Number of SNPS loci needed to detect population structure

Human Heredity

Volumn 55, Issue 1, 2003, Pages 37-45

  Turakulov, Rust ^a   Easteal, Simon ^a  

^a Biology and Environment   (Australia)

Author keywords

Genetic polymorphisms; Population stratification; Population structure; Population studies; Sample size; SNP

Indexed keywords

ARTICLE; ASIAN; CAUCASIAN; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; GEOGRAPHY; HUMAN; MODEL; NORMAL HUMAN; POLYMORPHIC LOCUS; POPULATION STRUCTURE; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES;

GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; VARIATION (GENETICS);

EID: 0043175282     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000071808     Document Type: Article

References (31)

1. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P: Association mapping in structured populations. Am J Hum Genet 2000;67:170-181.
2. Risch N, Burchard E, Ziv E, Tang H: Categorization of humans in biomedical research: genes, race and disease. Genome Biol 2002;3: comment 2007.
3. Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, Adebamowo CA, Griffin R, Williams T, Ukoli F, Adams-Campbell L, Kwagyan J, Isaacs W, Freeman V, Dunston GM: CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification? Hum Genet 2002;110:553-560.
4. Wacholder S, Rothman N, Caporaso N: Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst 2000;92: 1151-1158.
5. Reich DE, Goldstein DB: Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 2001;20:4-16.
6. Goldstein DB, Chikhi L: Human Migrations and Population Structure: What We Know and Why It Matters. Annu Rev Genomics Hum Genet 2002;4:4.
7. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD: Interrogating a high-density SNP map for signatures of natural selection. Genome Res 2002;12:1805-1814.
8. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR: Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001;294:1719-1723.
9. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002;296:2225-2229.
10. Ardlie KG, Lunetta KL, Seielstad M: Testing for population subdivision and association in four case-control studies. Am J Hum Genet 2002;71:304-311.
11. Thomas DC, Witte JS: Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 2002;11:505-512.
12. Lewontin RC: The Apportionment of Human Diversity. Evolutionary Biol 1972;61:381-398.
13. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL: An apportionment of human DNA diversity. Proc Natl Acad Sci USA 1997;94: 4516-4519.
14. Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST, Stoneking M, Batzer MA, Barbujani G: Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 2002;12:602-612.
15. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW: Genetic structure of human populations. Science 2002;298:2381-2385.
16. Pritchard JK, Donnelly P: Case-Control Studies of Association in Structured or Admixed Populations. Theor Popul Biol 2001;60:227-237.
17. Wilson JF, Weale ME, Smith AC, Gratrix F, Fletcher B, Thomas MG, Bradman N, Goldstein DB: Population genetic structure of variable drug response. Nat Genet 2001;29:265-269.
18. Kaufman L, Rousseeuw PJ: Finding Groups in Data: An Introduction to Cluster Analysis. New York., Wiley, 1990.
19. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000;155:945-959.
20. Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D: A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 2001;409:928-933.
21. Struyf A, Mia H, Rousseeuw PJ: Integrating robust clustering techniques in S-PLUS. Computational Statistics & Data Analysis 1997;26: 17-37.
22. Ripley BD: The R project in statistical computing. MSOR Connections. The newsletter of the LTSN Maths, Stats & OR Network. 2001;1: 23-25.
23. Ward JH: Hierarchical grouping to optimize an object function. J Am Statist Ass 1963;58:236-244.
24. Everitt B: Cluster Analysis. London, Heinemann Educ, 1974.
25. Romesburg C, H.: Cluster analysis for researchers. Belmont, Lifetime Learning Publications, 1984.
26. Felsenstein J: Phylogenies and the Comparative Method. Am Naturalist 1985;125:1-15.
27. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB: Human population genetic structure and inference of group membership. Am J Hum Genet 2003;72:578-589.
28. Wakeley J, Nielsen R, Liu-Cordero SN, Ardlie K: The discovery of single-nucleotide polymorphisms-and inferences about human demographic history. Am J Hum Genet 2001;69: 1332-1347.
29. Cavalli-Sforza LL: Genes, peoples, and languages. Proc Natl Acad Sci USA 1997;94: 7719-7724.
30. Rosenberg NA, Woolf E, Pritchard JK, Schaap T, Gefel D, Shpirer I, Lavi U, Bonne-Tamir B, Hillel J, Feldman MW: Distinctive genetic signatures in the Libyan Jews. Proc Natl Acad Sci USA 2001;98:858-863.
31. Mountain JL, Cavalli-Sforza LL: Multilocus genotypes, a tree of individuals, and human evolutionary history. Am J Hum Genet 1997; 61:705-718.