New approaches to disease mapping in admixed populations

Nature Reviews Genetics

Volumn 12, Issue 8, 2011, Pages 523-528

  Seldin, Michael F ^a   Pasaniuc, Bogdan ^b,c   Price, Alkes L ^b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ARTICLE; GENE MAPPING; GENETIC ANALYSIS; GENETIC DISORDER; GENOME; HISPANIC; HUMAN; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

AFRICAN AMERICANS; BIOLOGICAL MARKERS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HISPANIC AMERICANS; HUMANS; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 79960566302     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg3002     Document Type: Article

References (44)

1. Smith, M. W. et al. A high-density admixture map for disease gene discovery in African Americans. Am. J. Hum. Genet. 74, 1001-1013 (2004). (Pubitemid 38568970)
2. Tian, C. et al. A genomewide single-nucleotide-polymorphism panel with high ancestry information for African American admixture mapping. Am. J. Hum. Genet. 79, 640-649 (2006). (Pubitemid 44452741)
3. Haiman, C. A. et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nature Genet. 39, 638-644 (2007). (Pubitemid 46676106)
4. Bryc, K. et al. Colloquium paper: genome-wide patterns of population structure and admixture among Hispanic/Latino populations. Proc. Natl Acad. Sci. USA 107 (Suppl. 2), 8954-8961 (2010).
5. Xu, S., Huang, W., Qian, J. & Jin, L. Analysis of genomic admixture in Uyghur and its implication in mapping strategy. Am. J. Hum. Genet. 82, 883-894 (2008).
6. de Wit, E. et al. Genome-wide analysis of the structure of the South African Coloured population in the Western Cape. Hum. Genet. 128, 145-153 (2010).
7. Smith, M. W. & O'Brien, S. J. Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nature Rev. Genet. 6, 623-632 (2005). (Pubitemid 41044299)
8. Florez, J. C. et al. Strong association of socioeconomic status with genetic ancestry in Latinos: implications for admixture studies of type 2 diabetes. Diabetologia 52, 1528-1536 (2009).
9. Yang, J. J. et al. Ancestry and pharmacogenomics of relapse in acute lymphoblastic leukemia. Nature Genet. 43, 237-241 (2011).
10. Grossman, S. R. et al. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327, 883-886 (2010).
11. Price, A. L., Zaitlen, N. A., Reich, D. & Patterson, N. New approaches to population stratification in genome-wide association studies. Nature Rev. Genet. 11, 459-463 (2010).
12. Seldin, M. F. Admixture mapping as a tool in gene discovery. Curr. Opin. Genet. Dev. 17, 177-181 (2007). (Pubitemid 46850797)
13. Rosenberg, N. A. et al. Genome-wide association studies in diverse populations. Nature Rev. Genet. 11, 356-366 (2010).
14. Price, A. L. et al. A genomewide admixture map for Latino populations. Am. J. Hum. Genet. 80, 1024-1036 (2007). (Pubitemid 47579340)
15. Tian, C. et al. A genomewide single-nucleotide-polymorphism panel for Mexican American admixture mapping. Am. J. Hum. Genet. 80, 1014-1023 (2007). (Pubitemid 47579339)
16. Tang, H. et al. Recent genetic selection in the ancestral admixture of Puerto Ricans. Am. J. Hum. Genet. 81, 626-633 (2007). (Pubitemid 47330221)
17. Price, A. L. et al. Long-range LD can confound genome scans in admixed populations. Am. J. Hum. Genet. 83, 132-135; author reply 135-139 (2008). (Pubitemid 351905729)
18. Zhu, X. et al. Admixture mapping for hypertension loci with genome-scan markers. Nature Genet. 37, 177-181 (2005).
19. Freedman, M. L. et al. Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc. Natl Acad. Sci. USA 103, 14068-14073 (2006). (Pubitemid 44452981)
20. Kao, W. H. et al. MYH9 is associated with nondiabetic end-stage renal disease in African Americans. Nature Genet. 40, 1185-1192 (2008).
