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Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res 37: W600-W605

Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.
Nucleic Acids Research (Impact Factor: 9.11). 06/2009; 37(Web Server issue):W600-5. DOI: 10.1093/nar/gkp290
Source: PubMed

ABSTRACT We have developed a set of web-based SNP selection tools (freely available at http://www.niehs.nih.gov/snpinfo) where investigators can specify genes or linkage regions and select SNPs based on GWAS results, linkage disequilibrium (LD), and predicted functional characteristics of both coding and non-coding SNPs. The algorithm uses GWAS SNP P-value data and finds all SNPs in high LD with GWAS SNPs, so that selection is from a much larger set of SNPs than the GWAS itself. The program can also identify and choose tag SNPs for SNPs not in high LD with any GWAS SNP. We incorporate functional predictions of protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles of a SNP are likely to have differential effects on function. Users can assign weights for different functional categories of SNPs to further tailor SNP selection. The program accounts for LD structure of different populations so that a GWAS study from one ethnic group can be used to choose SNPs for one or more other ethnic groups. Finally, we provide an example using prostate cancer and demonstrate that this algorithm can select a small panel of SNPs that include many of the recently validated prostate cancer SNPs.

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    • "QIAamp DNA Mini Kit (Qiagen GmbH, Hilden, Germany). Selection of tag SNPs: tag SNPs were selected for TPH2 using National Institute of Environmental Health Sciences (NIEHS) Tag SNP selection tool using r 2 threshold of 0.8 [31] "
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    • "[30], GenomePipe (http:// snpinfo.niehs.nih.gov/snpfunc.htm) [31] FastSNP (http://fastsnp. ibms.sinica.edu.tw/), "
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    • "cs.queensu.ca/F-SNP/) (Lee & Shatkay 2008) and SNPinfo–FuncPred (http://snpinfo.niehs.nih.gov/snpinfo/snpfunc. htm/) (Xu & Taylor 2009 "
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