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. 2008 Jul 17:9:311.
doi: 10.1186/1471-2105-9-311.

Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge

Don L Armstrong  1 , Chaim O Jacob, Raphael Zidovetzki
Affiliations

Function2Gene: a gene selection tool to increase the power of genetic association studies by utilizing public databases and expert knowledge

Don L Armstrong et al. BMC Bioinformatics. .

Abstract

Background: Many common disorders have multiple genetic components which convey increased susceptibility. SNPs have been used to identify genetic components which are associated with a disease. Unfortunately, many studies using these methods suffer from low reproducibility due to lack of power.

Results: We present a set of programs which implement a novel method for searching for disease-associated genes using prior information to select and order genes from publicly available databases by their prior likelihood of association with the disease. These programs were used in a published study of childhood-onset SLE which yielded novel associations with modest sample size.

Conclusion: Using prior information to decrease the size of the problem space to an amount commensurate with available samples and resources while maintaining appropriate power enables researchers to increase their likelihood of discovering reproducible associations.

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Figures

Figure 1
Figure 1
Schematic of the gene selection process. Flow chart of the separate methodology and the scripts which enact the methodology, as described in the introduction and implementation sections.
See this image and copyright information in PMC

References

    1. MacDonald ME, Ambrose CM, Duyao MP, Myers RH, Lin C, Srinidhi L, Barnes G, Taylor SA, James M, Groot N, MacFarlane H, Jenkins B, Anderson MA, Wexler NS, Gusella JF, Bates GP, Baxendale S, Hummerich H, Kirby S, North M, Youngman S, Mott R, Zehetner G, Sedlacek Z, Poustka A, Frischauf AM, Lehrach H, Buckler AJ, Church D, Doucette-Stamm L, O'Donovan MC, Riba-Ramirez L, Shah M, Stanton VP, Strobel SA, Draths KM, Wales JL, Dervan P, Housman DE, Altherr M, Shiang R, Thompson L, Fielder T, Wasmuth JJ, Tagle D, Valdes J, Elmer L, Allard M, Castilla L, Swaroop M, Blanchard K, Collins FS, Snell R, Holloway T, Gillespie K, Datson N, Shaw D, Harper PS. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell. 1993;72:971–83. doi: 10.1016/0092-8674(93)90585-E. - DOI - PubMed
    1. Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, Huey B, King MC. Linkage of early-onset familial breast cancer to chromosome 17q21. Science. 1990;250:1684–9. doi: 10.1126/science.2270482. - DOI - PubMed
    1. Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science. 1996;273:1516–7. doi: 10.1126/science.273.5281.1516. - DOI - PubMed
    1. Colhoun HM, McKeigue PM, Smith GD. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–72. doi: 10.1016/S0140-6736(03)12715-8. - DOI - PubMed
    1. Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet. 2001;29:306–9. doi: 10.1038/ng749. - DOI - PubMed

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