ArticleNucleic acids research2013
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Detection of structural DNA variants in medulloblastomas using optical genome mapping.Acta neuropathologica communications · 2026Article
- Whole-exome sequencing reveals novel cancer genes and actionable targets in biliary tract cancers in primary sclerosing cholangitis.Hepatology communications · 2024Article
- Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking.BMC bioinformatics · 2024Article
- Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics.Bioinformatics (Oxford, England) · 2023Article
- Stage IV Colorectal Cancer Patients with High Risk Mutation Profiles Survived 16 Months Longer with Individualized Therapies.Cancers · 2020Article
- Rapid response of stage IV colorectal cancer with APC/TP53/KRAS mutations to FOLFIRI and Bevacizumab combination chemotherapy: a case report of use of liquid biopsy.BMC medical genetics · 2020Article
- Identification and characterization of two functional variants in the human longevity gene FOXO3.Nature communications · 2017Article
- Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut.BMC bioinformatics · 2017Article
- Article
- Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options.Nature genetics · 2015Article
- Quality control metrics improve repeatability and reproducibility of single-nucleotide variants derived from whole-genome sequencing.The pharmacogenomics journal · 2015Article
- Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data.Scientific reports · 2015Article
- Development of a high-resolution NGS-based HLA-typing and analysis pipeline.Nucleic acids research · 2015Article
- Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors.Molecules (Basel, Switzerland) · 2015Review
- Whole genome and exome sequencing of monozygotic twins discordant for Crohn's disease.BMC genomics · 2014Article
- GrabBlur--a framework to facilitate the secure exchange of whole-exome and -genome SNV data using VCF files.BMC genomics · 2014Article
- Assessment of whole genome amplification for sequence capture and massively parallel sequencing.PloS one · 2014Article
- Comparing somatic mutation-callers: beyond Venn diagrams.BMC bioinformatics · 2013Article
- Cancer genome landscapes.Science (New York, N.Y.) · 2013Review
- Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.BMC genomics · 2012Article
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18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5-60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts details on nucleotides from alignment files at user-specified coordinates and identifies reproducible genotypes, if present. In test cases pibase identifies genotypes at 99.98% specificity, 10-fold better than other tools. pibase also provides pair-wise comparisons between healthy and affected cells using nucleotide signals (10-fold more accurately than a genotype-based approach, as we show in our case study of monozygotic twins). This comparison tool also solves the problem of detecting allelic imbalance within heterozygous SNVs in copy number variation loci, or in heterogeneous tumor sequences.
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