{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,26]],"date-time":"2023-09-26T00:53:31Z","timestamp":1695689611237},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present a software tool called GenomeLaser that determines the haplotypes of each person from unphased high-throughput genotypes in family pedigrees. This method features high accuracy, chromosome-range phasing distance, linear computing, flexible pedigree types and flexible genetic marker types.<\/jats:p>\n               <jats:p>Availability and implementation: \u00a0http:\/\/www.4dgenome.com\/software\/genomelaser.html.<\/jats:p>\n               <jats:p>Contact: \u00a0qsong@msm.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv452","type":"journal-article","created":{"date-parts":[[2015,8,19]],"date-time":"2015-08-19T02:39:25Z","timestamp":1439951965000},"page":"3984-3987","source":"Crossref","is-referenced-by-count":3,"title":["GenomeLaser: fast and accurate haplotyping from pedigree genotypes"],"prefix":"10.1093","volume":"31","author":[{"given":"Wenzhi","family":"Li","sequence":"first","affiliation":[{"name":"1 Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061 China,"},{"name":"2 Cardiovascular Research Institute and Department of Medicine, Morehouse School of Medicine, Atlanta, GA, 30310 USA,"}]},{"given":"Guoxing","family":"Fu","sequence":"additional","affiliation":[{"name":"3 4DGENOME Inc, Atlanta, GA, 30033 USA and"}]},{"given":"Weinian","family":"Rao","sequence":"additional","affiliation":[{"name":"3 4DGENOME Inc, Atlanta, GA, 30033 USA and"}]},{"given":"Wei","family":"Xu","sequence":"additional","affiliation":[{"name":"2 Cardiovascular Research Institute and Department of Medicine, Morehouse School of Medicine, Atlanta, GA, 30310 USA,"}]},{"given":"Li","family":"Ma","sequence":"additional","affiliation":[{"name":"2 Cardiovascular Research Institute and Department of Medicine, Morehouse School of Medicine, Atlanta, GA, 30310 USA,"},{"name":"3 4DGENOME Inc, Atlanta, GA, 30033 USA and"}]},{"given":"Shiwen","family":"Guo","sequence":"additional","affiliation":[{"name":"1 Department of Neurosurgery, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061 China,"}]},{"given":"Qing","family":"Song","sequence":"additional","affiliation":[{"name":"2 Cardiovascular Research Institute and Department of Medicine, Morehouse School of Medicine, Atlanta, GA, 30310 USA,"},{"name":"3 4DGENOME Inc, Atlanta, GA, 30033 USA and"},{"name":"4 Center of Big Data and Bioinformatics, First Affiliated Hospital of Medical School, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061 China"}]}],"member":"286","published-online":{"date-parts":[[2015,8,18]]},"reference":[{"key":"2023051307183789000_btv452-B1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/ng786","article-title":"Merlin\u2014rapid analysis of dense genetic maps using sparse gene flow trees","volume":"30","author":"Abecasis","year":"2002","journal-title":"Nat. Genet."},{"key":"2023051307183789000_btv452-B2","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1038\/nrg3054","article-title":"Haplotype phasing: existing methods and new developments","volume":"12","author":"Browning","year":"2011","journal-title":"Nat. Rev. Genet."},{"key":"2023051307183789000_btv452-B3","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1101\/gr.142455.112","article-title":"Genotype calling and haplotyping in parent-offspring trios","volume":"23","author":"Chen","year":"2013","journal-title":"Genome Res."},{"key":"2023051307183789000_btv452-B4","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1534\/genetics.109.108431","article-title":"A hidden Markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping","volume":"184","author":"Druet","year":"2010","journal-title":"Genetics"},{"key":"2023051307183789000_btv452-B5","doi-asserted-by":"crossref","first-page":"1677","DOI":"10.1093\/bioinformatics\/btu859","article-title":"LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors","volume":"31","author":"Druet","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051307183789000_btv452-B6","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nbt.1739","article-title":"Whole-genome molecular haplotyping of single cells","volume":"29","author":"Fan","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2023051307183789000_btv452-B7","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1159\/000194978","article-title":"Haplotyping methods for pedigrees","volume":"67","author":"Gao","year":"2009","journal-title":"Hum. Hered."},{"key":"2023051307183789000_btv452-B8","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/7687","article-title":"Loss of information due to ambiguous haplotyping of SNPs","volume":"21","author":"Hodge","year":"1999","journal-title":"Nat. Genet."},{"key":"2023051307183789000_btv452-B9","doi-asserted-by":"crossref","first-page":"S64","DOI":"10.1186\/1753-6561-8-S1-S64","article-title":"Genotype imputation accuracy with different reference panels in admixed populations","volume":"8","author":"Huang","year":"2014","journal-title":"BMC Proc."},{"key":"2023051307183789000_btv452-B10","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1016\/j.ajhg.2009.01.013","article-title":"Genotype-imputation accuracy across worldwide human populations","volume":"84","author":"Huang","year":"2009","journal-title":"Am. J. Hum. Genet."},{"key":"2023051307183789000_btv452-B11","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1101\/gr.144600.112","article-title":"Sequencing of isolated sperm cells for direct haplotyping of a human genome","volume":"23","author":"Kirkness","year":"2013","journal-title":"Genome Res."},{"key":"2023051307183789000_btv452-B12","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nbt.1740","article-title":"Haplotype-resolved genome sequencing of a Gujarati Indian individual","volume":"29","author":"Kitzman","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2023051307183789000_btv452-B13","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1038\/ng.216","article-title":"Detection of sharing by descent, long-range phasing and haplotype imputation","volume":"40","author":"Kong","year":"2008","journal-title":"Nat. Genet"},{"key":"2023051307183789000_btv452-B14","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1755-8794-5-12","article-title":"Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs","volume":"5","author":"Krithika","year":"2012","journal-title":"BMC Med. Genomics"},{"key":"2023051307183789000_btv452-B15","first-page":"1347","article-title":"Parametric and nonparametric linkage analysis: a unified multipoint approach","volume":"58","author":"Kruglyak","year":"1996","journal-title":"Am. J. Hum. Genet."