Analysis and application of European genetic substructure using 300 K SNP information

PLoS Genetics

Volumn 4, Issue 1, 2008, Pages 0029-0039

  Tian, Chao ^a   Plenge, Robert M ^b,c   Ransom, Michael ^a   Lee, Annette ^d   Villoslada, Pablo ^e   Selmi, Carlo ^a,f   Klareskog, Lars ^g   Pulver, Ann E ^h   Qi, Lihong ^a,i   Gregersen, Peter K ^d   Seldin, Michael F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c BRIGHAM AND WOMEN S HOSPITAL   (United States)

^d FEINSTEIN INSTITUTE FOR MEDICAL RESEARCH   (United States)

^e UNIVERSITY OF NAVARRA   (Spain)

^f UNIVERSITY OF MILAN   (Italy)

^g KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

^h JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EUROPE; FALSE POSITIVE RESULT; GENE REPLICATION; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; GENOTYPE; GREECE; HUMAN; ITALY; JEW; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; RHEUMATOID ARTHRITIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPAIN; ALGORITHM; BAYES THEOREM; CASE CONTROL STUDY; CAUCASIAN; CLUSTER ANALYSIS; ETHNOLOGY; GENETICS; GEOGRAPHY; IRELAND; NEOPLASM; UNITED STATES;

DNA;

ALGORITHMS; ARTHRITIS, RHEUMATOID; BAYES THEOREM; CASE-CONTROL STUDIES; CLUSTER ANALYSIS; DNA; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC MARKERS; GENETICS, POPULATION; GEOGRAPHY; HUMANS; IRELAND; JEWS; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; UNITED STATES; VARIATION (GENETICS);

EID: 38949212271     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0040004     Document Type: Article

References (43)

1. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512-517.
2. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36: 388-393.
3. Campbell CD, Ogburn EL, Lunetta KL, Lyon HN, Freedman ML, et al. (2005) Demonstrating stratification in a European American population. Nat Genet 37: 868-872.
4. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, et al. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37: 1243-1246.
5. Helgason A, Yngvadottir B, Hrafnkelsson B, Gulcher J, Stefansson K (2005) An Icelandic example of the impact of population structure on association studies. Nat Genet 37: 90-95.
6. Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, et al. (2006) European population substructure: clustering of northern and southern populations. PLoS Genetics 2: e143. doi: 10.1371/journal.pgen.0020143
7. Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, et al. (2007) Measuring European population stratification with microarray genotype data. Am J Hum Genet 80: 948-956.
8. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67: 170-181.
9. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, et al. (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72: 1492-1504.
10. 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.
11. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38: 904-909.
12. Epstein MP, Allen AS, Satten GA (2007) A simple and improved correction for population stratification in case-control studies. Am J Hum Genet 80: 921-930.
13. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
14. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55: 997-1004.
15. Menozzi P, Piazza A, Cavalli-Sforza L (1978) Synthetic maps of human gene frequencies in Europeans. Science 201: 786-792.
16. Sokal RR, Oden NL, Wilson C (1991) Genetic evidence for the spread of agriculture in Europe by demic diffusion. Nature 351: 143-145.
17. Cavalli-Sforza LL, Menozzi P, Piazza A (1993) Demic expansions and human evolution. Science 259: 639-646.
18. Cavalli-Sforza LL, Menozzi P, Piazza A (1996) The history and geography of human genes. Princeton (New Jersey): Princeton University Press. xiii, 413 p.
19. Barbujani G, Bertorelle G (2001) Genetics and the population history of Europe. Proc Natl Acad Sci U S A 98: 22-25.
20. Belle EM, Landry PA, Barbujani G (2006) Origins and evolution of the Europeans' genome: evidence from multiple microsatellite loci. Proc Biol Sci 273: 1595-1602.
21. 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.
22. Rosenberg NA, Li LM, Ward R, Pritchard JK (2003) Informativeness of genetic markers for inference of ancestry. Am J Hum Genet 73: 1402-1422.
23. Plenge RM, Seielstad M, Padyukov L, Lee AT, Remmers EF, et al. (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis - a genomewide study. N Engl J Med 357: 1199-1209.
24. Giglio S, Broman KW, Matsumoto N, Calvari V, Gimelli G, et al. (2001) Olfactory receptor-gene clusters, genomic-inversion polymorphisms, and common chromosome rearrangements. Am J Hum Genet 68: 874-883.
25. Herva R, de la Chapelle A (1976) A large pericentric inversion of human chromosome 8. Am J Hum Genet 28: 208-212.
26. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
27. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129-137.
28. Macalister RAS (1935) Ancient Ireland. London: Benjamin Blom, Inc.
29. Snyder HL (1976) From the beginnings to the end of the middle ages.Orel H, editor. Irish history and culture. Lawrence (Kansas): The University Press of Kansas. pp. 25-41.
30. Klein U, Casola S, Cattoretti G, Shen Q, Lia M, et al. (2006) Transcription factor IRF4 controls plasma cell differentiation and class-switch recombination. Nat Immunol 7: 773-782.
31. Ma S, Turetsky A, Trinh L, Lu R (2006) IFN regulatory factor 4 and 8 promote Ig light chain kappa locus activation in pre-B cell development. J Immunol 177: 7898-7904.
32. Lohoff M, Mittrucker HW, Brustle A, Sommer F, Casper B, et al. (2004) Enhanced TCR-induced apoptosis in interferon regulatory factor 4-deficient CD4(+) Th cells. J Exp Med 200: 247-253.
33. Tailor P, Tamura T, Ozato K (2006) IRF family proteins and type I interferon induction in dendritic cells. Cell Res 16: 134-140.
34. Mitchell MK, Gregersen PK, Johnson S, Parsons R, Vlahov D (2004) The New York Cancer project: rationale, organization, design, and baseline characteristics. J Urban Health 81: 301-310.
35. Amos CI, Chen WV, Lee A, Li W, Kern M, et al. (2006) High-density SNP analysis of 642 Caucasian families with rheumatoid arthritis identifies two new linkage regions on 11p12 and 2q33. Genes Immun 7: 277-286.
36. Wolfe F, Michaud K, Gefeller O, Choi HK (2003) Predicting mortality in patients with rheumatoid arthritis. Arthritis Rheum 48: 1530-1542.
37. Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314: 1461-1463.
38. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (2001) GENETIX, software under WindowsTM for the genetic of populations. 4.02 ed. Montpellier, France: Laboratory Genome, Populations, Interactions CNRS UMR 5000, University of Montpellier II.
39. Weir B, Cockerham C (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
40. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
41. Spearman C (1910) Correlation calculated with faulty data. Br J Psychol 3: 271-295.
42. Royston P (1995) A remark on Algorithm AS 181: The W Test for normality. Appl Stat 44: 547-551.
43. Patterson N, Price AL, Reich D (2006) Population structure and Eigenanalysis. PLoS Genet 2: e190. doi: 10.1371/journal.pgen.0020190