Genome-wide association of breast cancer: Composite likelihood with imputed genotypes

European Journal of Human Genetics

Volumn 19, Issue 2, 2011, Pages 194-199

  Politopoulos, Ioannis ^a   Gibson, Jane ^a   Tapper, William ^a   Ennis, Sarah ^a   Eccles, Diana ^a   Collins, Andrew ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

association mapping; breast cancer; composite likelihood; FGFR2 gene; imputed genotypes

Indexed keywords

FIBROBLAST GROWTH FACTOR RECEPTOR 2; NEUROTENSIN RECEPTOR; NEUROTENSIN RECEPTOR 1; UNCLASSIFIED DRUG;

ARTICLE; BREAST CANCER; CASE CONTROL STUDY; CONTROLLED STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENE MUTATION; GENETIC ASSOCIATION; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MAXIMUM LIKELIHOOD METHOD; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

BREAST NEOPLASMS; CASE-CONTROL STUDIES; CHROMOSOME MAPPING; CONFIDENCE INTERVALS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; RECEPTOR, FIBROBLAST GROWTH FACTOR, TYPE 2; SOFTWARE;

EID: 78651395972     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.157     Document Type: Article

References (19)

1. Easton DF, Pooley KA, Dunning AM et al: Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007; 447: 1087-1093.
2. Hunter DJ, Kraft P, Jacobs KB et al: A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 2007; 39: 870-874.
3. Wellcome Trust Case Control Consortium (WTCCC): Genome-wide association study of .14000. cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661-678.
4. Zeggini E, Scott LJ, Saxena R et al: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 2008; 40: 638-645.
5. Gibson J, Tapper W, Cox D et al: A multimetric approach to analysis of genome-wide association by single markers and composite likelihood. Proc Natl Acad Sci USA 2008; 105: 2592-2597.
6. Morton N, Maniatis N, Zhang W, Ennis S, Collins A: Genome scanning by composite likelihood. Am J Hum Genet 2007; 80: 19-28.
7. Maniatis N, Collins A, Xu C-F et al: The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci USA 2002; 99: 2228-2233.
8. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575.
9. Collins A, Lau W: CHROMSCAN: genome-wide association using a linkage disequilibrium map. J Hum Genet 2008; 53: 121-126.
10. Maniatis N, Collins A, Gibson J, Zhang W, Tapper W, Morton NE: Positional cloning by linkage disequilibrium. Am J Hum Genet 2004; 74: 846-855.
11. Collins A, Lau W, De La Vega FM: Mapping genes for common diseases: the case for genetic (LD) maps. Hum Hered 2004; 58: 2-9.
12. Lau W, Kuo T-Y, Tapper W, Cox S, Collins A: Exploiting large scale computing to construct high resolution linkage disequilibrium maps of the human genome. Bioinformatics 2007; 23: 517-519.
13. Dupouy S, Viardot-Foucault V, Alifano M et al: The neurotensin receptor-1 pathway contributes to human ductal breast cancer progression. PLoS ONE 2009; 4: e4223.
14. Tapper W, Hammond V, Gerty S et al: The influence of genetic variation in 30 selected genes on the clinical characteristics of early onset breast cancer. Breast Cancer Res 2008; 10: R108.
15. Huang BE, Amos CI, Lin DY: Detecting haplotype effects in genomewide association studies. Genet Epidemiol 2007; 31: 803-812.
16. Hao K, Chudin E, McElwee J, Schadt E: Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet 2009; 10: 27.
17. Huang L, Wang C, Rosenberg NA: The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am J Hum Genet 2009; 85: 692-698.
18. Tapper W, Collins A, Morton N: Mapping a gene for rheumatoid arthritis on chromosome 18q21. BMC Proc 2007; 1: S18.
19. Boyarskikh UA, Zarubina NA, Biltueva JA et al: Association of FGFR2 gene polymorphisms with the risk of breast cancer in population of West Siberia. Eur J Hum Genet 2009; 17: 1688-1691.