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SVInterpreter: a web-based tool for structural variants inspection and identification of possible disease-causing candidate genes

2021-08-28Conference object Open access
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dc.contributor.authorFino, Joana
dc.contributor.authorMarques, Barbara
dc.contributor.authorDong, Zirui
dc.contributor.authorDavid, Dezso
dc.date.accessioned2022-01-24T19:10:55Z
dc.date.available2022-01-24T19:10:55Z
dc.date.issued2021-08-28
dc.description.abstractIntroduction: With the advent of genomic sequencing, the identification of structural variants (SVs) is no longer a challenge, being possible to detect an average of 5 K SVs by individual. Contrarily, the annotation of the genome is incomplete, and the data is scattered along different databases, making SV manual evaluation complicated and time-consuming. Also, the available tools are limited on their scope. Thus, to address the need of a comprehensive application to assist evaluation of clinical outcome of SVs, we developed Structural Variant Interpreter (SVInterpreter). Methods: SVInterpreter is a free Python-CGI developed Web application able to analyze SVs using Topologically Associated Domains as genome units, within which genome browsers data, medically actionable genes, virtual gene panels and HPO similarity results, among other information, is retrieved. Results: We started by re-analysing 220 published SVs, of which about 50% were previously classified as VUS. SVInterpreter corroborated the previous classification in about 84% of the SVs. In about 5% of the SVs, SVInterpreter gave indication of possible position effect, through phenotype similarity, disrupted chromatin loops or genome wide association studies. Then, we show the applicability of SVInterpreter on the clinical setting, by inspecting 15 cases analysed by chromosomal microarray or genome sequencing. Conclusions: To our knowledge, SVInterpreter is the most comprehensive TAD based tool to assist prediction of clinical outcome of SVs. Based on gathered information, identification of possible disease-causing candidate genes and SVs is easily achievable. SVInterpreter is available at http://dgrctools-insa.min-saude.pt/cgi-bin/SVInterpreter.pypt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.urihttp://hdl.handle.net/10400.18/7877
dc.language.isoengpt_PT
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/pt_PT
dc.subjectSVInterpreterpt_PT
dc.subjectIdentification of Structural Variantspt_PT
dc.subjectFerramenta Bioinformáticapt_PT
dc.subjectAssociação Genótipo-fenótipopt_PT
dc.subjectDoenças Genéticaspt_PT
dc.subjectGenómica Funcional e Estruturalpt_PT
dc.titleSVInterpreter: a web-based tool for structural variants inspection and identification of possible disease-causing candidate genespt_PT
dc.typeconference object
dspace.entity.typePublication
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/HMSP-ICT%2F0016%2F2013/PT
oaire.citation.conferencePlace(online)pt_PT
oaire.citation.titleEuropean Human Genetics Conference (EHGC 2021), Sociedade Portuguesa de Genética Humana, 28–31 August 2021pt_PT
oaire.fundingStream3599-PPCDT
person.familyNameVieira Fino
person.familyNameNunes Lopes Marques
person.familyNameDong
person.familyNameDavid
person.givenNameJoana Rita
person.givenNameBárbara Sofia
person.givenNameZirui Elvis
person.givenNameDezso
person.identifier.ciencia-idDE1B-2588-B3A8
person.identifier.ciencia-id581A-57C7-6B58
person.identifier.ciencia-id1B1D-C917-A0EF
person.identifier.orcid0000-0002-3266-9011
person.identifier.orcid0000-0002-4392-4858
person.identifier.orcid0000-0002-3626-6500
person.identifier.orcid0000-0003-2293-590X
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typeconferenceObjectpt_PT
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