{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:24Z","timestamp":1740185124671,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2020,11,2]],"date-time":"2020-11-02T00:00:00Z","timestamp":1604275200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"JSPS","doi-asserted-by":"publisher","award":["19H01021","20K21834"],"award-info":[{"award-number":["19H01021","20K21834"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"AMED","doi-asserted-by":"publisher","award":["JP20km0405211","JP20ek0109413","JP20ek0410075","JP20gm4010006","JP20km0405217"],"award-info":[{"award-number":["JP20km0405211","JP20ek0109413","JP20ek0410075","JP20gm4010006","JP20km0405217"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bioinformatics Initiative of Osaka University Graduate School of Medicine"},{"DOI":"10.13039\/100007449","name":"Takeda Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007449","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genetic linkage analysis has made a huge contribution to the genetic mapping of Mendelian diseases. However, most previously available linkage analysis methods have limited applicability. Since parametric linkage analysis requires predefined model of inheritance with a fixed set of parameters, it is inapplicable without fully structured pedigree information. Furthermore, the analytical results are dependent on the specification of model parameters. While non-parametric linkage analysis can avoid these problems, the runs of homozygosity (ROH) mapping, a widely used non-parametric linkage analysis method, can only deal with recessive inheritance. The implementation of non-parametric linkage analyses capable of dealing with both dominant and recessive inheritance has been required.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed the Obelisc (Observational linkage scan), a flexibly applicable user-friendly non-parametric linkage analysis tool, which also provides an intuitive visualization of the analytical results. Obelisc is based on the SNP streak approach, which does not require any predefined inheritance model with parameters. In contrast to the ROH mapping, the SNP streak approach is applicable to both dominant and recessive traits. To illustrate the performance of Obelisc, we generated a pseudo-pedigree from the publicly available BioBank Japan Project genome-wide genotype dataset (n\u2009&amp;gt;\u2009180\u00a0000). By applying Obelisc to this pseudo-pedigree, we successfully identified the regions with inherited identical-by-descent haplotypes shared among the members of the pseudo-pedigree, which was validated by the population-based haplotype phasing approach.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Obelisc is feely available at https:\/\/github.com\/qsonehara\/Obelisc as a python package with example datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa940","type":"journal-article","created":{"date-parts":[[2020,10,26]],"date-time":"2020-10-26T12:10:49Z","timestamp":1603714249000},"page":"5567-5570","source":"Crossref","is-referenced-by-count":2,"title":["Obelisc: an identical-by-descent mapping tool based on SNP streak"],"prefix":"10.1093","volume":"36","author":[{"given":"Kyuto","family":"Sonehara","sequence":"first","affiliation":[{"name":"Department of Statistical Genetics, Osaka University Graduate School of Medicine , Suita 565-0871, Japan"}]},{"given":"Yukinori","family":"Okada","sequence":"additional","affiliation":[{"name":"Department of Statistical Genetics, Osaka University Graduate School of Medicine , Suita 565-0871, Japan"},{"name":"Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University , Suita 565-0871, Japan"},{"name":"Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University , Suita 565-0871, Japan"}]}],"member":"286","published-online":{"date-parts":[[2020,11,2]]},"reference":[{"key":"2023062408145864000_btaa940-B1","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"2023062408145864000_btaa940-B2","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1002\/gepi.1370060148","article-title":"Linkage analysis with inbreeding","volume":"6","author":"Eerdewegh","year":"1989","journal-title":"Genet. 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