},{"key":"2023051307183789000_btv452-B16","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/nbt.2833","article-title":"Whole-genome haplotyping using long reads and statistical methods","volume":"32","author":"Kuleshov","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2023051307183789000_btv452-B17","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1142\/S0219720009004217","article-title":"An almost linear time algorithm for a general haplotype solution on tree pedigrees with no recombination and its extensions","volume":"7","author":"Li","year":"2009","journal-title":"J. Bioinform. Comput. Biol."},{"key":"2023051307183789000_btv452-B18","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1002\/gepi.20533","article-title":"MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes","volume":"34","author":"Li","year":"2010","journal-title":"Genet. Epidemiol."},{"key":"2023051307183789000_btv452-B19","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1002\/gepi.21690","article-title":"MaCH-admix: genotype imputation for admixed populations","volume":"37","author":"Liu","year":"2013","journal-title":"Genet. Epidemiol."},{"key":"2023051307183789000_btv452-B20","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1016\/S0065-2660(07)00414-2","article-title":"Haplotype-association analysis","volume":"60","author":"Liu","year":"2008","journal-title":"Adv. Genet."},{"key":"2023051307183789000_btv452-B21","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/nmeth.1443","article-title":"Direct determination of molecular haplotypes by chromosome microdissection","volume":"7","author":"Ma","year":"2010","journal-title":"Nat. Methods"},{"key":"2023051307183789000_btv452-B22","doi-asserted-by":"crossref","first-page":"5800","DOI":"10.1038\/srep05800","article-title":"Accurate inference of local phased ancestry of modern admixed populations","volume":"4","author":"Ma","year":"2014","journal-title":"Sci. Rep."},{"key":"2023051307183789000_btv452-B23","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1086\/338446","article-title":"Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms","volume":"70","author":"Niu","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"2023051307183789000_btv452-B24","doi-asserted-by":"crossref","first-page":"e1004234","DOI":"10.1371\/journal.pgen.1004234","article-title":"A general approach for haplotype phasing across the full spectrum of relatedness","volume":"10","author":"O'Connell","year":"2014","journal-title":"PLoS Genet."},{"key":"2023051307183789000_btv452-B25","doi-asserted-by":"crossref","first-page":"S64","DOI":"10.1002\/1098-2272(2000)19:1+<::AID-GEPI10>3.0.CO;2-G","article-title":"Zero-recombinant haplotyping: applications to fine mapping using SNPs","volume":"19","author":"O'Connell","year":"2000","journal-title":"Genet. Epidemiol."},{"key":"2023051307183789000_btv452-B26","doi-asserted-by":"crossref","first-page":"1242","DOI":"10.1086\/344207","article-title":"Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms","volume":"71","author":"Qin","year":"2002","journal-title":"Am. J. Hum. Genet."},{"key":"2023051307183789000_btv452-B27","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1038\/nmeth.2308","article-title":"High-resolution whole-genome haplotyping using limited seed data","volume":"10","author":"Rao","year":"2013","journal-title":"Nat. Methods"},{"key":"2023051307183789000_btv452-B28","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1038\/nbt.2728","article-title":"Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing","volume":"31","author":"Selvaraj","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"2023051307183789000_btv452-B29","first-page":"1323","article-title":"Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics","volume":"58","author":"Sobel","year":"1996","journal-title":"Am. J. Hum. Genet."},{"key":"2023051307183789000_btv452-B30","doi-asserted-by":"crossref","first-page":"1672","DOI":"10.1101\/gr.125047.111","article-title":"A comprehensively molecular haplotype-resolved genome of a European individual","volume":"21","author":"Suk","year":"2011","journal-title":"Genome Res."},{"key":"2023051307183789000_btv452-B31","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1073\/pnas.1016725108","article-title":"Completely phased genome sequencing through chromosome sorting","volume":"108","author":"Yang","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023051307183789000_btv452-B32","doi-asserted-by":"crossref","first-page":"339","DOI":"10.4310\/SII.2011.v4.n3.a8","article-title":"Practical consideration of genotype imputation: sample size, window size, reference choice, and untyped rate","volume":"4","author":"Zhang","year":"2011","journal-title":"Stat. Interface"},{"key":"2023051307183789000_btv452-B33","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1093\/bioinformatics\/bth388","article-title":"HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination","volume":"21","author":"Zhang","year":"2005","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/24\/3984\/50306949\/bioinformatics_31_24_3984.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/24\/3984\/50306949\/bioinformatics_31_24_3984.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T07:19:51Z","timestamp":1683962391000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/24\/3984\/196663"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,8,18]]},"references-count":33,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2015,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv452","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,12,15]]},"published":{"date-parts":[[2015,8,18]]}}}