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Improvement of large copy number variant detection by whole genome nanopore sequencing

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Title: Improvement of large copy number variant detection by whole genome nanopore sequencing
Authors: Javier Cuenca-Guardiola, Belén de la Morena-Barrio, Juan L. García, Alba Sanchis-Juan, Javier Corral, Jesualdo T. Fernández-Breis
Source: Journal of Advanced Research, Vol 50, Iss , Pp 145-158 (2023)
Publisher Information: Elsevier, 2023.
Publication Year: 2023
Collection: LCC:Medicine (General)
LCC:Science (General)
Subject Terms: Nanopore, Structural variant, Third-generation sequencing, SERPINC1, Medicine (General), R5-920, Science (General), Q1-390
More Details: Introduction: Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations. Methods: We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets. Results: We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers’ results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples. Conclusion: We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.
Document Type: article
File Description: electronic resource
Language: English
ISSN: 2090-1232
Relation: http://www.sciencedirect.com/science/article/pii/S2090123222002417; https://doaj.org/toc/2090-1232
DOI: 10.1016/j.jare.2022.10.012
Access URL: https://doaj.org/article/e0c75bf3cae14b18b5e67066ff4e599c
Accession Number: edsdoj.0c75bf3cae14b18b5e67066ff4e599c
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  Data: Introduction: Whole-genome sequencing using nanopore technologies can uncover structural variants, which are DNA rearrangements larger than 50 base pairs. Nanopore technologies can also characterize their boundaries with single-base accuracy, owing to the kilobase-long reads that encompass either full variants or their junctions. Other methods, such as next-generation short read sequencing or PCR assays, are limited in their capabilities to detect or characterize structural variants. However, the existing software for nanopore sequencing data analysis still reports incomplete variant sets, which also contain erroneous calls, a considerable obstacle for the molecular diagnosis or accurate genotyping of populations. Methods: We compared multiple factors affecting variant calling, such as reference genome version, aligner (minimap2, NGMLR, and lra) choice, and variant caller combinations (Sniffles, CuteSV, SVIM, and NanoVar), to find the optimal group of tools for calling large (>50 kb) deletions and duplications, using data from seven patients exhibiting gross gene defects on SERPINC1 and from a reference variant set as the control. The goal was to obtain the most complete, yet reasonably specific group of large variants using a single cell of PromethION sequencing, which yielded lower depth coverage than short-read sequencing. We also used a custom method for the statistical analysis of the coverage value to refine the resulting datasets. Results: We found that for large deletions and duplications (>50 kb), the existing software performed worse than for smaller ones, in terms of both sensitivity and specificity, and newer tools had not improved this. Our novel software, disCoverage, could polish variant callers’ results, improving specificity by up to 62% and sensitivity by 15%, the latter requiring other data or samples. Conclusion: We analyzed the current situation of >50-kb copy number variants with nanopore sequencing, which could be improved. The methods presented in this work could help to identify the known deletions and duplications in a set of patients, while also helping to filter out erroneous calls for these variants, which might aid the efforts to characterize a not-yet well-known fraction of genetic variability in the human genome.
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