European American stratification in ovarian cancer case control data: The utility of genome-wide data for inferring ancestry

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Raska, Paola ^a   Iversen, Edwin ^b   Chen, Ann ^c   Chen, Zhihua ^c   Fridley, Brooke L ^d   Permuth Wey, Jennifer ^c   Tsai, Ya Yu ^c   Vierkant, Robert A ^d   Goode, Ellen L ^d   Risch, Harvey ^e   Schildkraut, Joellen M ^f   Sellers, Thomas A ^c   Barnholtz Sloan, Jill ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Duke University   (United States)

^c H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

^d Mayo Clinic   (United States)

^e YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE CONTROL STUDY; CHROMOSOME 6; CONTROLLED STUDY; ETHNICITY; EUROPEAN AMERICAN; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; NORTH AMERICA; ONCOGENE; OVARY CANCER; PLESIOMORPHY; POPULATION STRUCTURE; PRINCIPAL COMPONENT ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; CAUCASIAN; CHROMOSOME 2; CLINICAL TRIAL; GENE LOCUS; GENETICS; MULTICENTER STUDY; NEOPLASM; OVARY TUMOR;

CASE-CONTROL STUDIES; CHROMOSOMES, HUMAN, PAIR 2; CHROMOSOMES, HUMAN, PAIR 6; EUROPEAN CONTINENTAL ANCESTRY GROUP; FEMALE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEOPLASMS, GLANDULAR AND EPITHELIAL; NORTH AMERICA; OVARIAN NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84860733538     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035235     Document Type: Article

References (29)

1. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, et al. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316: 1341-1345.
2. Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PIW, et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331-1336.
3. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, et al. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445: 881-885.
4. Burton PR, Clayton DG, Cardon LR, Craddock N, Deloukas P, et al. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
5. Marchini J, Cardon LR, Phillips MS, Donnelly P, (2004) The effects of human population structure on large genetic association studies. Nature Genetics 36: 512-517.
6. Ziv E, Burchard EG, (2003) Human population structure and genetic association studies. Pharmacogenomics 4: 431-441.
7. Bacanu SA, Devlin B, Roeder K, (2002) Association studies for quantitative traits in structured populations. Genetic Epidemiology 22: 78-93.
8. Zhu XF, Li SC, Cooper RS, Elston RC, (2008) A unified association analysis approach for family and unrelated samples correcting for stratification. American Journal of Human Genetics 82: 352-365.
9. Tiwari HK, Barnholtz-Sloan J, Wineinger N, Padilla MA, Vaughan LK, et al. (2008) Review and evaluation of methods correcting for population stratification with a focus on underlying statistical principles. Human Heredity 66: 67-86.
10. Barnholtz-Sloan JS, McEvoy B, Shriver MD, Rebbeck TR, (2008) Ancestry estimation and correction for population stratification in molecular epidemiologic association studies. Cancer Epidemiology Biomarkers & Prevention 17: 471-477.
11. Zhu XF, Zhang SL, Zhao HY, Cooper RS, (2002) Association mapping, using a mixture model for complex traits. Genetic Epidemiology 23: 181-196.
12. Seldin MF, Price AL, (2008) Application of ancestry informative markers to association studies in European Americans. Plos Genetics 4: 3.
13. 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: 1339-1351.
14. Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, et al. (2007) Measuring European population stratification with microarray genotype data. American Journal of Human Genetics 80: 948-956.
15. Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, et al. (2008) Analysis and application of European genetic substructure using 300 KSNP information. Plos Genetics 4: 11.
16. Price AL, Butler J, Patterson N, Capelli C, Pascali VL, et al. (2008) Discerning the ancestry of European Americans in genetic association studies. Plos Genetics 4: 9.
17. Paschou P, Drineas P, Lewis J, Nievergelt CM, Nickerson DA, et al. (2008) Tracing Sub-Structure in the European American Population with PCA-Informative Markers. Plos Genetics 4: 13.
18. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nature Genetics 38: 904-909.
19. Permuth-Wey J, Chen YA, Tsai Y-Y, Chen Z, Qu X, et al. (2011) Inherited Variants in Mitochondrial Biogenesis Genes May Influence Epithelial Ovarian Cancer Risk. Cancer Epidemiology Biomarkers & Prevention.
20. Clayton D"PrincipalComponentAnalysiswithsnpMatrix"Bioconductor, (2010) 17 Available: http://bioconductor.org/packages/2.6/bioc/vignettes/snpMatrix/inst/doc/pca-vignette.pdf. Accessed 2011 June.
21. Campbell CD, Ogburn EL, Lunetta KL, Lyon HN, Freedman ML, et al. (2005) Demonstrating stratification in a European American population. Nature Genetics 37: 868-872.
22. de Bakker PIW, McVean G, Sabeti PC, Miretti MM, Green T, et al. (2006) A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nature Genetics 38: 1166-1172.
23. Fellay J, Shianna KV, Ge DL, Colombo S, Ledergerber B, et al. (2007) A whole-genome association study of major determinants for host control of HIV-1. Science 317: 944-947.
24. Broman KW, Matsumoto N, Giglio S, Martin CL, Roseberry JA, et al. (2003) Common long human inversion polymorphism on chromosome 8p. Statistics and Science a Festschrift for Terry Speed. Hayward: Inst Mathematical Statistics pp. 237-245.
25. Zou F, Lee S, Knowles MR, Wright FA, (2010) Quantification of Population Structure Using Correlated SNPs by Shrinkage Principal Components. Human Heredity 70: 9-22.
26. Drineas P, Lewis J, Paschou P, (2010) Inferring Geographic Coordinates of Origin for Europeans Using Small Panels of Ancestry Informative Markers. PLoS ONE 5: e11892.
27. Diner H Learn NC"ImmigrationinUShistory"LEARNNorthCarolina, (2003) 17 Available: http://www.learnnc.org/lp/editions/nchist-newsouth/5690. Accessed 2011 June.
28. "When were the major waves of immigration to the United States?" History AnswersVisibleInkPress, (2005) Answers.com. 17 Available: http://www.answers.com/topic/when-were-the-major-waves-of-immigration-to-the-united-states. Accessed 2011 June.
29. "History of Immigration"TorontoHistoryGeography2UI3Section4, (2010) 17 Available: http://libwiki.mcmaster.ca/geo2ui3-section4/index.php/Toronto/History. Accessed 2011 June.