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

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...

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Bibliographic Details
Published in:Scientific reports 2021-03, Vol.11 (1), p.5697-5697, Article 5697
Main Authors: Arteche-López, A., Ávila-Fernández, A., Romero, R., Riveiro-Álvarez, R., López-Martínez, M. A., Giménez-Pardo, A., Vélez-Monsalve, C., Gallego-Merlo, J., García-Vara, I., Almoguera, Berta, Bustamante-Aragonés, A., Blanco-Kelly, F., Tahsin-Swafiri, S., Rodríguez-Pinilla, E., Minguez, P., Lorda, I., Trujillo-Tiebas, M. J., Ayuso, C.
Format: Article
Language:English
Subjects:
631/208/2489/1512
692/4017
Copy number
Disease
Genes
Genetics
Genomes
Genomics
Hospitals
Human error
Humanities and Social Sciences
Laboratories
multidisciplinary
Next-generation sequencing
Quality control
Science
Science (multidisciplinary)
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Summary: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).
ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-85182-w