{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T11:26:06Z","timestamp":1784805966814,"version":"3.55.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2018,5,31]],"date-time":"2018-05-31T00:00:00Z","timestamp":1527724800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011102","name":"European Union Seventh Frame-work Program","doi-asserted-by":"publisher","award":["FP7\/2007-2013"],"award-info":[{"award-number":["FP7\/2007-2013"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011102","name":"European Union Seventh Frame-work Program","doi-asserted-by":"publisher","award":["305,444"],"award-info":[{"award-number":["305,444"]}],"id":[{"id":"10.13039\/100011102","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,2]]},"DOI":"10.1093\/nar\/gky471","type":"journal-article","created":{"date-parts":[[2018,5,16]],"date-time":"2018-05-16T07:09:38Z","timestamp":1526454578000},"page":"W545-W553","source":"Crossref","is-referenced-by-count":175,"title":["VarAFT: a variant annotation and filtration system for human next generation sequencing data"],"prefix":"10.1093","volume":"46","author":[{"given":"Jean-Pierre","family":"Desvignes","sequence":"first","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc","family":"Bartoli","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Val\u00e9rie","family":"Delague","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Krahn","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"},{"name":"APHM, H\u00f4pital d\u2019Enfants de la Timone, D\u00e9partement de G\u00e9n\u00e9tique M\u00e9dicale et de Biologie Cellulaire, 13385 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morgane","family":"Miltgen","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"B\u00e9roud","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"},{"name":"APHM, H\u00f4pital d\u2019Enfants de la Timone, D\u00e9partement de G\u00e9n\u00e9tique M\u00e9dicale et de Biologie Cellulaire, 13385 Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5905-3591","authenticated-orcid":false,"given":"David","family":"Salgado","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, MMG, 13005,\u00a0Marseille, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,5,31]]},"reference":[{"key":"key\n\t\t\t\t20180630070745_B1","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180630070745_B2","first-page":"518","article-title":"[Orphanet: a European database for rare diseases]","volume":"152","author":"Weinreich","year":"2008","journal-title":"Ned. Tijdschr. Geneeskd."},{"key":"key\n\t\t\t\t20180630070745_B3","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/nbt.3237","article-title":"Good laboratory practice for clinical next-generation sequencing informatics pipelines","volume":"33","author":"Gargis","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20180630070745_B4","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.1002\/humu.23110","article-title":"How to identify pathogenic mutations among all those variations: variant annotation and filtration in the genome sequencing era","volume":"37","author":"Salgado","year":"2016","journal-title":"Hum. Mutat."},{"key":"key\n\t\t\t\t20180630070745_B5","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1038\/nrg.2017.52","article-title":"Settling the score: variant prioritization and Mendelian disease","volume":"18","author":"Eilbeck","year":"2017","journal-title":"Nat. Rev. Genet."},{"key":"key\n\t\t\t\t20180630070745_B6","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1111\/cge.12654","article-title":"Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care","volume":"89","author":"Sawyer","year":"2016","journal-title":"Clin. Genet."},{"key":"key\n\t\t\t\t20180630070745_B7","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1186\/s12859-017-1654-4","article-title":"QueryOR: a comprehensive web platform for genetic variant analysis and prioritization","volume":"18","author":"Bertoldi","year":"2017","journal-title":"BMC Bioinformatics"},{"issue":"Suppl. 2","key":"key\n\t\t\t\t20180630070745_B8","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1186\/s12864-016-2722-2","article-title":"VarElect: the phenotype-based variation prioritizer of the GeneCards Suite","volume":"17","author":"Stelzer","year":"2016","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20180630070745_B9","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1093\/bib\/bbv051","article-title":"VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files","volume":"17","author":"Hart","year":"2015","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20180630070745_B10","doi-asserted-by":"crossref","first-page":"W88","DOI":"10.1093\/nar\/gku407","article-title":"A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies","volume":"42","author":"Alem\u00e1n","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B11","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B12","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180630070745_B13","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.atg.2016.01.005","article-title":"Ethical issues in consumer genome sequencing: use of consumers' samples and data","volume":"8","author":"Niemiec","year":"2016","journal-title":"Appl. Transl. Genom."},{"key":"key\n\t\t\t\t20180630070745_B14","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.3324\/haematol.2016.160192","article-title":"Exome sequencing identifies recurrent BCOR gene alterations and the absence of KLF2, TNFAIP3 and MYD88 mutations in splenic diffuse red pulp small B-cell lymphoma","volume":"102","author":"Jallades","year":"2017","journal-title":"Haematologica"},{"key":"key\n\t\t\t\t20180630070745_B15","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.3324\/haematol.2016.153577","article-title":"Macrothrombocytopenia and dense granule deficiency associated with FLI1 variants: ultrastructural and pathogenic features","volume":"102","author":"Saultier","year":"2017","journal-title":"Haematologica"},{"key":"key\n\t\t\t\t20180630070745_B16","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.metabol.2017.03.011","article-title":"Exome sequencing reveals a de novo POLD1 mutation causing phenotypic variability in mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL)","volume":"71","author":"Elouej","year":"2017","journal-title":"Metab. Clin. Exp."