{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T14:19:51Z","timestamp":1774534791915,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005416","name":"Research Council of Norway","doi-asserted-by":"publisher","award":["321043"],"award-info":[{"award-number":["321043"]}],"id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Cosegregation analysis is a powerful tool for identifying pathogenic genetic variants, but its implementation remains challenging. Existing software is either limited in scope or too demanding for many end users. Moreover, current solutions lack methods for assessing the robustness of cosegregation evidence, which is important due to its reliance on uncertain estimates.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present shinyseg, a comprehensive web application for clinical cosegregation analysis. Our app streamlines penetrance specification based on either liability classes or epidemiological data such as risks, hazard ratios, and age of onset distribution. In addition, it incorporates sensitivity analyses to assess the robustness of cosegregation evidence, and offers support in clinical interpretation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The shinyseg app is freely available at https:\/\/chrcarrizosa.shinyapps.io\/shinyseg, with documentation and complete R source code on https:\/\/chrcarrizosa.github.io\/shinyseg and https:\/\/github.com\/chrcarrizosa\/shinyseg.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae201","type":"journal-article","created":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T18:13:20Z","timestamp":1712772800000},"source":"Crossref","is-referenced-by-count":3,"title":["shinyseg: a web application for flexible cosegregation and sensitivity analysis"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3919-0011","authenticated-orcid":false,"given":"Christian","family":"Carrizosa","sequence":"first","affiliation":[{"name":"Department of Medical Genetics, Oslo University Hospital and University of Oslo , 0424 Oslo, Norway"}]},{"given":"Dag E","family":"Undlien","sequence":"additional","affiliation":[{"name":"Department of Medical Genetics, Oslo University Hospital and University of Oslo , 0424 Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9134-4962","authenticated-orcid":false,"given":"Magnus D","family":"Vigeland","sequence":"additional","affiliation":[{"name":"Department of Forensic Sciences, Oslo University Hospital , 0424 Oslo, Norway"}]}],"member":"286","published-online":{"date-parts":[[2024,4,10]]},"reference":[{"key":"2024050409155892900_btae201-B1","doi-asserted-by":"crossref","first-page":"2052","DOI":"10.1038\/s41436-020-0920-4","article-title":"Considerations in assessing germline variant pathogenicity using cosegregation analysis","volume":"22","author":"Belman","year":"2020","journal-title":"Genet Med"},{"key":"2024050409155892900_btae201-B2","doi-asserted-by":"crossref","first-page":"948","DOI":"10.1038\/s41436-018-0285-0","article-title":"Splice-altering variant in COL11A1 as a cause of nonsyndromic hearing loss DFNA37","volume":"21","author":"Booth","year":"2019","journal-title":"Genet Med"},{"key":"2024050409155892900_btae201-B3","doi-asserted-by":"crossref","first-page":"1907","DOI":"10.1016\/j.ajhg.2021.09.003","article-title":"Classification of 101 BRCA1 and BRCA2 variants of uncertain significance by cosegregation study: a powerful approach","volume":"108","author":"Caputo","year":"2021","journal-title":"Am J Hum Genet"},{"key":"2024050409155892900_btae201-B4","author":"Chang","year":"2024"},{"key":"2024050409155892900_btae201-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.cancergen.2021.01.005","article-title":"Lynch syndrome and Muir-Torre phenotype associated with a recurrent variant in the 3'UTR of the MSH6 gene","volume":"254-255","author":"Cini","year":"2021","journal-title":"Cancer Genet"},{"key":"2024050409155892900_btae201-B6","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1016\/j.ajhg.2016.04.003","article-title":"Consideration of cosegregation in the pathogenicity classification of genomic variants","volume":"98","author":"Jarvik","year":"2016","journal-title":"Am J Hum Genet"},{"key":"2024050409155892900_btae201-B7","first-page":"460","article-title":"Easy calculations of lod scores and genetic risks on small computers","volume":"36","author":"Lathrop","year":"1984","journal-title":"Am J Hum Genet"},{"key":"2024050409155892900_btae201-B8","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/1471-2407-9-211","article-title":"A simple method for co-segregation analysis to evaluate the pathogenicity of unclassified variants; 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