{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T20:44:22Z","timestamp":1722890662127},"reference-count":10,"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":[[2013,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Y haplogroup analyses are an important component of genealogical reconstruction, population genetic analyses, medical genetics and forensics. These fields are increasingly moving towards use of low-coverage, high throughput sequencing. While there have been methods recently proposed for assignment of Y haplogroups on the basis of high-coverage sequence data, assignment on the basis of low-coverage data remains challenging.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We developed a new algorithm, YHap, which uses an imputation framework to jointly predict Y chromosome genotypes and assign Y haplogroups using low coverage population sequence data. We use data from the 1000 genomes project to demonstrate that YHap provides accurate Y haplogroup assignment with less than 2x coverage.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Borrowing information across multiple samples within a population using an imputation framework enables accurate Y haplogroup assignment.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-331","type":"journal-article","created":{"date-parts":[[2013,11,19]],"date-time":"2013-11-19T20:00:59Z","timestamp":1384891259000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data"],"prefix":"10.1186","volume":"14","author":[{"given":"Fan","family":"Zhang","sequence":"first","affiliation":[]},{"given":"Ruoyan","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Dongbing","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Xiaotian","family":"Yao","sequence":"additional","affiliation":[]},{"given":"Guoqing","family":"Li","sequence":"additional","affiliation":[]},{"given":"Yabin","family":"Jin","sequence":"additional","affiliation":[]},{"given":"Chang","family":"Yu","sequence":"additional","affiliation":[]},{"given":"Yingrui","family":"Li","sequence":"additional","affiliation":[]},{"given":"Lachlan JM","family":"Coin","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,11,19]]},"reference":[{"key":"6200_CR1","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1016\/j.cub.2009.07.032","volume":"19","author":"Y Xue","year":"2009","unstructured":"Xue Y, Wang Q, Long Q, Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y, et al: Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr Biol. 2009, 19: 1453-1457. 10.1016\/j.cub.2009.07.032.","journal-title":"Curr Biol"},{"key":"6200_CR2","doi-asserted-by":"publisher","first-page":"717","DOI":"10.1086\/367774","volume":"72","author":"T Zerjal","year":"2003","unstructured":"Zerjal T, Xue Y, Bertorelle G, Wells RS, Bao W, Zhu S, Qamar R, Ayub Q, Mohyuddin A, Fu S, et al: The genetic legacy of the Mongols. Am J Hum Genet. 2003, 72: 717-721. 10.1086\/367774.","journal-title":"Am J Hum Genet"},{"key":"6200_CR3","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/S0379-0738(03)00299-8","volume":"137","author":"JJ Sanchez","year":"2003","unstructured":"Sanchez JJ, Borsting C, Hallenberg C, Buchard A, Hernandez A, Morling N: Multiplex PCR and minisequencing of SNPs-a model with 35 Y chromosome SNPs. Forensic Sci Int. 2003, 137: 74-84. 10.1016\/S0379-0738(03)00299-8.","journal-title":"Forensic Sci Int"},{"key":"6200_CR4","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1086\/342096","volume":"71","author":"T Zerjal","year":"2002","unstructured":"Zerjal T, Wells RS, Yuldasheva N, Ruzibakiev R, Tyler-Smith C: A genetic landscape reshaped by recent events: Y-chromosomal insights into central Asia. Am J Hum Genet. 2002, 71: 466-482. 10.1086\/342096.","journal-title":"Am J Hum Genet"},{"issue":"1","key":"6200_CR5","first-page":"iii-iv","volume":"4","author":"A Turner","year":"2008","unstructured":"Turner A: SNPs on chips: a New source of data for Y-chromosome studies. Journal of Genetic Genealogy. 2008, 4 (1): iii-iv-","journal-title":"Journal of Genetic Genealogy"},{"key":"6200_CR6","doi-asserted-by":"publisher","first-page":"1021","DOI":"10.1093\/gbe\/evt066","volume":"5","author":"E Elhaik","year":"2013","unstructured":"Elhaik E, Greenspan E, Staats S, Krahn T, Tyler-Smith C, Xue Y, Tofanelli S, Francalacci P, Cucca F, Pagani L, et al: The GenoChip: a new tool for genetic anthropology. Genome Biol Evol. 2013, 5: 1021-1031. 10.1093\/gbe\/evt066.","journal-title":"Genome Biol Evol"},{"key":"6200_CR7","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/1471-2164-14-101","volume":"14","author":"A Van Geystelen","year":"2013","unstructured":"Van Geystelen A, Decorte R, Larmuseau MHD: AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications. BMC Genomics. 2013, 14: 101-10.1186\/1471-2164-14-101.","journal-title":"BMC Genomics"},{"issue":"5","key":"6200_CR8","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1101\/gr.7172008","volume":"18","author":"TM Karafet","year":"2008","unstructured":"Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF: New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008, 18 (5): 830-838. 10.1101\/gr.7172008.","journal-title":"Genome Res"},{"key":"6200_CR9","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"A McKenna","year":"2010","unstructured":"McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA, The 1000 Genomes Project Consortium: The 1000 genomes project consortium: a map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038\/nature09534.","journal-title":"Nature"},{"key":"6200_CR10","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1038\/nature09298","volume":"467","author":"DM Altshuler","year":"2010","unstructured":"Altshuler DM, Gibbs RA, Peltonen L, Altshuler DM, Gibbs RA, Peltonen L, Dermitzakis E, Schaffner SF, Yu F, International HapMap Consortium, et al: Integrating common and rare genetic variation in diverse human populations. Nature. 2010, 467: 52-58. 10.1038\/nature09298.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-331.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:12:59Z","timestamp":1630548779000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-331"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,11,19]]},"references-count":10,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["6200"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-331","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,11,19]]},"assertion":[{"value":"22 July 2013","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2013","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2013","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"331"}}