Publication
Detection of structural variants in the human genome using nanopore sequencing
| dc.contributor.author | Silva, Catarina | |
| dc.contributor.author | Vieira, Luís | |
| dc.date.accessioned | 2020-05-25T14:56:04Z | |
| dc.date.available | 2020-05-25T14:56:04Z | |
| dc.date.issued | 2019-05-10 | |
| dc.description.abstract | Nanopore sequencing is a recent technology that allows direct real-time sequencing of DNA/RNA molecules with read lengths as long as the size of the original fragments. The characteristics of nanopore sequencing make it well suited for whole genome sequencing and as a preferential tool to identify structural variants (SV), namely those associated with tumours. In this work, we present a complete workflow to detect SV in tumour samples using nanopore sequencing. We used a tumour sample to prepare DNA libraries using the Rapid Sequencing kit (Oxford Nanopore Technologies-ONT), sequenced those on the MinION device (ONT) and implemented a pipeline for SV detection using multiple bioinformatics tools. The MinION generated a total of 2.34 Gb of sequence. Overall, 87.8% of reads had a quality (Q) value >7 (quality threshold). The longest read obtained had 74369 bases and the mean read length was of 4508 bases. A total of 3470 SV were identified, including deletions, duplications, translocations, insertions and inversions. Nanopore sequencing is a fast and sensitive approach of great potential for human genomics research, namely in the detection of SV in the human genome. | pt_PT |
| dc.description.sponsorship | This work was supported by Centre for Toxicogenomics and Human Health - UID/BIM/00009/2019 - and GenomePT project – POCI-01-0145-FEDER-022184. | pt_PT |
| dc.description.version | info:eu-repo/semantics/publishedVersion | pt_PT |
| dc.identifier.uri | http://hdl.handle.net/10400.18/6795 | |
| dc.language.iso | eng | pt_PT |
| dc.peerreviewed | yes | pt_PT |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc/4.0/ | pt_PT |
| dc.subject | Nanopore Sequencing | pt_PT |
| dc.subject | Whole Genome Sequencing | pt_PT |
| dc.subject | Long Reads | pt_PT |
| dc.subject | Sequencing | pt_PT |
| dc.subject | Doenças Genéticas | pt_PT |
| dc.subject | Sequenciação | pt_PT |
| dc.title | Detection of structural variants in the human genome using nanopore sequencing | pt_PT |
| dc.type | conference object | |
| dspace.entity.type | Publication | |
| oaire.awardURI | info:eu-repo/grantAgreement/FCT/5876/UID%2FBIM%2F00009%2F2013/PT | |
| oaire.citation.conferencePlace | Vairão, Vila do Conde, Portugal | pt_PT |
| oaire.citation.title | GenomePT Symposium - CIBIO-InBIO, 10 May 2019 | pt_PT |
| oaire.fundingStream | 5876 | |
| 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 |
| relation.isProjectOfPublication | e9cc9728-4f09-4e3a-b30d-53d4429986fb | |
| relation.isProjectOfPublication.latestForDiscovery | e9cc9728-4f09-4e3a-b30d-53d4429986fb |
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