ArticleScientific reports2013
A practical method to detect SNVs and indels from whole genome and exome sequencing data.
Article in Scientific reports, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Novel Strategy for Structural Variant Genotyping by Short-Read Genomic Sequencing From Restriction-Circles: Experimental and Bioinformatics Proof-of-Concept.Human mutation · 2026Article
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
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- Hidden secrets of the cancer genome: unlocking the impact of non-coding mutations in gene regulatory elements.Cellular and molecular life sciences : CMLS · 2024Review
- Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States.Genes · 2023Article
- Evaluation of a Targeted Next-Generation Sequencing Panel for the Non-Invasive Detection of Variants in Circulating DNA of Colorectal Cancer.Journal of clinical medicine · 2021Article
- Comprehensive analysis of mutations and clonal evolution patterns in a cohort of patients with cytogenetically normal acute myeloid leukemia.Molecular cytogenetics · 2021Article
- Integrated Genome and Transcriptome Sequencing to Solve a Neuromuscular Puzzle: Miyoshi Muscular Dystrophy and Early Onset Primary Dystonia in Siblings of the Same Family.Frontiers in genetics · 2021Article
- Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer.PloS one · 2021Article
- Pharmacogenomics, How to Deal with Different Types of Variants in Next Generation Sequencing Data in the Personalized Medicine Area.Journal of clinical medicine · 2020Review
- 12 new susceptibility loci for prostate cancer identified by genome-wide association study in Japanese population.Nature communications · 2019Article
- Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls.Nature communications · 2018Article
- IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes.Nature communications · 2018Article
- IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis.Scientific reports · 2018Article
- Genetic variation in human drug-related genes.Genome medicine · 2017Article
- Improving somatic variant identification through integration of genome and exome data.BMC genomics · 2017Article
- Article
- SPAI: an interactive platform for indel analysis.BMC genomics · 2016Article
- [Clinical feature and ATP8B1 mutation analysis of a patient with progressive familial intrahepatic cholestasis type I].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2016Article
- Comprehensive genetic exploration of skeletal dysplasia using targeted exome sequencing.Genetics in medicine : official journal of the American College of Medical Genetics · 2016Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development of massively parallel sequencing technology has allowed the creation of comprehensive catalogs of genetic variation. However, due to the relatively high sequencing error rate for short read sequence data, sophisticated analysis methods are required to obtain high-quality variant calls. Here, we developed a probabilistic multinomial method for the detection of single nucleotide variants (SNVs) as well as short insertions and deletions (indels) in whole genome sequencing (WGS) and whole exome sequencing (WES) data for single sample calling. Evaluation with DNA genotyping arrays revealed a concordance rate of 99.98% for WGS calls and 99.99% for WES calls. Sanger sequencing of the discordant calls determined the false positive and false negative rates for the WGS (0.0068% and 0.17%) and WES (0.0036% and 0.0084%) datasets. Furthermore, short indels were identified with high accuracy (WGS: 94.7%, WES: 97.3%). We believe our method can contribute to the greater understanding of human diseases.
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