ArticleGenome medicine2013
A simple consensus approach improves somatic mutation prediction accuracy.
Article in Genome medicine, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 42 citations in OpenAlex.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- An Annotated Biobank of Triple-Negative Breast Cancer Patient-Derived Xenografts Features Treatment-Naïve and Longitudinal Samples during Neoadjuvant Chemotherapy.Cancer research · 2025Trial
- CHIP ahoy: charting a decade of discovery in clonal hematopoiesis.Haematologica · 2026Review
- Integrated genomic analysis of NF1-associated peripheral nerve sheath tumors: an updated biorepository dataset.Scientific data · 2025Article
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing.Briefings in bioinformatics · 2024Article
- A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.International journal of molecular sciences · 2024Article
- Prediction of Deleterious Single Amino Acid Polymorphisms with a Consensus Holdout Sampler.Current genomics · 2024Article
- Simple combination of multiple somatic variant callers to increase accuracy.Scientific reports · 2023Article
- Verification of prognostic expression biomarkers is improved by examining enriched leukemic blasts rather than mononuclear cells from acute myeloid leukemia patients.Biomarker research · 2023Article
- Computational cancer neoantigen prediction: current status and recent advances.Immuno-oncology technology · 2021Review
- SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.Scientific reports · 2020Article
- AML risk stratification models utilizing ELN-2017 guidelines and additional prognostic factors: a SWOG report.Biomarker research · 2020Article
- Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data.BMC medical genomics · 2019Article
- NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer.BMC medical genomics · 2019Article
- Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state.Science translational medicine · 2019Article
- High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer.Nature communications · 2018Article
- Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines.Cell systems · 2018Article
- Improving somatic variant identification through integration of genome and exome data.BMC genomics · 2017Article
- Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia.Nature communications · 2017Article
- ReliableGenome: annotation of genomic regions with high/low variant calling concordance.Bioinformatics (Oxford, England) · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Differentiating true somatic mutations from artifacts in massively parallel sequencing data is an immense challenge. To develop methods for optimal somatic mutation detection and to identify factors influencing somatic mutation prediction accuracy, we validated predictions from three somatic mutation detection algorithms, MuTect, JointSNVMix2 and SomaticSniper, by Sanger sequencing. Full consensus predictions had a validation rate of >98%, but some partial consensus predictions validated too. In cases of partial consensus, read depth and mapping quality data, along with additional prediction methods, aided in removing inaccurate predictions. Our consensus approach is fast, flexible and provides a high-confidence list of putative somatic mutations.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.