21. Nalls, M. A. et al. Admixture mapping of white cell count: genetic locus responsible for lower white blood cell count in the Health ABC and Jackson Heart studies. Am. J. Hum. Genet. 82, 81-87 (2008). (Pubitemid 351726080)
22. Reich, D. et al. Reduced neutrophil count in people of African descent is due to a regulatory variant in the Duffy antigen receptor for chemokines gene. PLoS Genet. 5, e1000360 (2009).
23. Tandon, A., Patterson, N. & Reich, D. Ancestry informative marker panels for African Americans based on subsets of commercially available SNP arrays. Genet. Epidemiol. 35, 80-83 (2011).
24. Sankararaman, S., Sridhar, S., Kimmel, G. & Halperin, E. Estimating local ancestry in admixed populations. Am. J. Hum. Genet. 82, 290-303 (2008). (Pubitemid 351726099)
25. Pasaniuc, B., Sankararaman, S., Kimmel, G. & Halperin, E. Inference of locus-specific ancestry in closely related populations. Bioinformatics 25, i213-i221 (2009).
26. Pugach, I., Matveyev, R., Wollstein, A., Kayser, M. & Stoneking, M. Dating the age of admixture via wavelet transform analysis of genome-wide data. Genome Biol. 12, R19 (2011).
27. Tang, H., Coram, M., Wang, P., Zhu, X. & Risch, N. Reconstructing genetic ancestry blocks in admixed individuals. Am. J. Hum. Genet. 79, 1-12 (2006). (Pubitemid 43927371)
28. Sundquist, A., Fratkin, E., Do, C. B. & Batzoglou, S. Effect of genetic divergence in identifying ancestral origin using HAPAA. Genome Res. 18, 676-682 (2008). (Pubitemid 351482793)
29. Price, A. L. et al. Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5, e1000519 (2009).
30. Li, N. & Stephens, M. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233 (2003). (Pubitemid 38040302)
31. Pasaniuc, B., Kennedy, J. & Mandoiu, I. Imputation-based local ancestry inference in admixed populations. Lect. Notes Comp. Sci. 5542, 221-233 (2009).
32. Pasaniuc, B. et al. Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium. PLoS Genet. 7, e1001371 (2011).
33. Adler, S. et al. Mexican-American admixture mapping analyses for diabetic nephropathy in type 2 diabetes mellitus. Semin. Nephrol. 30, 141-149 (2010).
34. Hancock, D. B. et al. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children. PLoS Genet. 5, e1000623 (2009).
35. Adeyemo, A. et al. A genome-wide association study of hypertension and blood pressure in African Americans. PLoS Genet. 5, e1000564 (2009).
36. Lettre, G. et al. Genome-wide association study of coronary heart disease and its risk factors in 8090 African Americans: the NHLBI CARe Project. PLoS Genet. 7, e1001300 (2011).
37. Tang, H., Siegmund, D. O., Johnson, N. A., Romieu, I. & London, S. J. Joint testing of genotype and ancestry association in admixed families. Genet. Epidemiol. 34, 783-791 (2010).
38. Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nature Rev. Genet. 11, 499-511 (2010).
39. Zaitlen, N., Pasaniuc, B., Gur, T., Ziv, E. & Halperin, E. Leveraging genetic variability across populations for the identification of causal variants. Am. J. Hum. Genet. 86, 23-33 (2010).
40. Udler, M. S. et al. FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation. Hum. Mol. Genet. 18, 1692-1703 (2009).
41. Teslovich, T. M. et al. Biological, clinical and population relevance of 95 loci for blood lipids. Nature 466, 707-713 (2010).
42. Waters, K. M. et al. Consistent association of type 2 diabetes risk variants found in europeans in diverse racial and ethnic groups. PLoS Genet. 6, e1001078 (2010).
43. Wang, X. et al. Adjustment for local ancestry in genetic association analysis of admixed populations. Bioinformatics 27, 670-677 (2011).
44. Shao, H. et al. Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis. Proc. Natl Acad. Sci. USA 105, 19910-19914 (2008).