SynthesisNature genetics2020
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
Synthesis in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
95 citing papers in PubMed, 3 syntheses or guidelines pooled it, 174 citations in OpenAlex.
- Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays.Annals of laboratory medicine · 2024Guideline
- Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).Genetics in medicine : official journal of the American College of Medical Genetics · 2022Guideline
- Text-mining clinically relevant cancer biomarkers for curation into the CIViC database.Genome medicine · 2019Pooled it
- Concordance in Molecular Tumor Board Case Reviews in the ASCO TAPUR Study.JCO precision oncology · 2024Trial
- Reclassification ofBiomolecules & biomedicine · 2026Article
- Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology.The Journal of molecular diagnostics : JMD · 2026Article
- IDAP: an integrated literature- and knowledge-graph-driven evidence prioritization pipeline for precision oncology.Bioinformatics (Oxford, England) · 2026Article
- The GA4GH Categorical Variation Representation Specification: A Unified Computational Framework for Reasoning over Genomic Variant Categories.bioRxiv : the preprint server for biology · 2026Article
- The Knowledge Connector decision support system for multiomics-based precision oncology.Nature communications · 2026Article
- Validation and clinical evaluation of a comprehensive circulating tumor DNA assay for genomic profiling in solid tumors.BMC cancer · 2025Article
- High-throughput characterization of 5886 HER2 variants identifies 112 new in cellulo gain-of-function mutations.Genomics · 2025Article
- Using artificial intelligence (AI) to model clinical variant reporting for next generation sequencing (NGS) oncology assays.BioData mining · 2025Article
- Need Analysis of Clinician-Oriented Integrated Precision Oncology Decision Support Tools: Qualitative Descriptive Study.JMIR human factors · 2025Article
- A highly annotated drug combination resource for catalyzing precision combinatorial therapy.Scientific data · 2025Article
- Onkopus: precise interpretation and prioritization of sequence variants for biomedical research and precision medicine.Nucleic acids research · 2025Article
- Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer.Molecular oncology · 2025Article
- Genomic analysis of small renal masses reveals mutations linked with renal cell carcinoma and fast-growing tumors.Journal of cancer research and clinical oncology · 2025Article
- New Gain-of-Function Mutations Prioritize Mechanisms of HER2 Activation.medRxiv : the preprint server for health sciences · 2025Article
- Unveiling the Digital Evolution of Molecular Tumor Boards.Targeted oncology · 2025Review
- Advancing precision oncology with AI-powered genomic analysis.Frontiers in pharmacology · 2025Review
35 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
40 authors at 20 institutions in 8 countries.
Funding
Abstract
Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
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What OpenQuestion holds
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.