},{"key":"key\n\t\t\t\t20180630070745_B17","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/infdis\/jix277","article-title":"Exome sequencing identifies two variants of the alkylglycerol monooxygenase gene (AGMO) as a cause of relapses in visceral leishmaniasis in children, in Sudan","volume":"216","author":"Marquet","year":"2017","journal-title":"J. Infect. Dis."},{"key":"key\n\t\t\t\t20180630070745_B18","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1002\/mus.25638","article-title":"Genetic Characterization of a French Cohort of GNE-mutation negative inclusion body myopathy patients with exome sequencing","volume":"56","author":"Cerino","year":"2017","journal-title":"Muscle Nerve"},{"key":"key\n\t\t\t\t20180630070745_B19","doi-asserted-by":"crossref","first-page":"E21","DOI":"10.3390\/cells5020021","article-title":"A heterozygous ZMPSTE24 mutation associated with severe metabolic syndrome, ectopic fat accumulation, and dilated cardiomyopathy","volume":"5","author":"Galant","year":"2016","journal-title":"Cells"},{"key":"key\n\t\t\t\t20180630070745_B20","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1002\/mds.26717","article-title":"Novel heterozygous mutation in ANO3 responsible for craniocervical dystonia","volume":"31","author":"Miltgen","year":"2016","journal-title":"Mov. Disord."},{"key":"key\n\t\t\t\t20180630070745_B21","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1182\/blood-2015-04-642496","article-title":"A mutation in the Gardos channel is associated with hereditary xerocytosis","volume":"126","author":"Rapetti-Mauss","year":"2015","journal-title":"Blood"},{"key":"key\n\t\t\t\t20180630070745_B22","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/gim.2016.190","article-title":"Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics","volume":"19","author":"Kalia","year":"2017","journal-title":"Genet. Med."},{"key":"key\n\t\t\t\t20180630070745_B23","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630070745_B24","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/humu.22932","article-title":"dbNSFP v3.0: a one-stop database of functional predictions and annotations for human nonsynonymous and splice-site SNVs","volume":"37","author":"Liu","year":"2016","journal-title":"Hum. Mutat."},{"key":"key\n\t\t\t\t20180630070745_B25","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM\u00ae), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B26","doi-asserted-by":"crossref","first-page":"D966","DOI":"10.1093\/nar\/gkt1026","article-title":"The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data","volume":"42","author":"K\u00f6hler","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B27","doi-asserted-by":"crossref","first-page":"D1049","DOI":"10.1093\/nar\/gku1179","article-title":"Gene Ontology Consortium: going forward","volume":"43","author":"Gene Ontology Consortium","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B28","doi-asserted-by":"crossref","first-page":"D481","DOI":"10.1093\/nar\/gkv1351","article-title":"The reactome pathway Knowledgebase","volume":"44","author":"Fabregat","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B29","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"Kanehisa","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B30","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkn653","article-title":"PID: the Pathway Interaction Database","volume":"37","author":"Schaefer","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B31","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1002\/humu.22965","article-title":"UMD-Predictor: a High throughput sequencing compliant system for pathogenicity prediction of any human cDNA substitution","volume":"37","author":"Salgado","year":"2016","journal-title":"Hum. Mutat."},{"key":"key\n\t\t\t\t20180630070745_B32","doi-asserted-by":"crossref","first-page":"e67","DOI":"10.1093\/nar\/gkp215","article-title":"Human Splicing Finder: an online bioinformatics tool to predict splicing signals","volume":"37","author":"Desmet","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630070745_B33","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief. Bioinform."},{"key":"key\n\t\t\t\t20180630070745_B34","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/ejhg.2015.226","article-title":"Guidelines for diagnostic next-generation sequencing","volume":"24","author":"Matthijs","year":"2016","journal-title":"Eur. J. Hum. Genet."},{"key":"key\n\t\t\t\t20180630070745_B35","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1136\/jnnp-2014-309663","article-title":"Improving molecular diagnosis of distal myopathies by targeted next-generation sequencing","volume":"87","author":"Sevy","year":"2015","journal-title":"J. Neurol. Neurosurg. Psychiatr."},{"key":"key\n\t\t\t\t20180630070745_B36","doi-asserted-by":"crossref","first-page":"e70151","DOI":"10.1371\/journal.pone.0070151","article-title":"Filtering for compound heterozygous sequence variants in non-consanguineous pedigrees","volume":"8","author":"Kamphans","year":"2013","journal-title":"PLoS One"},{"key":"key\n\t\t\t\t20180630070745_B37","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/ng.2892","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180630070745_B38","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1111\/jns.12175","article-title":"Screening for SH3TC2 gene mutations in a series of demyelinating recessive Charcot-Marie-Tooth disease (CMT4)","volume":"21","author":"Piscosquito","year":"2016","journal-title":"J. Peripher. Nerv. Syst."},{"issue":"Suppl. 3","key":"key\n\t\t\t\t20180630070745_B39","doi-asserted-by":"crossref","first-page":"S780","DOI":"10.1007\/s11606-014-2908-8","article-title":"RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research","volume":"29","author":"Thompson","year":"2014","journal-title":"J. Gen. Intern. Med."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/W1\/W545\/25110397\/gky471.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,17]],"date-time":"2019-10-17T23:15:05Z","timestamp":1571354105000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W545\/5025894"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,31]]},"references-count":39,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2018,5,31]]},"published-print":{"date-parts":[[2018,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky471","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,2]]},"published":{"date-parts":[[2018,5,31]]}}}