Repository logo
 
Publication

Comparative analysis of hybrid‑SNP microarray and nanopore sequencing for detection of large‑sized copy number variants in the human genome

2025-07-23Journal article Open access
Simple item page
datacite.subject.fosCiências Naturais::Ciências Biológicas
datacite.subject.sdg03:Saúde de Qualidade
dc.contributor.authorSilva, Catarina
dc.contributor.authorFerrão, José
dc.contributor.authorMarques, Bárbara
dc.contributor.authorPedro, Sónia
dc.contributor.authorCorreia, Hildeberto
dc.contributor.authorValente, Ana
dc.contributor.authorRodrigues, António Sebastião
dc.contributor.authorVieira, Luís
dc.date.accessioned2025-11-10T13:23:17Z
dc.date.available2025-11-10T13:23:17Z
dc.date.issued2025-07-23
dc.description.abstractBackground: Nanopore sequencing is a technology that holds great promise for identifying all types of human genome variations, particularly structural variations. In this work, we used nanopore sequencing technology to sequence 2 human cell lines at low depth of coverage to call copy number variations (CNV), and compared the results variant by variant with chromosomal microarray (CMA) results. Results: We analysed sequencing data using CuteSV and Sniffles2 variant callers, compared breakpoints based on hybrid-SNP microarray, nanopore sequencing and Sanger sequencing, and analysed CNV coverage. From a total of 48 high confidence variants (truth set), variant calling detected 79% of the truth set variants, increasing to 86% for interstitial CNV. Simultaneous use of the 2 callers slightly increased variant calling. Both callers performed better when calling CNV losses than gains. Variant sizes from CMA and nanopore sequencing showed an excellent correlation, with breakpoints determined by nanopore sequencing differing by only 20 base pairs on average from Sanger sequencing. Nanopore sequencing also revealed that four variants concealed genomic inversions undetectable by CMA. In the 10 CNV not called in nanopore sequencing, 8 showed coverage evidence of genomic loss or gain, highlighting the need to improve SV calling algorithms performance. Conclusions: Nanopore sequencing offers advantages over CMA for structural variant detection, including the identification of multiple variant types and their breakpoints with increased precision. However, further improvements in variant calling algorithms are still needed for nanopore sequencing to become a highly robust and standardized approach for a comprehensive analysis of genomic structural variation.eng
dc.description.sponsorshipThis work is a result of the GenomePT project (POCI-01–0145-FEDER-022184), supported by COMPETE 2020—Operational Programme for Competitiveness and Internationalization (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 Fundação para a Ciência e a Tecnologia within the scope of the project UID/BIM/00009/2019 (Centre for Toxicogenomics and Human Health -ToxOmics).
dc.identifier.citationMol Cytogenet. 2025 Jul 23;18(1):18. doi: 10.1186/s13039-025-00721-8
dc.identifier.doi10.1186/s13039-025-00721-8
dc.identifier.issn1755-8166
dc.identifier.pmid40702511
dc.identifier.urihttp://hdl.handle.net/10400.18/10573
dc.language.isoeng
dc.peerreviewedyes
dc.publisherBioMed Central
dc.relationCentre for Toxicogenomics and Human Health
dc.relationPOCI-01-0145-FEDER-022184
dc.relation.hasversionhttps://molecularcytogenetics.biomedcentral.com/articles/10.1186/s13039-025-00721-8
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectCopy Number Variation
dc.subjectHybrid-SNP Microarray
dc.subjectNanopore Sequencing
dc.subjectStructural Variation
dc.subjectThird-Generation Sequencing
dc.subjectVariant Calling
dc.subjectWhole Genome Sequencing
dc.subjectTecnologias de Análise de DNA
dc.titleComparative analysis of hybrid‑SNP microarray and nanopore sequencing for detection of large‑sized copy number variants in the human genomeeng
dc.typejournal article
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM1_ESM.pptx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM2_ESM.pptx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM3_ESM.pptx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM4_ESM.pptx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM5_ESM.pptx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM6_ESM.pdf
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM7_ESM.pdf
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM8_ESM.docx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM9_ESM.docx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM10_ESM.docx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM11_ESM.docx
dcterms.referenceshttps://static-content.springer.com/esm/art%3A10.1186%2Fs13039-025-00721-8/MediaObjects/13039_2025_721_MOESM12_ESM.docx
dspace.entity.typePublication
oaire.awardTitleCentre for Toxicogenomics and Human Health
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F00009%2F2019/PT
oaire.citation.issue1
oaire.citation.startPage18
oaire.citation.titleMolecular Cytogenetics
oaire.citation.volume18
oaire.fundingStream6817 - DCRRNI ID
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
relation.isProjectOfPublicationda24f146-9eb6-459d-8a8d-8adef9929107
relation.isProjectOfPublication.latestForDiscoveryda24f146-9eb6-459d-8a8d-8adef9929107

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
s13039-025-00721-8.pdf
Size:
3.07 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
4.03 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

DGH - Artigos em revistas internacionais
INSA - Artigos em revistas internacionais