{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T08:04:47Z","timestamp":1769328287134,"version":"3.49.0"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Since the completion of the HapMap project, huge numbers of individual genotypes have been generated from many kinds of laboratories. The efforts of finding or interpreting genetic association between disease and SNPs\/haplotypes have been on-going widely. So, the necessity of the capability to analyze huge data and diverse interpretation of the results are growing rapidly.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We have developed an advanced tool to perform linkage disequilibrium analysis, and genetic association analysis between disease and SNPs\/haplotypes in an integrated web interface. It comprises of four main analysis modules: (i) data import and preprocessing, (ii) haplotype estimation, (iii) LD blocking and (iv) association analysis. Hardy-Weinberg Equilibrium test is implemented for each SNPs in the data preprocessing. Haplotypes are reconstructed from unphased diploid genotype data, and linkage disequilibrium between pairwise SNPs is computed and represented by D', r<jats:sup>2<\/jats:sup> and LOD score. Tagging SNPs are determined by using the square of Pearson's correlation coefficient (r<jats:sup>2<\/jats:sup>). If genotypes from two different sample groups are available, diverse genetic association analyses are implemented using additive, codominant, dominant and recessive models. Multiple verified algorithms and statistics are implemented in parallel for the reliability of the analysis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>SNPAnalyzer 2.0 performs linkage disequilibrium analysis and genetic association analysis in an integrated web interface using multiple verified algorithms and statistics. Diverse analysis methods, capability of handling huge data and visual comparison of analysis results are very comprehensive and easy-to-use.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-290","type":"journal-article","created":{"date-parts":[[2008,6,24]],"date-time":"2008-06-24T06:13:07Z","timestamp":1214287987000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":85,"title":["SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis"],"prefix":"10.1186","volume":"9","author":[{"given":"Jinho","family":"Yoo","sequence":"first","affiliation":[]},{"given":"Youngbok","family":"Lee","sequence":"additional","affiliation":[]},{"given":"Yujung","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Sun Young","family":"Rha","sequence":"additional","affiliation":[]},{"given":"Yangseok","family":"Kim","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,6,23]]},"reference":[{"issue":"15","key":"2275_CR1","doi-asserted-by":"publisher","first-page":"1928","DOI":"10.1093\/bioinformatics\/btl268","volume":"22","author":"X Sole","year":"2006","unstructured":"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\u20131929. 10.1093\/bioinformatics\/btl268","journal-title":"Bioinformatics"},{"key":"2275_CR2","doi-asserted-by":"crossref","unstructured":"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\u2013488. 10.1093\/nar\/gki428","DOI":"10.1093\/nar\/gki428"},{"issue":"5","key":"2275_CR3","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1002\/gepi.20216","volume":"31","author":"BL Browning","year":"2007","unstructured":"Browning BL, Browning SR: Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering. Genet Epidemiol 2007, 31(5):365\u2013375. 10.1002\/gepi.20216","journal-title":"Genet Epidemiol"},{"issue":"3","key":"2275_CR4","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1086\/519795","volume":"81","author":"S Purcell","year":"2007","unstructured":"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\u2013575. 10.1086\/519795","journal-title":"Am J Hum Genet"},{"issue":"1","key":"2275_CR5","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1093\/bioinformatics\/bth482","volume":"21","author":"K Zhang","year":"2005","unstructured":"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\u2013134. 10.1093\/bioinformatics\/bth482","journal-title":"Bioinformatics"},{"issue":"2","key":"2275_CR6","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","volume":"21","author":"JC Barrett","year":"2005","unstructured":"Barrett JC, Fry B, Maller J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263\u2013265. 10.1093\/bioinformatics\/bth457","journal-title":"Bioinformatics"},{"key":"2275_CR7","unstructured":"SNPAnalyzer 2.0 homepage[http:\/\/snp.istech21.com\/snpanalyzer\/2.0\/]"},{"issue":"5","key":"2275_CR8","first-page":"921","volume":"12","author":"L Excoffier","year":"1995","unstructured":"Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995, 12(5):921\u2013927.","journal-title":"Mol Biol Evol"},{"issue":"1","key":"2275_CR9","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1086\/338446","volume":"70","author":"T Niu","year":"2002","unstructured":"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\u2013169. 10.1086\/338446","journal-title":"Am J Hum Genet"},{"issue":"2","key":"2275_CR10","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1006\/geno.1995.9003","volume":"29","author":"B Devlin","year":"1995","unstructured":"Devlin B, Risch N: A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 1995, 29(2):311\u2013322. 10.1006\/geno.1995.9003","journal-title":"Genomics"},{"issue":"5576","key":"2275_CR11","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1126\/science.1069424","volume":"296","author":"SB Gabriel","year":"2002","unstructured":"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\u20132229. 10.1126\/science.1069424","journal-title":"Science"},{"issue":"16","key":"2275_CR12","doi-asserted-by":"publisher","first-page":"9440","DOI":"10.1073\/pnas.1530509100","volume":"100","author":"JD Storey","year":"2003","unstructured":"Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100(16):9440\u20139445. 10.1073\/pnas.1530509100","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6","key":"2275_CR13","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.1086\/380204","volume":"73","author":"MP Epstein","year":"2003","unstructured":"Epstein MP, Satten GA: Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 2003, 73(6):1316\u20131329. 10.1086\/380204","journal-title":"Am J Hum Genet"},{"issue":"2","key":"2275_CR14","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1093\/bioinformatics\/btl580","volume":"23","author":"S Purcell","year":"2007","unstructured":"Purcell S, Daly MJ, Sham PC: WHAP: haplotype-based association analysis. Bioinformatics 2007, 23(2):255\u2013256. 10.1093\/bioinformatics\/btl580","journal-title":"Bioinformatics"},{"issue":"2","key":"2275_CR15","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1086\/338688","volume":"70","author":"DJ Schaid","year":"2002","unstructured":"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\u2013434. 10.1086\/338688","journal-title":"Am J Hum Genet"},{"issue":"Pt 2","key":"2275_CR16","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1046\/j.1529-8817.2003.00085.x","volume":"68","author":"DA Tregouet","year":"2004","unstructured":"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\u2013177. 10.1046\/j.1529-8817.2003.00085.x","journal-title":"Ann Hum Genet"},{"key":"2275_CR17","unstructured":"THESIAS software program[http:\/\/www.genecanvas.org]"},{"key":"2275_CR18","unstructured":"Haplo Stats software program[http:\/\/mayoresearch.mayo.edu\/mayo\/research\/schaid_lab\/software.cfm]"},{"issue":"4","key":"2275_CR19","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1086\/319501","volume":"68","author":"M Stephens","year":"2001","unstructured":"Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001, 68(4):978\u2013989. 10.1086\/319501","journal-title":"Am J Hum Genet"},{"key":"2275_CR20","unstructured":"dbSNP database at NCBI[http:\/\/www.ncbi.nlm.nih.gov\/SNP\/]"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-290.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T11:03:00Z","timestamp":1630494180000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-290"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,23]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2275"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-290","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,6,23]]},"assertion":[{"value":"23 February 2008","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 June 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"290"}}