ArticlePloS one2014
Comprehensive analysis to improve the validation rate for single nucleotide variants detected by next-generation sequencing.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Germline or somatic mutations in genes encoding microRNAs as biomarkers predicting the risk of adult T-cell leukemia/lymphoma.Journal of human genetics · 2026Article
- A preliminary computational outputs versus experimental results: Application of sTRAP, a biophysical tool for the analysis of SNPs of transcription factor-binding sites.Molecular genetics & genomic medicine · 2020Article
- Empirical design of a variant quality control pipeline for whole genome sequencing data using replicate discordance.Scientific reports · 2019Article
- PKD1 Duplicated regions limit clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of Autosomal Dominant Polycystic Kidney Disease.Scientific reports · 2019Article
- Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Valection: design optimization for validation and verification studies.BMC bioinformatics · 2018Article
- Genetic analysis of parathyroid and pancreatic tumors in a patient with multiple endocrine neoplasia type 1 using whole-exome sequencing.BMC medical genetics · 2017Article
- Review
- Pitfalls of exome sequencing: a case study of the attribution of HABP2 rs7080536 in familial non-medullary thyroid cancer.NPJ genomic medicine · 2017Article
- Next generation sequencing (NGS) in glucose-6-phosphate dehydrogenase (G6PD) deficiency studies.Bioinformation · 2016Article
- Comparing targeted exome and whole exome approaches for genetic diagnosis of neuromuscular disorders.Applied & translational genomics · 2015Article
- VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering.BMC genomics · 2015Article
- Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein-Coding Regions.Human mutation · 2015Article
- Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.BMC genomics · 2015Article
- A thesaurus of genetic variation for interrogation of repetitive genomic regions.Nucleic acids research · 2015Article
- Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition.PloS one · 2015Article
- Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics.Frontiers in oncology · 2014Review
- Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing.Journal of Zhejiang University. Science. BArticle
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) has enabled the high-throughput discovery of germline and somatic mutations. However, NGS-based variant detection is still prone to errors, resulting in inaccurate variant calls. Here, we categorized the variants detected by NGS according to total read depth (TD) and SNP quality (SNPQ), and performed Sanger sequencing with 348 selected non-synonymous single nucleotide variants (SNVs) for validation. Using the SAMtools and GATK algorithms, the validation rate was positively correlated with SNPQ but showed no correlation with TD. In addition, common variants called by both programs had a higher validation rate than caller-specific variants. We further examined several parameters to improve the validation rate, and found that strand bias (SB) was a key parameter. SB in NGS data showed a strong difference between the variants passing validation and those that failed validation, showing a validation rate of more than 92% (filtering cutoff value: alternate allele forward [AF] ≥ 20 and AF<80 in SAMtools, SB<-10 in GATK). Moreover, the validation rate increased significantly (up to 97-99%) when the variant was filtered together with the suggested values of mapping quality (MQ), SNPQ and SB. This detailed and systematic study provides comprehensive recommendations for improving validation rates, saving time and lowering cost in NGS analyses.
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