ArticleCommunications biology2018
Genome-wide somatic variant calling using localized colored de Bruijn graphs.
Article in Communications biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
What it found
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Who cites it
95 citing papers in PubMed.
- Increased Synthetic Cytotoxicity of Combinatorial Chemoradiation Therapy in Homologous Recombination Deficient Tumors.International journal of radiation oncology, biology, physics · 2025Trial
- The BRCA1 coiled-coil domain is dispensable for suppression of tandem duplications and tolerance of FANCM loss.The EMBO journal · 2026Article
- Article
- 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
- A High-Fidelity and Ancestrally Inclusive Patient-Derived Organoid Platform Resolves Cancer Cell Plasticity in Uterine Carcinosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Geospatial genetic evolution and phenotypic plasticity in triple-negative breast cancer.Genome medicine · 2026Article
- Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.NAR genomics and bioinformatics · 2026Article
- Resolving the Haplotype Complexity of Colorectal Cancer Genomes with Droplet Barcode Sequencing.Life (Basel, Switzerland) · 2026Article
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- A Single-Cell Atlas of Uterine Carcinosarcoma from Diverse Ancestries.bioRxiv : the preprint server for biology · 2026Article
- Microglandular adenosis, triple negative breast carcinoma and DNA repair defects.Journal of clinical pathology · 2026Article
- Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers.Cell genomics · 2026Article
- Article
- Metastatic progression of pheochromocytoma and paraganglioma occurs via parallel evolution.NPJ precision oncology · 2026Article
- Comparative Evaluation of Mutect2, Strelka2, and FreeBayes for Somatic SNV Detection in Synthetic and Clinical Whole-Exome Sequencing Data.Biomolecules · 2025Article
- Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data.bioRxiv : the preprint server for biology · 2025Article
- Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.Cell reports. Medicine · 2025Article
- Whole-genome sequencing reveals three follicular lymphoma subtypes with distinct cell of origin and patient outcomes.Cell reports. Medicine · 2025Article
- The Open Pediatric Cancer Project.bioRxiv : the preprint server for biology · 2025Article
35 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzing reads from tumor and matched normal samples using colored de Bruijn graphs. We demonstrate, through extensive experimental comparison on synthetic and real whole-genome sequencing datasets, that Lancet has better accuracy, especially for indel detection, than widely used somatic callers, such as MuTect, MuTect2, LoFreq, Strelka, and Strelka2. Lancet features a reliable variant scoring system, which is essential for variant prioritization, and detects low-frequency mutations without sacrificing the sensitivity to call longer insertions and deletions empowered by the local-assembly engine. In addition to genome-wide analysis, Lancet allows inspection of somatic variants in graph space, which augments the traditional read alignment visualization to help confirm a variant of interest. Lancet is available as an open-source program at https://github.com/nygenome/lancet.
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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.