SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Yoo, Jinho ^a   Lee, Youngbok ^c   Kim, Yujung ^c   Rha, Sun Young ^a   Kim, Yangseok ^b  

^a Yonsei University College of Medicine   (South Korea)

^b Kyung Hee University   (South Korea)

^c ISTECH Inc   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS METHOD; ASSOCIATION ANALYSIS; DATA PREPROCESSING; HARDY-WEINBERG EQUILIBRIUM; LINKAGE DISEQUILIBRIUM; PEARSON'S CORRELATION COEFFICIENTS; VISUAL COMPARISON; WEB INTERFACE;

ALGORITHMS; CORRELATION METHODS; DATA HANDLING; RELIABILITY ANALYSIS;

DATA FLOW ANALYSIS;

ALGORITHM; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; DIPLOIDY; GENE LINKAGE DISEQUILIBRIUM; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; HAPLOTYPE MAP; INTERMETHOD COMPARISON; INTERNET; RELIABILITY; SINGLE NUCLEOTIDE POLYMORPHISM; HAPLOTYPE; HUMAN; STATISTICAL ANALYSIS;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 47249133881     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-290     Document Type: Article

References (20)

1. Sole X Guino E Valls J Iniesta R Moreno V SNPStats: A web tool for the analysis of association studies Bioinformatics 2006, 22:15. 1928 1929 10.1093/bioinformatics/btl268 16720584
2. Yoo J Seo B Kim Y SNPAnalyzer: A web-based integrated workbench for single-nucleotide polymorphism analysis Nucleic Acids Res 2005, 33(Web Server):W483-488. 1160189 15980517 10.1093/nar/gki428
3. Browning BL Browning SR Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering Genet Epidemiol 2007, 31(5):365-375. 10.1002/gepi.20216 17326099
4. Purcell S Neale B Todd-Brown K Thomas L Ferreira MAR Bender D Maller J de Bakker PIW Daly MJ Sham PC PLINK: A toolset for whole-genome association and population-based linkage analyses Am J Hum Genet 2007, 81(3):559-575. 1950838 17701901 10.1086/519795
5. Zhang K Qin Z Chen T Liu JS Waterman MS Sun F HapBlock: Haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms Bioinformatics 2005, 21(1):131-134. 10.1093/ bioinformatics/bth482 15333454
6. Barrett JC Fry B Maller J Daly MJ Haploview: Analysis and visualization of LD and haplotype maps Bioinformatics 2005, 21(2):263-265. 10.1093/ bioinformatics/bth457 15297300
7. SNPAnalyzer 2.0 homepage http://snp.istech21.com/snpanalyzer/2.0/
8. Excoffier L Slatkin M Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population Mol Biol Evol 1995, 12(5):921-927. 7476138
9. Niu T Qin ZS Xu X Liu JS Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms Am J Hum Genet 2002, 70(1):157-169. 448439 11741196 10.1086/338446
10. Devlin B Risch N A comparison of linkage disequilibrium measures for fine-scale mapping Genomics 1995, 29(2):311-322. 10.1006/geno.1995.9003 8666377
11. Gabriel SB Schaffner SF Nguyen H Moore JM Roy J Blumenstiel B Higgins J DeFelice M Lochner A Faggart M Liu-Cordero SN Rotimi C Adeyemo A Cooper R Ward R Lander ES Daly MJ Altshuler D The structure of haplotype blocks in the human genome Science 2002, 296(5576):2225-2229. 10.1126/ science.1069424 12029063
12. Storey JD Tibshirani R Statistical significance for genomewide studies Proc Natl Acad Sci USA 2003, 100(16):9440-9445. 170937 12883005 10.1073/ pnas.1530509100
13. Epstein MP Satten GA Inference on haplotype effects in case-control studies using unphased genotype data Am J Hum Genet 2003, 73(6):1316-1329. 1180397 14631556 10.1086/380204
14. Purcell S Daly MJ Sham PC WHAP: Haplotype-based association analysis Bioinformatics 2007, 23(2):255-256. 10.1093/bioinformatics/btl580 17118959
15. Schaid DJ Rowland CM Tines DE Jacobson RM Poland GA Score tests for association between traits and haplotypes when linkage phase is ambiguous Am J Hum Genet 2002, 70(2):425-434. 384917 11791212 10.1086/ 338688
16. Tregouet DA Escolano S Tiret L Mallet A Golmard JL A new algorithm for haplotype-based association analysis: The Stochastic-EM algorithm Ann Hum Genet 2004, 68(Pt 2):165-177. 10.1046/j.1529-8817.2003.00085.x 15008795
17. THESIAS software program http://www.genecanvas.org
18. Haplo Stats software program http://mayoresearch.mayo.edu/mayo/research/ schaid_lab/software.cfm
19. Stephens M Smith NJ Donnelly P A new statistical method for haplotype reconstruction from population data Am J Hum Genet 2001, 68(4):978-989. 1275651 11254454 10.1086/319501
20. dbSNP database at NCBI http://www.ncbi.nlm.nih.gov/SNP/