ArticleGenome medicine2016
Somatic cancer variant curation and harmonization through consensus minimum variant level data.
Article in Genome medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.Nature genetics · 2020Pooled it
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- A review of genetic variant databases and machine learning tools for predicting the pathogenicity of breast cancer.Briefings in bioinformatics · 2023Review
- Actionability classification of variants of unknown significance correlates with functional effect.NPJ precision oncology · 2023Article
- CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.Nucleic acids research · 2023Article
- Feasibility and outcome of reproducible clinical interpretation of high-dimensional molecular data: a comparison of two molecular tumor boards.BMC medicine · 2022Article
- Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays.Scientific reports · 2021Article
- Clinical cancer genomic profiling.Nature reviews. Genetics · 2021Review
- Clinical practice guidance for next-generation sequencing in cancer diagnosis and treatment (edition 2.1).International journal of clinical oncology · 2021Article
- Evidence-Based Network Approach to Recommending Targeted Cancer Therapies.JCO clinical cancer informatics · 2020Article
- A virtual molecular tumor board to improve efficiency and scalability of delivering precision oncology to physicians and their patients.JAMIA open · 2019Article
- A case for expert curation: an overview of cancer curation in the Clinical Genome Resource (ClinGen).Cold Spring Harbor molecular case studies · 2019Article
- Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants.Genome medicine · 2019Article
- "Somatic" and "pathogenic" - is the classification strategy applicable in times of large-scale sequencing?Haematologica · 2019Article
- UniProt genomic mapping for deciphering functional effects of missense variants.Human mutation · 2019Article
- Validity of an NGS-based multiple gene panel in identifying actionable mutations for patients with NSCLC in a Chinese hospital.Oncology letters · 2019Article
- Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study.Nature medicine · 2019Article
- Development of Clinical Domain Working Groups for the Clinical Genome Resource (ClinGen): lessons learned and plans for the future.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- Clinical validation of the tempus xT next-generation targeted oncology sequencing assay.Oncotarget · 2019Article
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19 authors.
Funding
Abstract
backgroundTo truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG) of the Clinical Genome Resource (ClinGen), in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD). MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice.
methodsWe developed MVLD through a consensus approach by i) reviewing clinical actionability interpretations from institutions participating in the WG, ii) conducting extensive literature search of clinical somatic interpretation schemas, and iii) survey of cancer variant web portals. A forthcoming guideline on cancer variant interpretation, from the Association of Molecular Pathology (AMP), can be incorporated into MVLD.
resultsAlong with harmonizing standardized terminology for allele interpretive and descriptive fields that are collected by many databases, the MVLD includes unique fields for cancer variants such as Biomarker Class, Therapeutic Context and Effect. In addition, MVLD includes recommendations for controlled semantics and ontologies. The Somatic WG is collaborating with ClinVar to evaluate MVLD use for somatic variant submissions. ClinVar is an open and centralized repository where sequencing laboratories can report summary-level variant data with clinical significance, and ClinVar accepts cancer variant data.
conclusionsWe expect the use of the MVLD to streamline clinical interpretation of cancer variants, enhance interoperability among multiple redundant curation efforts, and increase submission of somatic variants to ClinVar, all of which will enhance translation to clinical oncology practice.
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