Practical population group assignment with selected informative markers: Characteristics and properties of Bayesian clustering via STRUCTURE

Genetic Epidemiology

Volumn 28, Issue 4, 2005, Pages 302-312

  Yang, Bao Zhu ^a,b   Zhao, Hongyu ^a   Kranzier, Henry R ^c   Gelernter, Joel ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b VA CONNECTICUT HEALTHCARE SYSTEM   (United States)

^c UNIVERSITY OF CONNECTICUT SCHOOL OF MEDICINE   (United States)

Author keywords

African American; Case control; European American; Population stratification; Short tandem repeats; STRUCTURE

Indexed keywords

ACCURACY; AFRICAN AMERICAN; ARTICLE; BAYES THEOREM; EUROPEAN AMERICAN; GENE CLUSTER; GENETIC MARKER; GENOTYPE; HUMAN; POPULATION GENETIC STRUCTURE; SHORT TANDEM REPEAT; UNITED STATES;

AFRICAN AMERICANS; ALGORITHMS; BAYES THEOREM; CLUSTER ANALYSIS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPE; HUMANS; MODELS, GENETIC; SAMPLE SIZE;

EID: 17644416423     PISSN: 07410395     EISSN: None     Source Type: Journal    
DOI: 10.1002/gepi.20070     Document Type: Article

References (37)

1. ABI, Applied Biosystems. 2001. AmpFLSTR® Identifier™ PCR Amplification Kit: User's Manual., User manual number 4323291B. Foster City, CA: Applied Biosystems.
2. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB. 2003. Human population genetic structure and inference of group membership. Am J Hum Genet 72:578-589.
3. Cardon LR, Palmer LJ. 2003. Population stratification and spurious allelic association. Lancet 361:598-604.
4. Chen HS, Zhu X, Zhao H, Zhang S. 2003. Qualitative semi-parametric test to detect genetic association in case-control design under structured population. Ann Hum Genet 67:250-264.
5. Corander J, Waldmann P, Sillanpaa MJ. 2003. Bayesian analysis of genetic differentiation between populations. Genetics 163:367-374.
6. Corander J, Waldmann P, Marttinen P, Sillanpaa MJ. 2004. BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20:2363-2369.
7. Covault J, Gelernter J, Hesselbrock V, Nellissery M, Kranzler HR. 2004. Allelic and haplotypic association of GABRA2 with alcohol dependence. Am J Med Genet 129B:104-109.
8. Dawson KJ, Belkhir K. 2001. A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res 78:59-77.
9. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55:997-1004.
10. 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.
11. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, Gabriel SB, Topol EJ, Smoller JW, Pato CN, Pato MT, Petryshen TL, Kolonel LN, Lander ES, Sklar P, Henderson B, Hirschhorn JN, Altshuler D. 2004. Assessing the impact of population stratification on genetic association studies. Nat Genet. 36:388-393.
12. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM. 2003. Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72:1492-1504.
13. 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.
14. Lappalainen J, Kranzler HR, Malison R, Price LH, Van Dyck C, Rosenheck RA, Cramer J, Southwick S, Charney D, Krystal J, and Gelernter J. 2002. A functional neuropeptide Y Leu7Pro polymorphism is associated with alcohol dependence in a large population sample from the US. Arch Gen Psychiatry 59:825-831.
15. Lautenberger JA, Stephens JC, O'Brien SJ, Smith MW. 2000. Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet 66:969-978.
16. Luo X, Klempan TA, Lappalainen J, Rosenheck RA, Charney DS, Erdos J, van Kammen DP, Kranzler HR, Kennedy JL, Gelernter J. 2004. NOTCH4 gene haplotype is associated with schizophrenia in African-Americans. Biol Psychiatry 55:112-117.
17. Pfaff C, Kittles R, Shriver MD. 2002. Adjusting for population structure in admixed populations. Genet Epidemiol 22:196-198.
18. Pritchard JK, Stephens M, Donnelly P. 2000a. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
19. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000b. Association mapping in structured populations. Am J Hum Genet 67:170-181.
20. Reich DE, Goldstein DB. 2001. Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 20:4-16.
21. Ripatti S, Pitkaniemi J, Sillanpaa MJ. 2001. Joint modeling of genetic association and population stratification using latent class models. Genet Epidemiol 21(Suppl 1):S409-414.
22. Risch NJ. 2000. Searching for genetic determinants in the new millennium. Nature 405:847-856.
23. Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST, Stoneking M, Batzer MA, Barbujani G. 2002. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 12:602-612.
24. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MA, Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmers K, Weigend S. 2001. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159:699-713.
25. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW. 2002. Genetic structure of human populations. Science 298:2381-2385.
26. Rosenberg NA, Li LM, Ward R, Pritchard JK. 2003. Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73:1402-1422.
27. Satten GA, Flanders WD, Yang Q. 2001. Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 68:466-477.
28. Sillanpaa MJ, Kilpikari R, Ripatti S, Onkamo P, Uimari P. 2001. Bayesian association mapping for quantitative traits in a mixture of two populations. Genet Epidemiol. 21(Suppl 1):S692-699.
29. Small KM, Wagoner LE, Levin AM, Kardia SL, Liggett SB. 2002. Synergistic polymorphisms of betal- and alpha2C-adrenergic receptors and the risk of congestive heart failure. N Engl J Med 347:1135-1142.
30. Smith MW, Lautenberger JA, Shin HD, Chretien JP, Shrestha S, Gilbert DA, O'Brien SJ. 2001. Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations. Am J Hum Genet 69:1080-1094.
31. Thomas DC, Witte JS. 2002. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 11:505-512.
32. Turakulov R, Easteal S. 2003. Number of SNPS loci needed to detect population structure. Human Hered 55:37-45.
33. Wacholder S, Rothman N, Caporaso N. 2002. Counterpoint: bias from population stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and cancer. Cancer Epidemiol Biomark Prev 11:513-520.
34. Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AE, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB. 2003. Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res 13:1607-1618.
35. Wilson JF, Weale ME, Smith AC, Gratrix F, Fletcher B, Thomas MG, Bradman N, Goldstein DB. 2001. Population genetic structure of variable drug response. Nature Genet 29:265-269.
36. Zhang S, Zhao H. 2001. Quantitative similarity-based association test using population samples. Am J Hum Genet 69:601-614.
37. Zhang S, Zhu X, Zhao H. 2003. On a semi-parametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 24:44-56.