ArticleScientific reports2020
SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Enhanced neoepitope-specific immunity following neoadjuvant PD-L1 and TGF-β blockade in HPV-unrelated head and neck cancer.The Journal of clinical investigation · 2022Trial
- Dual PD-L1 and TGF-b blockade in patients with recurrent respiratory papillomatosis.Journal for immunotherapy of cancer · 2021Trial
- fourSynergy: ensemble-based interaction calling on 4C-seq data using gradient-free optimization.BioData mining · 2026Article
- CHIP ahoy: charting a decade of discovery in clonal hematopoiesis.Haematologica · 2026Review
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
- MutAnt: mutation annotation tool predicts deleteriousness of missense mutations and improves mutation calling from transcriptomics.Human genetics · 2025Article
- Multi-omic characterization of consensus molecular subtype 1 (CMS1) colorectal cancer with dampened immune response improves precision medicine.Molecular oncology · 2025Article
- Prevalence and biological impact of clinically relevant gene fusions in head and neck cancers.NPJ precision oncology · 2025Article
- Article
- Predicting high confidence ctDNA somatic variants with ensemble machine learning models.Scientific reports · 2025Article
- Identifying genetic errors of immunity due to mosaicism.The Journal of experimental medicine · 2025Review
- Genetic diversity analysis and conservation strategy recommendations for ex situ conservation of Cupressus chengiana.BMC plant biology · 2025Article
- Inferring active mutational processes in cancer using single cell sequencing and evolutionary constraints.bioRxiv : the preprint server for biology · 2025Article
- Unveiling the molecular profile of a prostate carcinoma: implications for personalized medicine.Biology direct · 2024Article
- A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing.Briefings in bioinformatics · 2024Article
- The Genomic Landscape of Benign and Malignant Thyroid Tumors from Individuals Carrying Germline PTEN Variants Is Distinct from Sporadic Thyroid Cancers.Cancer research · 2024Article
- A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer.International journal of molecular sciences · 2024Article
- Molecular profiling of a bladder cancer with very high tumour mutational burden.Cell death discovery · 2024Article
- DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors.Cell reports · 2024Article
- Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity.Nature genetics · 2023Article
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Authors and funding
10 authors.
Funding
Abstract
It is challenging to identify somatic variants from high-throughput sequence reads due to tumor heterogeneity, sub-clonality, and sequencing artifacts. In this study, we evaluated the performance of eight primary somatic variant callers and multiple ensemble methods using both real and synthetic whole-genome sequencing, whole-exome sequencing, and deep targeted sequencing datasets with the NA12878 cell line. The test results showed that a simple consensus approach can significantly improve performance even with a limited number of callers and is more robust and stable than machine learning based ensemble approaches. To fully exploit the multi-callers, we also developed a software package, SomaticCombiner, that can combine multiple callers and integrates a new variant allelic frequency (VAF) adaptive majority voting approach, which can maintain sensitive detection for variants with low VAFs.
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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.