Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.

Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical...

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Autores principales:	John Bartlett, Yutaka Amemiya, Heleen Arts, Jane Bayani, Barry Eng, Daria Grafodatskaya, Suzanne Kamel Reid, Mathieu Lariviere, Bryan Lo, Rebecca McClure, Vinay Mittal, Bekim Sadikovic, Seth Sadis, Arun Seth, Jeff Smith, Xiao Zhang, Harriet Feilotter
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2461c7df1ca54a0aa3c235e5ca730d3c
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spelling	oai:doaj.org-article:2461c7df1ca54a0aa3c235e5ca730d3c2021-12-02T20:17:24ZMultisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.1932-620310.1371/journal.pone.0258188https://doaj.org/article/2461c7df1ca54a0aa3c235e5ca730d3c2021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0258188https://doaj.org/toc/1932-6203Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present. However, data on reproducibility between laboratories is limited. Using a ring study, we evaluated the performance of 7 Ontario laboratories using targeted sequencing panels. All laboratories analysed a series of control and clinical samples for SNVs/CNVs and gene fusions. High concordance was observed across laboratories for measured CNVs and SNVs. Over 97% of SNV calls in clinical samples were detected by all laboratories. Whilst only a single CNV was detected in the clinical samples tested, all laboratories were able to reproducibly report both the variant and copy number. Concordance for information derived from RNA was lower than observed for DNA, due largely to decreased quality metrics associated with the RNA components of the assay, suggesting that the RNA portions of comprehensive NGS assays may be more vulnerable to variations in approach and workflow. Overall the results of this study support the use of the OFA for targeted sequencing for testing of clinical samples and suggest specific internal quality metrics that can be reliable indicators of assay failure. While we believe this evidence can be interpreted to support deep targeted sequencing in general, additional studies should be performed to confirm this.John BartlettYutaka AmemiyaHeleen ArtsJane BayaniBarry EngDaria GrafodatskayaSuzanne Kamel ReidMathieu LariviereBryan LoRebecca McClureVinay MittalBekim SadikovicSeth SadisArun SethJeff SmithXiao ZhangHarriet FeilotterPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 10, p e0258188 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q John Bartlett Yutaka Amemiya Heleen Arts Jane Bayani Barry Eng Daria Grafodatskaya Suzanne Kamel Reid Mathieu Lariviere Bryan Lo Rebecca McClure Vinay Mittal Bekim Sadikovic Seth Sadis Arun Seth Jeff Smith Xiao Zhang Harriet Feilotter Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
description	Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present. However, data on reproducibility between laboratories is limited. Using a ring study, we evaluated the performance of 7 Ontario laboratories using targeted sequencing panels. All laboratories analysed a series of control and clinical samples for SNVs/CNVs and gene fusions. High concordance was observed across laboratories for measured CNVs and SNVs. Over 97% of SNV calls in clinical samples were detected by all laboratories. Whilst only a single CNV was detected in the clinical samples tested, all laboratories were able to reproducibly report both the variant and copy number. Concordance for information derived from RNA was lower than observed for DNA, due largely to decreased quality metrics associated with the RNA components of the assay, suggesting that the RNA portions of comprehensive NGS assays may be more vulnerable to variations in approach and workflow. Overall the results of this study support the use of the OFA for targeted sequencing for testing of clinical samples and suggest specific internal quality metrics that can be reliable indicators of assay failure. While we believe this evidence can be interpreted to support deep targeted sequencing in general, additional studies should be performed to confirm this.
format	article
author	John Bartlett Yutaka Amemiya Heleen Arts Jane Bayani Barry Eng Daria Grafodatskaya Suzanne Kamel Reid Mathieu Lariviere Bryan Lo Rebecca McClure Vinay Mittal Bekim Sadikovic Seth Sadis Arun Seth Jeff Smith Xiao Zhang Harriet Feilotter
author_facet	John Bartlett Yutaka Amemiya Heleen Arts Jane Bayani Barry Eng Daria Grafodatskaya Suzanne Kamel Reid Mathieu Lariviere Bryan Lo Rebecca McClure Vinay Mittal Bekim Sadikovic Seth Sadis Arun Seth Jeff Smith Xiao Zhang Harriet Feilotter
author_sort	John Bartlett
title	Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
title_short	Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
title_full	Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
title_fullStr	Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
title_full_unstemmed	Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
title_sort	multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/2461c7df1ca54a0aa3c235e5ca730d3c
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Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours.

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