ArticleNucleic acids research2016
VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06680791 (Molecular Classification in Relation to Prevention of Endometrial Cancer Recurrence and Lifestyle Factors), which is not on this map. Cited by 611 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Molecular Classification in Relation to Prevention of Endometrial Cancer Recurrence and Lifestyle Factors
Who cites it
611 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.Scientific reports · 2024Pooled it
- Neoadjuvant camrelizumab combined with metronomic chemotherapy in patients with advanced esophageal squamous cell carcinoma: a pilot randomized phase 2 trial.BMC medicine · 2026Trial
- Circulating tumor DNA as a prognostic biomarker in metastatic colorectal cancer: Post-hoc analysis of treatment response and survival outcomes in the ALTER-C-002 study.Biomolecules & biomedicine · 2026Trial
- Tumor-Informed ctDNA in Guiding First-Line Immunochemotherapy in Advanced Non-Small Cell Lung Cancers.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Trial
- Clonal Hematopoiesis and Cardiovascular Disease and Bleeding Risk and the Effectiveness of Aspirin.JAMA cardiology · 2025Trial
- Efficacy and safety of pyrotinib in patients with previously treated HER2-positive non-breast solid tumors: a phase 2, open-label basket trial.The oncologist · 2025Trial
- Molecular residual disease analysis of adjuvant osimertinib in resected EGFR-mutated stage IB-IIIA non-small-cell lung cancer.Nature medicine · 2025Trial
- Dynamics of clonal hematopoiesis under DNA-damaging treatment in patients with ovarian cancer.Leukemia · 2024Trial
- Combination of acalabrutinib with lenalidomide and rituximab in relapsed/refractory aggressive B-cell non-Hodgkin lymphoma: a single-arm phase II trial.Nature communications · 2024Trial
- Efficacy and safety of anlotinib combined with the STUPP regimen in patients with newly diagnosed glioblastoma: a multicenter, single-arm, phase II trial.Cancer biology & medicine · 2024Trial
- xinguangA preliminary characterization of PI4K/PIPK alterations across solid tumors: an exploratory framework for prognostic and therapeutic stratification.Cancer biology & therapy · 2026Article
- Germline homologous recombination deficiency influences TP53-mutant clonal hematopoiesis fitness during platinum and PARP inhibitor treatment.Nature genetics · 2026Article
- TERT drives liver tumorigenesis beyond telomere elongation.Life science alliance · 2026Article
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- Development of an homologous recombination deficiency scoring algorithm for unmatched ovarian tumor sample based on next-generation sequencing.Journal of gynecologic oncology · 2026Article
- Review
- Genome-wide annotation of human multi-nucleotide variants reveals widespread functional differences from single nucleotide variants.Nature communications · 2026Article
- Chemically induced skin tumors arise from long-lived stem cells of the upper hair follicle.Science (New York, N.Y.) · 2026Article
- Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation.Cell reports · 2026Article
- Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.Genome research · 2026Article
551 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls SNV, MNV, InDels, complex and structural variants, expanding the detected genetic driver landscape of tumors. It performs local realignments on the fly for more accurate allele frequency estimation. VarDict performance scales linearly to sequencing depth, enabling ultra-deep sequencing used to explore tumor evolution or detect tumor DNA circulating in blood. In addition, VarDict performs amplicon aware variant calling for polymerase chain reaction (PCR)-based targeted sequencing often used in diagnostic settings, and is able to detect PCR artifacts. Finally, VarDict also detects differences in somatic and loss of heterozygosity variants between paired samples. VarDict reprocessing of The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma dataset called known driver mutations in KRAS, EGFR, BRAF, PIK3CA and MET in 16% more patients than previously published variant calls. We believe VarDict will greatly facilitate application of NGS in clinical cancer research.
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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.