ArticleNature methods2015
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 204 papers, 3 of them syntheses that pooled it.
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Who cites it
204 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- TMBserval: a statistical explainable learning model reveals weighted tumor mutation burden better categorizing therapeutic benefits.Frontiers in immunology · 2023Pooled it
- The application of crowdsourcing approaches to cancer research: a systematic review.Cancer medicine · 2017Pooled it
- Integrated clinical and genomic evaluation of guadecitabine (SGI-110) in peripheral T-cell lymphoma.Leukemia · 2022Trial
- Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.Nature communications · 2021Trial
- Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data.The Lancet. Oncology · 2017Trial
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- AI-driven neoantigen identification: a comprehensive review from somatic variant calling to T cell recognition.Journal of translational medicine · 2026Review
- VariantMedium: sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental data.Genome medicine · 2026Article
- Accurate detection of tumor clonality and ongoing expansion mode from genomic data.bioRxiv : the preprint server for biology · 2026Article
- A complete human pancreatic cancer genome.bioRxiv : the preprint server for biology · 2026Article
- Characterization of de novo germline mutations suggests a strong male mutation bias in coppery titi monkeys (Plecturocebus cupreus).Molecular biology and evolution · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution.bioRxiv : the preprint server for biology · 2026Article
- NanoVar: a comprehensive workflow for structural variant detection to uncover the genome's hidden patterns.Nature protocols · 2026Review
- Analytical Validation of an Annotation Tool for WGS-Based Pharmacogenomics: Preparing for Clinical Implementation in Pediatric Oncology.Clinical and translational science · 2026Article
- Eduomics: a Nextflow pipeline to simulate -omics data for education.NAR genomics and bioinformatics · 2026Article
- Scalable and comprehensive mosaic variant calling using DRAGEN.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Synth4bench: generating synthetic data for benchmarking tumor-only somatic variant calling algorithms.Frontiers in bioinformatics · 2026Article
144 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
Abstract
The detection of somatic mutations from cancer genome sequences is key to understanding the genetic basis of disease progression, patient survival and response to therapy. Benchmarking is needed for tool assessment and improvement but is complicated by a lack of gold standards, by extensive resource requirements and by difficulties in sharing personal genomic information. To resolve these issues, we launched the ICGC-TCGA DREAM Somatic Mutation Calling Challenge, a crowdsourced benchmark of somatic mutation detection algorithms. Here we report the BAMSurgeon tool for simulating cancer genomes and the results of 248 analyses of three in silico tumors created with it. Different algorithms exhibit characteristic error profiles, and, intriguingly, false positives show a trinucleotide profile very similar to one found in human tumors. Although the three simulated tumors differ in sequence contamination (deviation from normal cell sequence) and in subclonality, an ensemble of pipelines outperforms the best individual pipeline in all cases. BAMSurgeon is available at https://github.com/adamewing/bamsurgeon/.
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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.