Comparison of admixture and association mapping in admixed families

Genetic Epidemiology

Volumn 31, Issue 7, 2007, Pages 763-775

  Clarke, Geraldine ^a   Whittemore, Alice S ^b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Admixture mapping; Efficient score; Likelihood; Linkage; Linkage disequilibrium; Transmission disequilibrium test

Indexed keywords

ALLELE; ARTICLE; CHROMOSOME; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENOTYPE; HUMAN; INHERITANCE; MATHEMATICAL COMPUTING; PEDIGREE; PHENOTYPE; SCORING SYSTEM; TECHNIQUE;

CHROMOSOMES, HUMAN; FAMILY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI;

EID: 36248984858     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20239     Document Type: Article

References (20)

1. Amundadottir LT, Sulem P, Gudmundsson J, Helgason A, Baker A, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Cazier JB, Sainz J, Jakobsdottir M, Kostic J, Magnusdottir DN, Ghosh S, Agnarsson K, Birgisdottir B, Le Roux L, Olafsdottir A, Blondal T, Andresdottir M, Gretarsdottir OS, Bergthorsson JT, Gudbjartsson D, Gylfason A, Thorleifsson G, Manolescu A, Kristjansson K, Geirsson G, Isaksson H, Douglas J, Johansson JE, Balter K, Wiklund F, Montie JE, Yu X, Suarez BK, Ober C, Cooney KA, Gronberg H, Catalona WJ, Einarsson GV, Barkardottir RB, Gulcher JR, Kong A, Thorsteinsdottir U, Stafannsson K. 2006. A common variant associated with prostate cancer in European and African populations. Nat Genet 38:652-658.
2. Chakraborty R, Weiss KM. 1988. Admixture as a tool for finding linked genes and detecting that difference from allelic association between loci. Proc Natl Acad Sci USA 85:3031-3074.
3. Ewens WJ, Spielman RS. 1995. The transmission/disequilibrium test: history, subdivision, and admixture. Am J Hum Genet 57:455-464.
4. Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567-1587.
5. Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardlie K, John EM, Oakley-Girvan I, Whittemore AS, Cooney KA, Ingles SA, Altshuler D, Henderson BE, Reich D. 2006. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Natl Acad Sci USA 103:14068-14073.
6. Hoggart CJ, Shriver MD, Kittles RA, Clayton DG, McKeigue PM. 2004. Design and analysis of admixture mapping studies. Am J Hum Genet 74:965-978.
7. McKeigue PM. 1997. Mapping genes underlying ethnic differences in disease risk by linkage disequilibrium in recently admixed populations. Am J Hum Genet 60:188-196.
8. McKeigue PM. 1998. Mapping genes that underlie ethnic differences in disease risk: methods for detecting linkage in admixed populations, by conditioning on parental admixture. Am J Hum Genet 63:241-251.
9. McKeigue PM. 2000. Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet 64:171-186.
10. Montana G, Pritchard JK. 2004. Statistical tests for admixture mapping with case-control and cases-only data. Am J Hum Genet 75:771-789.
11. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly MJ, Reich D. 2004. Methods for high-density admixture mapping of disease genes. Am J Hum Genet 74:979-1000.
12. Reich D, Patterson N. 2005. Will admixture mapping work to find disease genes? Philos Trans R Soc Lond B Biol Sci 360:1605-1607.
13. Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Paff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA. 2003. Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112:387-399.
14. Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De Teh G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Alshuler D, Gilbert DA, O'Brien SJ, Reich D. 2004. A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 74:1001-1013.
15. Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506-516.
16. Tang H, Peng J, Wang P, Risch NJ. 2005. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28:289-301.
17. Tang H, Coram M, Wang P, Zhu X, Risch N. 2006. Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet 79:1-12.
18. Terwilliger JD, Ott J. 1992. A haplotype-based "haplotype relative risk" approach to detecting allelic associations. Hum Hered 42:337-346.
19. Tu IP, Whittemore AS. 1999. Power of association and linkage tests when the disease alleles are unobserved. Am J Hum Genet 64:641-649.
20. Zhang C, Chen K, Seldin MF, Li H. 2004. A hidden Markov modeling approach for admixture mapping based on case-control data. Genet Epidemiol 27:225-239.