{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,26]],"date-time":"2026-04-26T08:43:27Z","timestamp":1777193007895,"version":"3.51.4"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,3]],"date-time":"2024-12-03T00:00:00Z","timestamp":1733184000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["16\/SPP\/3324"],"award-info":[{"award-number":["16\/SPP\/3324"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000025","name":"National Institutes of Mental Health","doi-asserted-by":"crossref","award":["R01MH124875"],"award-info":[{"award-number":["R01MH124875"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000025","name":"National Institutes of Mental Health","doi-asserted-by":"crossref","award":["U01MH109499-04"],"award-info":[{"award-number":["U01MH109499-04"]}],"id":[{"id":"10.13039\/100000025","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Next-generation sequencing is widely applied to the investigation of pedigree data for gene discovery. However, identifying plausible disease-causing variants within a robust statistical framework is challenging. Here, we introduce BICEP: a Bayesian inference tool for rare variant causality evaluation in pedigree-based cohorts. BICEP calculates the posterior odds that a genomic variant is causal for a phenotype based on the variant cosegregation as well as a priori evidence such as deleteriousness and functional consequence. BICEP can correctly identify causal variants for phenotypes with both Mendelian and complex genetic architectures, outperforming existing methodologies. Additionally, BICEP can correctly down-weight common variants that are unlikely to be involved in phenotypic liability in the context of a pedigree, even if they have reasonable cosegregation patterns. The output metrics from BICEP allow for the quantitative comparison of variant causality within and across pedigrees, which is not possible with existing approaches.<\/jats:p>","DOI":"10.1093\/bib\/bbae624","type":"journal-article","created":{"date-parts":[[2024,12,14]],"date-time":"2024-12-14T11:08:43Z","timestamp":1734174523000},"source":"Crossref","is-referenced-by-count":2,"title":["BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5717-0508","authenticated-orcid":false,"given":"Cathal","family":"Ormond","sequence":"first","affiliation":[{"name":"Neuropsychiatric Genetics Research Group , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 ,","place":["Ireland"]},{"name":"Trinity College Dublin , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 ,","place":["Ireland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niamh M","family":"Ryan","sequence":"additional","affiliation":[{"name":"Neuropsychiatric Genetics Research Group , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 ,","place":["Ireland"]},{"name":"Trinity College Dublin , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 ,","place":["Ireland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathieu","family":"Cap","sequence":"additional","affiliation":[{"name":"Neuropsychiatric Genetics Research Group , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 ,","place":["Ireland"]},{"name":"Trinity College Dublin , Department of Psychiatry, Trinity Centre for Health Sciences, , St James\u2019s Hospital, Dublin 8 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