{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T07:42:47Z","timestamp":1707982967861},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recently, investigators have proposed state-of-the-art Identity-by-descent (IBD) mapping methods to detect IBD segments between purportedly unrelated individuals. The IBD information can then be used for association testing in genetic association studies. One approach for this IBD association testing strategy is to test for excessive IBD between pairs of cases (\u2018pairwise method\u2019). However, this approach is inefficient because it requires a large number of permutations. Moreover, a limited number of permutations define a lower bound for P-values, which makes fine-mapping of associated regions difficult because, in practice, a much larger genomic region is implicated than the region that is actually associated.<\/jats:p>\n               <jats:p>Results: In this article, we introduce a new pairwise method \u2018Fast-Pairwise\u2019. Fast-Pairwise uses importance sampling to improve efficiency and enable approximation of extremely small P-values. Fast-Pairwise method takes only days to complete a genome-wide scan. In the application to the WTCCC type 1 diabetes data, Fast-Pairwise successfully fine-maps a known human leukocyte antigen gene that is known to cause the disease.<\/jats:p>\n               <jats:p>Availability: Fast-Pairwise is publicly available at: http:\/\/genetics.cs.ucla.edu\/graphibd.<\/jats:p>\n               <jats:p>Contact: \u00a0eeskin@cs.ucla.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt609","type":"journal-article","created":{"date-parts":[[2013,10,25]],"date-time":"2013-10-25T04:43:23Z","timestamp":1382676203000},"page":"206-213","source":"Crossref","is-referenced-by-count":5,"title":["Fast pairwise IBD association testing in genome-wide association studies"],"prefix":"10.1093","volume":"30","author":[{"given":"Buhm","family":"Han","sequence":"first","affiliation":[{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"}]},{"given":"Eun Yong","family":"Kang","sequence":"additional","affiliation":[{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"}]},{"given":"Soumya","family":"Raychaudhuri","sequence":"additional","affiliation":[{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, 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Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"}]},{"given":"Paul I. W.","family":"de Bakker","sequence":"additional","affiliation":[{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and Women\u2019s Hospital, Harvard Medical School, Boston, MA 02115, USA, 3Partners Center for Personalized Genetic Medicine, Boston, MA 02115, USA, 4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA, 5Computer Science Department, University of California, Los Angeles, CA 90095, USA, 6Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK, 7Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands, 8Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands and 9Department of Human Genetics, University of California, Los Angeles, CA 90095, USA"},{"name":"1 Division of Genetics, Brigham and Women\u2019s Hospital and 2Division of Rheumatology, Brigham and 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