Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes

Abstract Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively...

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Autores principales: A. Arteche-López, A. Ávila-Fernández, R. Romero, R. Riveiro-Álvarez, M. A. López-Martínez, A. Giménez-Pardo, C. Vélez-Monsalve, J. Gallego-Merlo, I. García-Vara, Berta Almoguera, A. Bustamante-Aragonés, F. Blanco-Kelly, S. Tahsin-Swafiri, E. Rodríguez-Pinilla, P. Minguez, I. Lorda, M. J. Trujillo-Tiebas, C. Ayuso
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Publicado: Nature Portfolio 2021
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Acceso en línea:https://doaj.org/article/3232ae8192614cb485634017846e2717
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spelling oai:doaj.org-article:3232ae8192614cb485634017846e27172021-12-02T13:35:03ZSanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes10.1038/s41598-021-85182-w2045-2322https://doaj.org/article/3232ae8192614cb485634017846e27172021-03-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-85182-whttps://doaj.org/toc/2045-2322Abstract Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively assessed this need in 1109 variants from 825 clinical exomes, the largest sample set to date assessed using Illumina chemistry reported. With a concordance of 100%, we conclude that Sanger sequencing can be very useful as an internal quality control, but not so much as a verification method for high-quality single-nucleotide and small insertion/deletions variants. Laboratories might validate and establish their own thresholds before discontinuing Sanger confirmation studies. We also expand and validate 23 copy number variations detected by exome sequencing in 20 samples, observing a concordance of 95.65% (22/23).A. Arteche-LópezA. Ávila-FernándezR. RomeroR. Riveiro-ÁlvarezM. A. López-MartínezA. Giménez-PardoC. Vélez-MonsalveJ. Gallego-MerloI. García-VaraBerta AlmogueraA. Bustamante-AragonésF. Blanco-KellyS. Tahsin-SwafiriE. Rodríguez-PinillaP. MinguezI. LordaM. J. Trujillo-TiebasC. AyusoNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-7 (2021)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
A. Arteche-López
A. Ávila-Fernández
R. Romero
R. Riveiro-Álvarez
M. A. López-Martínez
A. Giménez-Pardo
C. Vélez-Monsalve
J. Gallego-Merlo
I. García-Vara
Berta Almoguera
A. Bustamante-Aragonés
F. Blanco-Kelly
S. Tahsin-Swafiri
E. Rodríguez-Pinilla
P. Minguez
I. Lorda
M. J. Trujillo-Tiebas
C. Ayuso
Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
description Abstract Despite the improved accuracy of next-generation sequencing (NGS), it is widely accepted that variants need to be validated using Sanger sequencing before reporting. Validation of all NGS variants considerably increases the turnaround time and costs of clinical diagnosis. We comprehensively assessed this need in 1109 variants from 825 clinical exomes, the largest sample set to date assessed using Illumina chemistry reported. With a concordance of 100%, we conclude that Sanger sequencing can be very useful as an internal quality control, but not so much as a verification method for high-quality single-nucleotide and small insertion/deletions variants. Laboratories might validate and establish their own thresholds before discontinuing Sanger confirmation studies. We also expand and validate 23 copy number variations detected by exome sequencing in 20 samples, observing a concordance of 95.65% (22/23).
format article
author A. Arteche-López
A. Ávila-Fernández
R. Romero
R. Riveiro-Álvarez
M. A. López-Martínez
A. Giménez-Pardo
C. Vélez-Monsalve
J. Gallego-Merlo
I. García-Vara
Berta Almoguera
A. Bustamante-Aragonés
F. Blanco-Kelly
S. Tahsin-Swafiri
E. Rodríguez-Pinilla
P. Minguez
I. Lorda
M. J. Trujillo-Tiebas
C. Ayuso
author_facet A. Arteche-López
A. Ávila-Fernández
R. Romero
R. Riveiro-Álvarez
M. A. López-Martínez
A. Giménez-Pardo
C. Vélez-Monsalve
J. Gallego-Merlo
I. García-Vara
Berta Almoguera
A. Bustamante-Aragonés
F. Blanco-Kelly
S. Tahsin-Swafiri
E. Rodríguez-Pinilla
P. Minguez
I. Lorda
M. J. Trujillo-Tiebas
C. Ayuso
author_sort A. Arteche-López
title Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
title_short Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
title_full Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
title_fullStr Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
title_full_unstemmed Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes
title_sort sanger sequencing is no longer always necessary based on a single-center validation of 1109 ngs variants in 825 clinical exomes
publisher Nature Portfolio
publishDate 2021
url https://doaj.org/article/3232ae8192614cb485634017846e2717
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