SNPselector:: a web tool for selecting SNPs for genetic association studies

被引：88

作者：

Xu, H ^{[1
]}

Gregory, SG ^{[1
]}

Hauser, ER ^{[1
]}

Stenger, JE ^{[1
]}

Pericak-Vance, MA ^{[1
]}

Vance, JM ^{[1
]}

Züchner, S ^{[1
]}

Hauser, MA ^{[1
]}

机构：

[1] Duke Univ, Med Ctr, Duke Ctr Human Genet, Durham, NC 27710 USA

来源：

BIOINFORMATICS | 2005年 / 21卷 / 22期

关键词：

D O I：

10.1093/bioinformatics/bti682

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Single nucleotide polymorphisms (SNPs) are commonly used for association studies to find genes responsible for complex genetic diseases. With the recent advance of SNP technology, researchers are able to assay thousands of SNPs in a single experiment. But the process of manually choosing thousands of genotyping SNPs for tens or hundreds of genes is time consuming. We have developed a web-based program, SNPselector, to automate the process. SNPselector takes a list of gene names or a list of genomic regions as input and searches the Ensembl genes or genomic regions for available SNPs. It prioritizes these SNPs on their tagging for linkage disequilibrium, SNP allele frequencies and source, function, regulatory potential and repeat status. SNPselector outputs result in compressed Excel spreadsheet files for review by the user.

引用

页码：4181 / 4186

页数：6

共 17 条

[1] An overview of ensembl [J].

Birney, E ;

Andrews, TD ;

Bevan, P ;

Caccamo, M ;

Chen, Y ;

Clarke, L ;

Coates, G ;

Cuff, J ;

Curwen, V ;

Cutts, T ;

Down, T ;

Eyras, E ;

Fernandez-Suarez, XM ;

Gane, P ;

Gibbins, B ;

Gilbert, J ;

Hammond, M ;

Hotz, HR ;

Iyer, V ;

Jekosch, K ;

Kahari, A ;

Kasprzyk, A ;

Keefe, D ;

Keenan, S ;

Lehvaslaiho, H ;

McVicker, G ;

Melsopp, C ;

Meidl, P ;

Mongin, E ;

Pettett, R ;

Potter, S ;

Proctor, G ;

Rae, M ;

Searle, S ;

Slater, G ;

Smedley, D ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Storey, R ;

Ureta-Vidal, A ;

Woodwark, KC ;

Cameron, G ;

Durbin, R ;

Cox, A ;

Hubbard, T ;

Clamp, M .

GENOME RESEARCH, 2004, 14 (05) :925-928

[2] Aligning multiple genomic sequences with the threaded blockset aligner [J].

Blanchette, M ;

Kent, WJ ;

Riemer, C ;

Elnitski, L ;

Smit, AFA ;

Roskin, KM ;

Baertsch, R ;

Rosenbloom, K ;

Clawson, H ;

Green, ED ;

Haussler, D ;

Miller, W .

GENOME RESEARCH, 2004, 14 (04) :708-715

[3] Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium [J].

Carlson, CS ;

Eberle, MA ;

Rieder, MJ ;

Yi, Q ;

Kruglyak, L ;

Nickerson, DA .

AMERICAN JOURNAL OF HUMAN GENETICS, 2004, 74 (01) :106-120

[4] Association of a single nucleotide polymorphism in the TIGR/MYOCILIN gene promoter with the severity of primary open-angle glaucoma [J].

Colomb, E ;

Nguyen, TD ;

Béchetoille, A ;

Dascotte, JC ;

Valtot, F ;

Brézin, AP ;

Berkani, M ;

Copin, B ;

Gomez, L ;

Polansky, JR ;

Garchon, HJ .

CLINICAL GENETICS, 2001, 60 (03) :220-225

[5] PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level [J].

Conde, L ;

Vaquerizas, JM ;

Santoyo, J ;

Al-Shahrour, F ;

Ruiz-Llorente, S ;

Robledo, M ;

Dopazo, J .

NUCLEIC ACIDS RESEARCH, 2004, 32 :W242-W248

[6] Pharmacogenetics goes genomic [J].

Goldstein, DB ;

Tate, SK ;

Sisodiya, SM .

NATURE REVIEWS GENETICS, 2003, 4 (12) :937-947

[7] Hierarchical patterns of global human Y-chromosome diversity [J].

Hammer, MF ;

Karafet, TM ;

Redd, AJ ;

Jarjanazi, H ;

Santachiara-Benerecetti, S ;

Soodyall, H ;

Zegura, SL .

MOLECULAR BIOLOGY AND EVOLUTION, 2001, 18 (07) :1189-1203

[8] Whole-genome patterns of common DNA variation in three human populations [J].

Hinds, DA ;

Stuve, LL ;

Nilsen, GB ;

Halperin, E ;

Eskin, E ;

Ballinger, DG ;

Frazer, KA ;

Cox, DR .

SCIENCE, 2005, 307 (5712) :1072-1079

[9] LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources [J].

Karchin, R ;

Diekhans, M ;

Kelly, L ;

Thomas, DJ ;

Pieper, U ;

Eswar, N ;

Haussler, D ;

Sali, A .

BIOINFORMATICS, 2005, 21 (12) :2814-2820

[10] The UCSC Genome Browser Database [J].

Karolchik, D ;

Baertsch, R ;

Diekhans, M ;

Furey, TS ;

Hinrichs, A ;

Lu, YT ;

Roskin, KM ;

Schwartz, M ;

Sugnet, CW ;

Thomas, DJ ;

Weber, RJ ;

Haussler, D ;

Kent, WJ .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :51-54

← 1 2 →