View