Publication
TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangements
| dc.contributor.author | Fino, Joana | |
| dc.contributor.author | David, Dezso | |
| dc.date.accessioned | 2021-03-13T17:23:15Z | |
| dc.date.available | 2021-03-13T17:23:15Z | |
| dc.date.issued | 2020-02 | |
| dc.description.abstract | With the advance of genome sequencing technologies, it is currently possible to identify a large number of chromosomal or genomic structural variants in a single individual. Therefore, the validation and manual assessment of structural variants clinical significance becomes unpractical and time consuming when performed with previous methodologies. In order to assist the validation process, we developed two clinically inspired bioinformatics tools - TADGConTool and CNV-ConTool. They were developed in python with a Common Gateway Interface that allows easy and user-friendly access through any standards compliant web browser (available at: http://dgrctools.insa.min- saude.pt/). TAD-GConTool collects genomic information of breakpoint regions, using topological associated domains (TADs) as reference. It then accesses public databases to retrieve elements found inside TADs, and the associated clinical phenotypes, highlighting those causing dominant disorders. CNV-ConTool searches for overlaps between patient-specific breakpoints and CNVs, and those reported in several public databases. These tools were already successfully applied to about 40 cases studied under the project “Next-gen cytogenetics enters clinical care and annotates the human genome” (HMSPICT/0016/2013) and are now being made available to the broader scientific community. These tools allowed a faster and more informed evaluation of the genomic structural variants, helping select potential pathogenic variants, either by identifying phenotype- associated genes, or by overlapping deletions and duplications with already described benign or pathogenic CNVs. As genome sequencing is becoming more and more a routine method for identification of chromosomal and genomic structural variants, such clinically oriented bioinformatics tools are crucial and represent the first level of analysis toward personalized genomic medicine. This research was supported by national funds through FCT - Fundação para a Ciência e a Tecnologia, Research Grant HMSP-ICT/0016/2013. | pt_PT |
| dc.description.sponsorship | Study supported by Fundação para a Ciência e Tecnologia project HMSP-ICT/0016/2013. | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.citation | Fino J, David D. TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangements. Bioinformatic Open Days, Braga - Portugal, 2020 | pt_PT |
| dc.identifier.uri | http://hdl.handle.net/10400.18/7473 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | pt_PT |
| dc.subject | Bioinformatic Tools | pt_PT |
| dc.subject | Genomics | pt_PT |
| dc.subject | Structural Variants | pt_PT |
| dc.subject | Phenotypic Outcome Prediction | pt_PT |
| dc.subject | Genómica Funcional e Estrutural | pt_PT |
| dc.title | TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangements | pt_PT |
| dc.type | conference object | |
| dspace.entity.type | Publication | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/3599-PPCDT/HMSP-ICT%2F0016%2F2013/PT | |
| oaire.citation.conferencePlace | Braga, Portugal | pt_PT |
| oaire.citation.title | Bioinformatic Open Days 2020, 19-21 February 2020 | pt_PT |
| oaire.fundingStream | 3599-PPCDT | |
| person.familyName | Vieira Fino | |
| person.familyName | David | |
| person.givenName | Joana Rita | |
| person.givenName | Dezso | |
| person.identifier.ciencia-id | DE1B-2588-B3A8 | |
| person.identifier.orcid | 0000-0002-3266-9011 | |
| 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.rights | openAccess | pt_PT |
| rcaap.type | conferenceObject | pt_PT |
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