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Detection of copy number variants in the human genome: Is long-read sequencing an alternative to genomic microarrays?

2023-11Conference object Restricted access
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dc.contributor.authorSilva, Catarina
dc.contributor.authorFerrão, José
dc.contributor.authorMarques, Barbara
dc.contributor.authorPedro, Sónia
dc.contributor.authorCorreia, Hildeberto
dc.contributor.authorRodrigues, António Sebastião
dc.contributor.authorVieira, Luís
dc.date.accessioned2024-02-27T17:26:22Z
dc.date.available2024-02-27T17:26:22Z
dc.date.issued2023-11
dc.description.abstractIntroduction: Copy number variations (CNVs) represent ~13% of the human genome and can harbour important genes and regulatory elements. High-resolution whole genome microarray (MA) analysis is the gold standard tool for detection of CNVs associated with genetic disorders. While short-read sequencing (SRS) can address SV detection, the use of long-read sequencing as proven to overcome SRS mapping inaccuracy in highly repetitive DNA regions and improve genome contiguity. We applied whole genome nanopore sequencing (NS) to call CNVs and compared the results with those obtained by microarray. Methodology: Genomic DNA from 2 cell lines (EOL-1 and 697) were processed using the CytoSan HD Array (Affymetrix) and ChAS software (ThermoFisher). A minimum CNV calling size threshold of 35 Kb was used. DNA was also sequenced on the MinION device (Oxford Nanopore Technologies) following a rapid library preparation method. Sequencing data were basecalled using Guppy, mapped with LRA, and SVs called using both CuteSV and Sniffles2. Sanger sequencing was performed to demonstrate breakpoint positions for 3 CNVs. R packages were used to perform comparisons between MA and NS data. Results: A total of 49 CNVs were confirmed after curated MA analysis in both cell lines, ranging in size from 35 Kb to 79 Mb. From those, 43 CNVs (87.7%) were called in nanopore data by either one (4 CNVs) or both (39 CNVs) callers with a mean whole genome coverage of ~12X. Six of 43 CNVs were called as inversions instead. In 3 CNVs the size of the variant was found to be smaller (ranging from ~5 to 22 Kb) than the threshold of MA analysis. The correlation between CNV sizes obtained with MA and NS was of 0.71 with Sniffles2 and 0.74 with CuteSV, whereas the correlation between callers was of 0.99. The breakpoint precision obtained for NS was much higher (ranging for CuteSV from 2 to 42 bp; and for Sniffles2 from 0 to 87 bp) than the one obtained for MA (ranging from 774 to 7618 bp). Conclusions: NS technology proved to be technically effective in the detection of CNVs of different types and sizes and thus posing itself as an alternative to MA in the detection of pathogenic SVs associated with genetic diseases. However, NS data analysis requires fine-tuning of the analysis conditions as well as the use of different methods, for greater reliability of results in a clinical context.pt_PT
dc.description.sponsorshipFunding: This work is a result of the GenomePT project (POCI-01- 0145-FEDER-022184), supported by COMPETE 2020 – Operational Programme for Competitiveness and Internationalisation (POCI), Lisboa Portugal Regional Operational Programme (Lisboa2020), Algarve Portugal Regional Operational Programme (CRESC Algarve2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF), and by Fundação para a Ciência e a Tecnologia (FCT). This work was also supported by Fundos FEDER through the Programa Operacional Factores de Competitividade – COMPETE and by Fundos Nacionais through the FCT within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health-ToxOmicspt_PT
dc.description.versionN/Apt_PT
dc.identifier.urihttp://hdl.handle.net/10400.18/9152
dc.language.isoengpt_PT
dc.relationNational Facility for genome sequencing and analysis
dc.relationCentre for Toxicogenomics and Human Health
dc.subjectLong-Read Sequencingpt_PT
dc.subjectWhole Human Genome Sequencingpt_PT
dc.subjectStructural Variationpt_PT
dc.subjectBioinformaticspt_PT
dc.subjectNanopore Sequencingpt_PT
dc.subjectTecnologias de Análise de DNApt_PT
dc.titleDetection of copy number variants in the human genome: Is long-read sequencing an alternative to genomic microarrays?pt_PT
dc.typeconference object
dspace.entity.typePublication
oaire.awardTitleNational Facility for genome sequencing and analysis
oaire.awardTitleCentre for Toxicogenomics and Human Health
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/9444 - RNIIIE/PINFRA%2F22184%2F2016/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F00009%2F2019/PT
oaire.citation.conferencePlaceLisboa, Portugalpt_PT
oaire.citation.title3rd GenomePT Symposium 2023 - Symposium of the National Research infrastructure for Genome Sequencing and Analysis, 17 novembro 2023pt_PT
oaire.fundingStream9444 - RNIIIE
oaire.fundingStream6817 - DCRRNI ID
person.familyNameSilva
person.familyNamede Oliveira Alves Ferrão
person.familyNameNunes Lopes Marques
person.familyNameRodrigues
person.familyNameVieira
person.givenNameCatarina
person.givenNameJosé Cândido
person.givenNameBárbara Sofia
person.givenNameAntónio Sebastião
person.givenNameLuís
person.identifierA-1930-2013
person.identifier.ciencia-idF316-76B8-6216
person.identifier.ciencia-idC01F-F31D-F997
person.identifier.ciencia-id581A-57C7-6B58
person.identifier.ciencia-id9012-44BE-F79D
person.identifier.orcid0000-0002-0864-2572
person.identifier.orcid0000-0002-2553-7467
person.identifier.orcid0000-0002-4392-4858
person.identifier.orcid0000-0002-8139-4595
person.identifier.orcid0000-0002-7703-1409
person.identifier.scopus-author-id36130557500
person.identifier.scopus-author-id55781566100
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsrestrictedAccesspt_PT
rcaap.typeconferenceObjectpt_PT
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