Publication
SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants
| dc.contributor.author | Fino, Joana | |
| dc.contributor.author | Marques, Barbara | |
| dc.contributor.author | Dong, Zirui | |
| dc.contributor.author | David, Dezso | |
| dc.date.accessioned | 2022-03-09T18:05:36Z | |
| dc.date.available | 2022-03-09T18:05:36Z | |
| dc.date.issued | 2021-12-01 | |
| dc.description | Erratum Front Genet. 2022 Feb 25;13:868306. doi: 10.3389/fgene.2022.868306. eCollection 2022. | |
| dc.description.abstract | With the advent of genomic sequencing, a number of balanced and unbalanced structural variants (SVs) can be detected per individual. Mainly due to incompleteness and the scattered nature of the available annotation data of the human genome, manual interpretation of the SV’s clinical significance is laborious and cumbersome. Since bioinformatic tools developed for this task are limited, a comprehensive tool to assist clinical outcome prediction of SVs is warranted. Herein, we present SVInterpreter, a free Web application, which analyzes both balanced and unbalanced SVs using topologically associated domains (TADs) as genome units. Among others, gene-associated data (as function and dosage sensitivity), phenotype similarity scores, and copy number variants (CNVs) scoring metrics are retrieved for an informed SV interpretation. For evaluation, we retrospectively applied SVInterpreter to 97 balanced (translocations and inversions) and 125 unbalanced (deletions, duplications, and insertions) previously published SVs, and 145 SVs identified from 20 clinical samples. Our results showed the ability of SVInterpreter to support the evaluation of SVs by (1) confirming more than half of the predictions of the original studies, (2) decreasing 40% of the variants of uncertain significance, and (3) indicating several potential position effect events. To our knowledge, SVInterpreter is the most comprehensive TAD-based tool to identify the possible disease-causing candidate genes and to assist prediction of the clinical outcome of SVs. SVInterpreter is available at http://dgrctools-insa.min-saude.pt/cgi-bin/SVInterpreter.py. | pt_PT |
| dc.description.sponsorship | This research was supported by national funds through FCT—Fundação para a Ciência e a Tecnologia, Research Grant HMSP-ICT/0016/2013 of the Harvard Medical School—Portugal Program in Translational Research and Information | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | Front Genet. 2021 Dec 1;12:757170. doi: 10.3389/fgene.2021.757170 | pt_PT |
| dc.identifier.doi | 10.3389/fgene.2021.757170 | pt_PT |
| dc.identifier.eissn | 1664-8021 | |
| dc.identifier.uri | http://hdl.handle.net/10400.18/7980 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.publisher | Frontiers Media | pt_PT |
| dc.relation.publisherversion | https://www.frontiersin.org/articles/10.3389/fgene.2021.757170/full | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | pt_PT |
| dc.subject | SVInterpreter | pt_PT |
| dc.subject | Balanced Structural Variants | pt_PT |
| dc.subject | Bioinformatic Web-Tool | pt_PT |
| dc.subject | Clinical Outcome Prediction | pt_PT |
| dc.subject | Copy Number Variants | pt_PT |
| dc.subject | Phenotypic Comparison | pt_PT |
| dc.subject | Topologically Associated Domains | pt_PT |
| dc.subject | Doenças Genéticas | pt_PT |
| dc.subject | Genómica Funcional e Estrutural | pt_PT |
| dc.title | SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants | pt_PT |
| dc.type | journal article | |
| dspace.entity.type | Publication | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/3599-PPCDT/HMSP-ICT%2F0016%2F2013/PT | |
| oaire.citation.startPage | 757170 | pt_PT |
| oaire.citation.title | Frontiers in Genetics | pt_PT |
| oaire.citation.volume | 12 | pt_PT |
| oaire.fundingStream | 3599-PPCDT | |
| person.familyName | Vieira Fino | |
| person.familyName | Nunes Lopes Marques | |
| person.familyName | Dong | |
| person.familyName | David | |
| person.givenName | Joana Rita | |
| person.givenName | Bárbara Sofia | |
| person.givenName | Zirui Elvis | |
| person.givenName | Dezso | |
| person.identifier.ciencia-id | DE1B-2588-B3A8 | |
| person.identifier.ciencia-id | 581A-57C7-6B58 | |
| person.identifier.ciencia-id | 1B1D-C917-A0EF | |
| person.identifier.orcid | 0000-0002-3266-9011 | |
| person.identifier.orcid | 0000-0002-4392-4858 | |
| person.identifier.orcid | 0000-0002-3626-6500 | |
| person.identifier.orcid | 0000-0003-2293-590X | |
| project.funder.identifier | http://doi.org/10.13039/501100001871 | |
| project.funder.name | Fundação para a Ciência e a Tecnologia | |
| rcaap.embargofct | Acesso de acordo com política editorial da revista. | pt_PT |
| rcaap.rights | openAccess | pt_PT |
| rcaap.type | article | pt_PT |
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