{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T02:40:34Z","timestamp":1738723234492,"version":"3.37.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2865,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: A two-stage association study is the most commonly used method among multistage designs to efficiently identify disease susceptibility genes. Recently, some SNP studies have utilized more than two stages to detect disease genes. However, there are few available programs for calculating statistical powers and positive predictive values (PPVs) of arbitrary n-stage designs.<\/jats:p><jats:p>Results: We developed programs for a multistage case\u2013control association study using R language. In our programs, input parameters include numbers of samples and candidate loci, genome-wide false positive rate and proportions of samples and loci to be selected at the k-th stage (k=1,\u2026, n). The programs output statistical powers, PPVs and numbers of typings in arbitrary n-stage designs. The programs can contribute to prior simulations under various conditions in planning a genome-wide association study.<\/jats:p><jats:p>Availability: The R programs are freely available for academic users and can be downloaded from http:\/\/www.med.niigata-u.ac.jp\/eng\/resources\/informatics\/gwa.html<\/jats:p><jats:p>Contact: \u00a0nktmr@m12.alpha-net.ne.jp<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn616","type":"journal-article","created":{"date-parts":[[2008,11,30]],"date-time":"2008-11-30T01:14:08Z","timestamp":1228007648000},"page":"272-273","source":"Crossref","is-referenced-by-count":1,"title":["Programs for calculating the statistical powers of detecting susceptibility genes in case\u2013control studies based on multistage designs"],"prefix":"10.1093","volume":"25","author":[{"given":"Nobutaka","family":"Kitamura","sequence":"first","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kouhei","family":"Akazawa","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akinori","family":"Miyashita","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryozo","family":"Kuwano","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shin-ichi","family":"Toyabe","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junichiro","family":"Nakamura","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norihito","family":"Nakamura","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tatsuhiko","family":"Sato","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. Aminul","family":"Hoque","sequence":"additional","affiliation":[{"name":"1 Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata 951-8520, 2Genome Science Branch, Center of Bioresource-Based Researches, Brain Research Institute, Niigata University, Niigata 951-8585, Japan and 3Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,11,28]]},"reference":[{"key":"2023013110002770000_B1","doi-asserted-by":"crossref","DOI":"10.1002\/9781119941750.ch7","article-title":"Statistics","volume-title":"An Introduction Using R.","author":"Crawley","year":"2005"},{"key":"2023013110002770000_B2","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1080\/10618600.1992.10477010","article-title":"Numerical computation of multivariate normal probabilities","volume":"1","author":"Genz","year":"1992","journal-title":"J. Comput. Graph. 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Genet."},{"key":"2023013110002770000_B4","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1093\/biostatistics\/kxj020","article-title":"Aspects of the design and analysis of high-dimensional SNP studies for disease risk estimation","volume":"7","author":"Prentice","year":"2006","journal-title":"Biostatistics"},{"key":"2023013110002770000_B5","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.0006-341X.2002.00163.x","article-title":"Two-stage designs for gene-disease association studies","volume":"58","author":"Satagopan","year":"2002","journal-title":"Biometrics"},{"key":"2023013110002770000_B6","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/ng1706","article-title":"Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies","volume":"38","author":"Skol","year":"2006","journal-title":"Nat. Genet."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/2\/272\/48982805\/bioinformatics_25_2_272.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/2\/272\/48982805\/bioinformatics_25_2_272.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,5]],"date-time":"2025-02-05T01:30:49Z","timestamp":1738719049000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/2\/272\/220758"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,11,28]]},"references-count":6,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2009,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn616","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"type":"electronic","value":"1367-4811"},{"type":"print","value":"1367-4803"}],"subject":[],"published-other":{"date-parts":[[2009,1,15]]},"published":{"date-parts":[[2008,11,28]]}}}