ArticleGenome medicine2018
From somatic variants towards precision oncology: Evidence-driven reporting of treatment options in molecular tumor boards.
Article in Genome medicine, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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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.
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Who cites it
26 citing papers in PubMed.
- Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic.Nature biotechnology · 2026Article
- Somatic likelihood tiering: an interpretable post-calling triage protocol for tumor-only whole-exome variant review.Briefings in bioinformatics · 2026Article
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.Nature communications · 2025Article
- Discovery of molecularly-informed therapeutic strategies for mature T-cell leukemias and lymphomas.Blood advances · 2025Article
- Advancing personalized cancer therapy: Onko_DrugCombScreen-a novel Shiny app for precision drug combination screening.NAR genomics and bioinformatics · 2025Article
- Unveiling the Digital Evolution of Molecular Tumor Boards.Targeted oncology · 2025Review
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
- DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.bioRxiv : the preprint server for biology · 2024Article
- Utility of public knowledge bases for the interpretation of comprehensive tumor molecular profiling results.Clinical and experimental medicine · 2023Article
- Consensus Statements on Precision Oncology in the China Greater Bay Area.JCO precision oncology · 2023Article
- The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards.BMC bioinformatics · 2023Article
- Implementation and Clinical Adoption of Precision Oncology Workflows Across a Healthcare Network.The oncologist · 2022Article
- Bioinformatics roadmap for therapy selection in cancer genomics.Molecular oncology · 2022Review
- Knowledge bases and software support for variant interpretation in precision oncology.Briefings in bioinformatics · 2021Article
- Diagnostic and Prognostic Value of Circulating Cell-Free DNA for Cholangiocarcinoma.Diagnostics (Basel, Switzerland) · 2021Article
- Routine Molecular Pathology Diagnostics in Precision Oncology.Deutsches Arzteblatt international · 2021Article
- Explaining decisions of graph convolutional neural networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer.Genome medicine · 2021Article
- Review
- ClinVAP: a reporting strategy from variants to therapeutic options.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundA comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene-drug interactions complicates the task of assigning clinical significance to genomic variants.
methodsHere we present a method that automatically matches patient-specific genomic alterations to treatment options. The method relies entirely on public knowledge of somatic variants with predictive evidence on drug response. The output report is aimed at supporting clinicians in the task of finding the clinical meaning of genomic variants. We applied the method to 1) The Cancer Genome Atlas (TCGA) and Genomics Evidence Neoplasia Information Exchange (GENIE) cohorts and 2) 11 patients from the NCT MASTER trial whose treatment discussions included information on their genomic profiles.
resultsOur reporting strategy showed a substantial number of patients with actionable variants in the analyses of TCGA and GENIE samples. Notably, it was able to reproduce experts' treatment suggestions in a retrospective study of 11 patients from the NCT MASTER trial. Our results establish a proof of concept for comprehensive, evidence-based reports as a supporting tool for discussing treatment options in tumor boards.
conclusionsWe believe that a standardized method to report actionable somatic variants will smooth the incorporation of NGS in the clinical context. We anticipate that tools like the one we present here will become essential in summarizing for clinicians the growing evidence in the field of precision medicine. The R code of the presented method is provided in Additional file 6 and available at https://github.com/jperera-bel/MTB-Report .
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