ArticleMolecular genetics & genomic medicine2019
A comprehensive assessment of Next-Generation Sequencing variants validation using a secondary technology.
Article in Molecular genetics & genomic medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Performance Evaluation of Targeted Nanopore Sequencing in Non-Tuberculous Mycobacteria Identification: A Comparative Study in Shenzhen, China.Infection and drug resistance · 2026Article
- Sanger validation of WGS variants.Scientific reports · 2025Article
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- Article
- Pharmacogenomic profile of actionable molecular variants related to drugs commonly used in anesthesia: WES analysis reveals new mutations.Frontiers in pharmacology · 2023Article
- Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice.Biomedicines · 2022Review
- Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis.BMC genomics · 2022Article
- Sanger sequencing is no longer always necessary based on a single-center validation of 1109 NGS variants in 825 clinical exomes.Scientific reports · 2021Article
- Hsa_circ_0008537 facilitates liver carcinogenesis by upregulating MCL1 and Snail1 expression via miR‑153‑3p.Oncology reports · 2021Observational
- Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing.Biomolecules · 2021Article
- Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches.BMC bioinformatics · 2020Article
- Sanger Validation of High-Throughput Sequencing in Genetic Diagnosis: Still the Best Practice?Frontiers in genetics · 2020Article
- A comprehensive assessment of Next-Generation Sequencing variants validation using a secondary technology.Molecular genetics & genomic medicine · 2019Article
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19 authors.
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Abstract
backgroundRecently, increasing innovations improved the accuracy of next generation sequencing (NGS) data. However, the validation of all NGS variants increased the cost and turn-around time of clinical diagnosis, and therefore limited the further development of clinical applications. We aimed to comprehensively assess the necessity of validating NGS variants.
methodsValidation data of 7,601 NGS variants involving 1,045 genes were collected from 5,190 clinical samples and sequenced by one of five targeted capture panels and two NGS chemistries, respectively. These genes and variants were widely distributed in 24 human chromosomes and mitochondrial genome. Variants validation was firstly processed by Sanger sequencing. If validation results were unavailable or inconsistent with NGS calls, another validation test would be performed by mass spectrometry genotyping.
resultsA total of 6,939 high quality NGS variants with ≥35 × depth coverage and ≥35% heterozygous ratio were 100% confirmed by a secondary methodology. 5,775 heterozygous variants were separated from 760 homozygous variants and 404 hemizygous variants by 80% heterozygous ratio. A total of 1.5% (98/6,939) of NGS variants were validated by mass spectrometry genotyping.
conclusionConsidering of the above comprehensive assessment, a new variant with high quality from a well-validated capture-based NGS workflow can be reported directly without validation.
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