Marker selection for genetic case-control association studies

Nature Protocols

Volumn 4, Issue 5, 2009, Pages 743-752

  Pettersson, Fredrik H ^a   Anderson, Carl A ^a   Clarke, Geraldine M ^a   Barrett, Jeffrey C ^a   Cardon, Lon R ^a   Morris, Andrew P ^a   Zondervan, Krina T ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CASE CONTROL STUDY; COMPUTER PROGRAM; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC MARKER; GENOMICS; GENOTYPE; HUMAN; HUMAN GENOME; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; GENETIC MARKERS; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 67649397907     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.38     Document Type: Article

References (23)

1. Lander, E.S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
2. Zondervan, K.T. & Cardon, L.R. Designing candidate gene and genome-wide case- control association studies. Nat. Protoc. 2, 2492-2501 (2007).
3. Kruglyak, L. & Nickerson, D.A. Variation is the spice of life. Nat. Genet. 27, 234-236 (2001).
4. Scherer, S.W. et al. Challenges and standards in integrating surveys of structural variation. Nat. Genet. 39, 7-15 (2007).
5. Sachidanandam, R. etal. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933 (2001).
6. Gabriel, S.B. et al. The structure of haplotype blocks in the human genome. Science 296, 2225-2229 (2002).
7. The International HapMap Consortium. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
8. Johnson, G.C.L. et al. Haplotype tagging forthe identification ofcommon disease genes. Nat. Genet. 29, 233-237 (2001).
9. The International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861 (2007).
10. Hirschhorn, J.N., Lohmueller, K., Byrne, E. & Hirschhorn, K. A comprehensive review of genetic association studies. Genet. Med. 4, 45-61 (2002).
11. Kuhn, R.M. et al. The UCSC Genome Browser Database: Update 2007. Nucleic Acids Res. 35, 668-673 (2007).
12. Evans, D.E., Barrett, J.C. & Cardon, L.R. To what extent do scans of nonsynonymous SNPs complement denser genome-wide association studies? Eur. J. Hum. Genet. 16, 718-23 (2008).
13. Perkel, J. SNP genotyping: six technologies that keyed a revolution. Nat. Methods 5, 447-453 (2008).
14. Syvanen, A.C. Toward genome-wide SNP genotyping. Nat. Genet. 37, 5-10 (2005).
15. Kingsmore, S.F., Lindquist, I.E., Mudge, J., Gessler, D.D. & Beavis, W.D. Genomewide association studies: progress and potential for drug discovery and development. Nat. Rev. Drug Discov. 7, 221-30 (2008).
16. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661-678 (2007).
17. Barrett, J.C. & Cardon, L.R. Evaluating coverage of genome-wide association studies. Nat. Genet. 38, 659-662 (2006).
18. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 441, 799-816 (2007).
19. Anderson, C.A. et al. Evaluating the effects of imputation on the power, coverage and cost-efficiency of genome-wide SNP platforms. Am. J. Hum. Genet. 83, 112-119 (2008).
20. Marchini, J., Howie, B., Myers, S., McVean, G. & Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007).
21. Altshuler, D. et al. The common PPAR gamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nat. Genet. 26, 76-80 (2000).
22. Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).
23. Pettersson, F., Morris, A.P., Barnes, M.R. & Cardon, L.R. Goldsurfer2 (Gs2): A comprehensive toolforthe analysis and visualization of genome wide association studies. BMC Bioinformatics 9 (2008).