{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,19]],"date-time":"2023-08-19T05:05:22Z","timestamp":1692421522927},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":3056,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Detailed analyses of the population-genetic nature of copy number variations (CNVs) and the linkage disequilibrium between CNV and single nucleotide polymorphism (SNP) loci from high-throughput experimental data require a computational tool to accurately infer alleles of CNVs and haplotypes composed of both CNV alleles and SNP alleles. Here we developed a new tool to infer population frequencies of such alleles and haplotypes from observed copy numbers and SNP genotypes, using the expectation\u2013maximization algorithm. This tool can also handle copy numbers ambiguously determined, such as 2 or 3 copies, due to experimental noise.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/emu.src.riken.jp\/MOCSphaser\/MOCSphaser.zip<\/jats:p>\n               <jats:p>Contact: \u00a0tsunoda@src.riken.jp<\/jats:p>\n               <jats:p>Supplementary information: Additional materials can be found at http:\/\/emu.src.riken.jp\/MOCSphaser\/SuppInfor.doc<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn242","type":"journal-article","created":{"date-parts":[[2008,5,21]],"date-time":"2008-05-21T02:49:19Z","timestamp":1211338159000},"page":"1645-1646","source":"Crossref","is-referenced-by-count":13,"title":["MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data"],"prefix":"10.1093","volume":"24","author":[{"given":"Mamoru","family":"Kato","sequence":"first","affiliation":[{"name":"1 SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045 and 2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Yusuke","family":"Nakamura","sequence":"additional","affiliation":[{"name":"1 SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045 and 2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"},{"name":"1 SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045 and 2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Tatsuhiko","family":"Tsunoda","sequence":"additional","affiliation":[{"name":"1 SNP Research Center, RIKEN, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, Kanagawa 230-0045 and 2Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan"}]}],"member":"286","published-online":{"date-parts":[[2008,5,20]]},"reference":[{"key":"2023020210482206000_B1","first-page":"1","article-title":"Trisomic phase inference","volume-title":"Computational Methods for SNPs and Haplotype Inference, Lecture Notes in Bioinformatics 2983","author":"Clark","year":"2004"},{"key":"2023020210482206000_B2","doi-asserted-by":"crossref","first-page":"S30","DOI":"10.1038\/ng2042","article-title":"The population genetics of structural variation","volume":"39","author":"Conrad","year":"2007","journal-title":"Nat. Genet"},{"key":"2023020210482206000_B3","first-page":"921","article-title":"Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population","volume":"12","author":"Excoffier","year":"1995","journal-title":"Mol. Biol. Evol"},{"key":"2023020210482206000_B4","doi-asserted-by":"crossref","first-page":"R57","DOI":"10.1093\/hmg\/ddl057","article-title":"Structural variants: changing the landscape of chromosomes and design of disease studies","volume":"15","author":"Feuk","year":"2006","journal-title":"Hum. Mol. Genet"},{"key":"2023020210482206000_B5","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1002\/humu.20609","article-title":"Multiplex PCR-based real-time invader assay (mPCR-RETINA): a novel SNP-based method for detecting allelic asymmetries within copy number variation regions","volume":"29","author":"Hosono","year":"2008","journal-title":"Hum. Mutat"},{"key":"2023020210482206000_B6","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1101\/gr.5629106","article-title":"Genome-wide detection of human copy number variations using high-density DNA oligonucleotide arrays","volume":"16","author":"Komura","year":"2006","journal-title":"Genome Res"},{"key":"2023020210482206000_B7","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/gepi.20024","article-title":"Algorithms for inferring haplotypes","volume":"27","author":"Niu","year":"2004","journal-title":"Genet. Epidemiol"},{"key":"2023020210482206000_B8","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature05329","article-title":"Global variation in copy number in the human genome","volume":"444","author":"Redon","year":"2006","journal-title":"Nature"},{"key":"2023020210482206000_B9","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1038\/nature06258","article-title":"A second generation human haplotype map of over 3.1 million SNPs","volume":"449","author":"The International HapMap Consortium","year":"2007","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/14\/1645\/49048000\/bioinformatics_24_14_1645.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/14\/1645\/49048000\/bioinformatics_24_14_1645.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T12:29:46Z","timestamp":1675340986000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/14\/1645\/182014"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,5,20]]},"references-count":9,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2008,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn242","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,7,15]]},"published":{"date-parts":[[2008,5,20]]}}}