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Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing

More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore seque...

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Autores principales: Nowak, Albina, Murik, Omer, Mann, Tzvia, Zeevi, David A., Altarescu, Gheona
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8595663/
https://www.ncbi.nlm.nih.gov/pubmed/34785703
http://dx.doi.org/10.1038/s41598-021-01749-7
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author Nowak, Albina
Murik, Omer
Mann, Tzvia
Zeevi, David A.
Altarescu, Gheona
author_facet Nowak, Albina
Murik, Omer
Mann, Tzvia
Zeevi, David A.
Altarescu, Gheona
author_sort Nowak, Albina
collection PubMed
description More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease.
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spelling pubmed-85956632021-11-17 Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing Nowak, Albina Murik, Omer Mann, Tzvia Zeevi, David A. Altarescu, Gheona Sci Rep Article More than 900 variants have been described in the GLA gene. Some intronic variants and copy number variants in GLA can cause Fabry disease but will not be detected by classical Sanger sequence. We aimed to design and validate a method for sequencing the GLA gene using long-read Oxford Nanopore sequencing technology. Twelve Fabry patients were blindly analyzed, both by conventional Sanger sequence and by long-read sequencing of a 13 kb PCR amplicon. We used minimap2 to align the long-read data and Nanopolish and Sniffles to call variants. All the variants detected by Sanger (including a deep intronic variant) were also detected by long-read sequencing. One patient had a deletion that was not detected by Sanger sequencing but was detected by the new technology. Our long-read sequencing-based method was able to detect missense variants and an exonic deletion, with the added advantage of intronic analysis. It can be used as an efficient and cost-effective tool for screening and diagnosing Fabry disease. Nature Publishing Group UK 2021-11-16 /pmc/articles/PMC8595663/ /pubmed/34785703 http://dx.doi.org/10.1038/s41598-021-01749-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Nowak, Albina
Murik, Omer
Mann, Tzvia
Zeevi, David A.
Altarescu, Gheona
Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title_full Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title_fullStr Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title_full_unstemmed Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title_short Detection of single nucleotide and copy number variants in the Fabry disease-associated GLA gene using nanopore sequencing
title_sort detection of single nucleotide and copy number variants in the fabry disease-associated gla gene using nanopore sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8595663/
https://www.ncbi.nlm.nih.gov/pubmed/34785703
http://dx.doi.org/10.1038/s41598-021-01749-7
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