{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T17:08:01Z","timestamp":1776013681342,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T00:00:00Z","timestamp":1709251200000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R03CA230366"],"award-info":[{"award-number":["R03CA230366"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA237562"],"award-info":[{"award-number":["R01CA237562"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U2CHL138346"],"award-info":[{"award-number":["U2CHL138346"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R03CA287169"],"award-info":[{"award-number":["R03CA287169"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics\u2014Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5\/BP6). This tool facilitates large-scale, clinically focused classification of germline sequence variants in a research setting.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>AutoGVP is an open source dockerized workflow implemented in R and freely available on GitHub at https:\/\/github.com\/diskin-lab-chop\/AutoGVP.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae114","type":"journal-article","created":{"date-parts":[[2024,2,27]],"date-time":"2024-02-27T01:26:24Z","timestamp":1708997184000},"source":"Crossref","is-referenced-by-count":12,"title":["AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6274-2841","authenticated-orcid":false,"given":"Jung","family":"Kim","sequence":"first","affiliation":[{"name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute , Rockville, MD 20850, United States"}]},{"given":"Ammar S","family":"Naqvi","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Ryan J","family":"Corbett","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Rebecca S","family":"Kaufman","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Health Informatics, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Oncology, Children's Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Zalman","family":"Vaksman","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Health Informatics, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Oncology, Children's Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Miguel A","family":"Brown","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Daniel P","family":"Miller","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2771-2572","authenticated-orcid":false,"given":"Saksham","family":"Phul","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Zhuangzhuang","family":"Geng","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Phillip B","family":"Storm","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Adam C","family":"Resnick","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"given":"Douglas R","family":"Stewart","sequence":"additional","affiliation":[{"name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute , Rockville, MD 20850, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2171-3627","authenticated-orcid":false,"given":"Jo Lynne","family":"Rokita","sequence":"additional","affiliation":[{"name":"Center for Data-Driven Discovery in Biomedicine, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Neurosurgery, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7200-8939","authenticated-orcid":false,"given":"Sharon J","family":"Diskin","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Health Informatics, Children\u2019s Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Division of Oncology, Children's Hospital of Philadelphia , Philadelphia, PA 19104, United States"},{"name":"Department of Pediatrics, University of Pennsylvania , Philadelphia, PA 19104, United States"}]}],"member":"286","published-online":{"date-parts":[[2024,2,29]]},"reference":[{"key":"2024032107582598900_btae114-B1","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1002\/humu.23626","article-title":"Recommendations for interpreting the loss of function PVS1 ACMG\/AMP variant criterion","volume":"39","author":"Abou Tayoun","year":"2018","journal-title":"Hum. Mutat"},{"key":"2024032107582598900_btae114-B2","author":"Adam","year":"2023"},{"key":"2024032107582598900_btae114-B3","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.1038\/gim.2018.42","article-title":"The ACMG\/AMP reputable source criteria for the interpretation of sequence variants","volume":"20","author":"Biesecker","year":"2018","journal-title":"Genet. 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Engl. J. Med"},{"key":"2024032107582598900_btae114-B8","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for molecular pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. 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