{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T15:51:32Z","timestamp":1783612292893,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2020,6,4]],"date-time":"2020-06-04T00:00:00Z","timestamp":1591228800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Barts Charity - Strategic Research Large Project","award":["MGU0344"],"award-info":[{"award-number":["MGU0344"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and molecular processes. We have further expanded the range of user directed annotation fields available for the study of cancer sequencing data. These new additions facilitate investigations into cancer driver variants and targetable molecular alterations within input datasets. New user directed filtering options have been coupled with the addition of interactive graphical and visualization tools. These improvements streamline the analysis of variants derived from large sequencing datasets for the identification of biologically and clinically significant subsets in the data. SNPnexus is the most comprehensible web-based application currently available and these new set of updates ensures that it remains a state-of-the-art tool for researchers. SNPnexus is freely available at https:\/\/www.snp-nexus.org.<\/jats:p>","DOI":"10.1093\/nar\/gkaa420","type":"journal-article","created":{"date-parts":[[2020,5,12]],"date-time":"2020-05-12T13:18:51Z","timestamp":1589289531000},"page":"W185-W192","source":"Crossref","is-referenced-by-count":266,"title":["SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update)"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6862-6753","authenticated-orcid":false,"given":"Jorge","family":"Oscanoa","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lavanya","family":"Sivapalan","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emanuela","family":"Gadaleta","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abu Z","family":"Dayem\u00a0Ullah","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas\u00a0R","family":"Lemoine","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude","family":"Chelala","sequence":"first","affiliation":[{"name":"Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,6,4]]},"reference":[{"key":"2020062614044605900_B1","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1093\/bioinformatics\/btn653","article-title":"SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms","volume":"25","author":"Chelala","year":"2009","journal-title":"Bioinformatics"},{"key":"2020062614044605900_B2","doi-asserted-by":"crossref","first-page":"W65","DOI":"10.1093\/nar\/gks364","article-title":"SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)","volume":"40","author":"Dayem\u00a0Ullah","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020062614044605900_B3","doi-asserted-by":"crossref","first-page":"W109","DOI":"10.1093\/nar\/gky399","article-title":"SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine","volume":"46","author":"Dayem\u00a0Ullah","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020062614044605900_B4","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13073-018-0531-8","article-title":"Cancer genome interpreter annotates the biological and clinical relevance of tumor alterations","volume":"10","author":"Tamborero","year":"2018","journal-title":"Genome Med"},{"key":"2020062614044605900_B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nprot.2015.123","article-title":"SIFT missense predictions for genomes","volume":"11","author":"Vaser","year":"2016","journal-title":"Nat. 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