{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T12:11:14Z","timestamp":1774527074033,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Performing experiments with simulated data is an inexpensive approach to evaluating competing experimental designs and analysis methods in genome-wide association studies. Simulation based on resampling known haplotypes is fast and efficient and can produce samples with patterns of linkage disequilibrium (LD), which mimic those in real data. However, the inability of current methods to simulate multiple nearby disease SNPs on the same chromosome can limit their application.<\/jats:p>\n               <jats:p>Results: We introduce a new simulation algorithm based on a successful resampling method, HAPGEN, that can simulate multiple nearby disease SNPs on the same chromosome. The new method, HAPGEN2, retains many advantages of resampling methods and expands the range of disease models that current simulators offer.<\/jats:p>\n               <jats:p>Availability: HAPGEN2 is freely available from http:\/\/www.stats.ox.ac.uk\/~marchini\/software\/gwas\/gwas.html.<\/jats:p>\n               <jats:p>Contact: \u00a0zhan@well.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr341","type":"journal-article","created":{"date-parts":[[2011,6,9]],"date-time":"2011-06-09T00:23:48Z","timestamp":1307579028000},"page":"2304-2305","source":"Crossref","is-referenced-by-count":305,"title":["HAPGEN2: simulation of multiple disease SNPs"],"prefix":"10.1093","volume":"27","author":[{"given":"Zhan","family":"Su","sequence":"first","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN and 2Department of Statistics, University of Oxford, Oxford OX1 3TG, UK"}]},{"given":"Jonathan","family":"Marchini","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN and 2Department of Statistics, University of Oxford, Oxford OX1 3TG, UK"},{"name":"1 Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN and 2Department of Statistics, University of Oxford, Oxford OX1 3TG, UK"}]},{"given":"Peter","family":"Donnelly","sequence":"additional","affiliation":[{"name":"1 Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN and 2Department of Statistics, University of Oxford, Oxford OX1 3TG, UK"},{"name":"1 Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN and 2Department of Statistics, University of Oxford, Oxford OX1 3TG, UK"}]}],"member":"286","published-online":{"date-parts":[[2011,6,8]]},"reference":[{"key":"2023012511515176300_B1","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/bth457","article-title":"Haploview: analysis and visualization of LD and haplotype maps","volume":"21","author":"Barrett","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012511515176300_B2","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1093\/bioinformatics\/18.2.337","article-title":"Generating samples under a Wright-Fisher neutral model","volume":"18","author":"Hudson","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012511515176300_B3","doi-asserted-by":"crossref","first-page":"1821","DOI":"10.1093\/bioinformatics\/btn317","article-title":"ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth","volume":"24","author":"Lambert","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511515176300_B4","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1093\/bioinformatics\/btm549","article-title":"GWAsimulator: a rapid whole-genome simulation program","volume":"24","author":"Li","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012511515176300_B5","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1093\/genetics\/165.4.2213","article-title":"Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data","volume":"165","author":"Li","year":"2003","journal-title":"Genetics"},{"key":"2023012511515176300_B6","doi-asserted-by":"crossref","first-page":"e1000477","DOI":"10.1371\/journal.pgen.1000477","article-title":"Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip","volume":"5","author":"Spencer","year":"2009","journal-title":"PLoS Genet."},{"key":"2023012511515176300_B7","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1038\/ng.694","article-title":"A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1","volume":"42","author":"Strange","year":"2010","journal-title":"Nat. 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