Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome
Abstract Background 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...
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BMC
2025-07-01
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| Series: | Molecular Cytogenetics |
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| Online Access: | https://doi.org/10.1186/s13039-025-00721-8 |
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| author | Catarina Silva José Ferrão Bárbara Marques Sónia Pedro Hildeberto Correia Ana Valente António Sebastião Rodrigues Luís Vieira |
| author_facet | Catarina Silva José Ferrão Bárbara Marques Sónia Pedro Hildeberto Correia Ana Valente António Sebastião Rodrigues Luís Vieira |
| author_sort | Catarina Silva |
| collection | DOAJ |
| description | Abstract Background 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. |
| format | Article |
| id | doaj-art-dd10d2498abc47b6963dd94785b830fe |
| institution | Kabale University |
| issn | 1755-8166 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | Molecular Cytogenetics |
| spelling | doaj-art-dd10d2498abc47b6963dd94785b830fe2025-08-20T04:03:07ZengBMCMolecular Cytogenetics1755-81662025-07-0118111510.1186/s13039-025-00721-8Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genomeCatarina Silva0José Ferrão1Bárbara Marques2Sónia Pedro3Hildeberto Correia4Ana Valente5António Sebastião Rodrigues6Luís Vieira7Technology and Innovation Unit, Human Genetics Department, National Institute of Health, Avenida Padre CruzTechnology and Innovation Unit, Human Genetics Department, National Institute of Health, Avenida Padre CruzCytogenetics Unit, Human Genetics Department, National Institute of HealthCytogenetics Unit, Human Genetics Department, National Institute of HealthCytogenetics Unit, Human Genetics Department, National Institute of HealthResearch and Development Unit, Human Genetics Department, National Institute of Health, Avenida Padre CruzComprehensive Health Research Centre, NOVA Medical School, Universidade NOVA de LisboaTechnology and Innovation Unit, Human Genetics Department, National Institute of Health, Avenida Padre CruzAbstract Background 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.https://doi.org/10.1186/s13039-025-00721-8Third-generation sequencingWhole genome sequencingNanopore SequencingHybrid-SNP microarrayStructural variationCopy number variation |
| spellingShingle | Catarina Silva José Ferrão Bárbara Marques Sónia Pedro Hildeberto Correia Ana Valente António Sebastião Rodrigues Luís Vieira Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome Molecular Cytogenetics Third-generation sequencing Whole genome sequencing Nanopore Sequencing Hybrid-SNP microarray Structural variation Copy number variation |
| title | Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome |
| title_full | Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome |
| title_fullStr | Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome |
| title_full_unstemmed | Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome |
| title_short | Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome |
| title_sort | comparative analysis of hybrid snp microarray and nanopore sequencing for detection of large sized copy number variants in the human genome |
| topic | Third-generation sequencing Whole genome sequencing Nanopore Sequencing Hybrid-SNP microarray Structural variation Copy number variation |
| url | https://doi.org/10.1186/s13039-025-00721-8 |
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