{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,9,16]],"date-time":"2023-09-16T04:52:30Z","timestamp":1694839950005},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1937,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Accurate inference of genealogical relationships between pairs of individuals is paramount in association studies, forensics and evolutionary analyses of wildlife populations. Current methods for relationship inference consider only a small set of close relationships and have limited to no power to distinguish between relationships with the same number of meioses separating the individuals under consideration (e.g. aunt\u2013niece versus niece\u2013aunt or first cousins versus great aunt\u2013niece).<\/jats:p>\n               <jats:p>Results: We present CARROT (ClAssification of Relationships with ROTations), a novel framework for relationship inference that leverages linkage information to differentiate between rotated relationships, that is, between relationships with the same number of common ancestors and the same number of meioses separating the individuals under consideration. We demonstrate that CARROT clearly outperforms existing methods on simulated data. We also applied CARROT on four populations from Phase III of the HapMap Project and detected previously unreported pairs of third- and fourth-degree relatives.<\/jats:p>\n               <jats:p>Availability: Source code for CARROT is freely available at http:\/\/carrot.stanford.edu.<\/jats:p>\n               <jats:p>Contact: \u00a0sofiakp@stanford.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr243","type":"journal-article","created":{"date-parts":[[2011,6,17]],"date-time":"2011-06-17T23:32:32Z","timestamp":1308353552000},"page":"i333-i341","source":"Crossref","is-referenced-by-count":14,"title":["Reconstruction of genealogical relationships with applications to Phase III of HapMap"],"prefix":"10.1093","volume":"27","author":[{"given":"Sofia","family":"Kyriazopoulou-Panagiotopoulou","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dorna","family":"Kashef Haghighi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah J.","family":"Aerni","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"},{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Sundquist","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"},{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sivan","family":"Bercovici","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Serafim","family":"Batzoglou","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Stanford University, 2Biomedical Informatics Training Program, Stanford University School of Medicine, Stanford, CA 94305 and 3DNAnexus, Inc., Palo Alto, CA 94301, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,6,14]]},"reference":[{"key":"2023012512153665900_B1","doi-asserted-by":"crossref","first-page":"i175","DOI":"10.1093\/bioinformatics\/btq204","article-title":"Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping","volume":"26","author":"Bercovici","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512153665900_B2","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1093\/bioinformatics\/btm219","article-title":"Reconstructing sibling relationships in wild populations","volume":"23","author":"Berger-Wolf","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512153665900_B3","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/S0169-5347(03)00225-8","article-title":"DNA-based methods for pedigree reconstruction and kinship analysis in natural populations","volume":"18","author":"Blouin","year":"2003","journal-title":"Trends Ecol. 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