Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

Li, Marilyn M.; Datto, Michael B.; Duncavage, Eric J.; Kulkarni, Shashikant; Lindeman, Neal I.; Roy, Somak; Tsimberidou, Apostolia M.; Vnencak‐Jones, Cindy L.; Wolff, Daynna J.; Younes, Anas; Nikiforova, Marina N.

doi:10.1016/j.jmoldx.2016.10.002

Cited by 1,314 publications

(841 citation statements)

References 113 publications

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“…The definition of evidence level for individual genomic mutations acquired by gene panel testing should not differ greatly from the definitions standardized in the USA and EU 4. The definitions adopted in this guidance (Table S1) have been developed to be suitable for the medical system in Japan, while paying attention to maintaining consistency with those published in the USA and EU.…”

Section: Handling Of Gene Panel Testing At the Postanalysis Stagementioning

confidence: 99%

Clinical practice guidance for next‐generation sequencing in cancer diagnosis and treatment (Edition 1.0)

et al. 2018

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In Japan, the social (medical) health‐care system is on the way to being developed to advance personalized medicine through the implementation of cancer genomic medicine, known as “cancer clinical sequencing,” which uses a next‐generation sequencer. However, no Japanese guidance for cancer genomic testing exists. Gene panel testing can be carried out to help determine patient treatment, confirm diagnosis, and evaluate prognostic predictions of patients with mainly solid cancers for whom no standard treatment is available. This guidance describes how to utilize gene panel testing according to the type of cancer: childhood cancer, rare cancer, carcinoma of unknown primary, and other cancers. The level of evidence classification for unified use in Japan is also detailed. This guidance establishes the basic principles of the quality control of specimens, requirements of medical institutions, informed consent, handling of data during the postanalysis stage, and treatment options based on the evidence level. In Japan, gene panel testing for cancer treatment and diagnosis is recommended to comply with this guidance. This is a collaborative work of the Japanese Society of Medical Oncology, Japan Society of Clinical Oncology, and the Japanese Cancer Association.

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Section: Handling Of Gene Panel Testing At the Postanalysis Stagementioning

confidence: 99%

Clinical practice guidance for next‐generation sequencing in cancer diagnosis and treatment (Edition 1.0)

et al. 2018

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“…MVLD formatted variants contain AMP somatic variant interpretation guidelines as one of their central fields in the “Level of Evidence” element (Li et al., 2017; Ritter et al., 2016). AMP somatic variant interpretation guidelines assign a Tier and Level to classify a somatic variant.…”

Section: Resultsmentioning

confidence: 99%

“…For a somatic variant, the Level of Evidence captures the interpretation framework used for variant assessment and is conceptually similar to the “assertion criteria” in ClinVar. Although initially published with an example in the Level of Evidence field from the Cancer Driver Log (CanDL), the MVLD has been updated and adopted the interpretive tiers from the AMP guidelines (Damodaran et al., 2015; Li et al., 2017). It is important to note that many somatic variant interpretive schemata could be recorded in the Level of Evidence field (Parsons et al., 2016).…”

Section: Methodsmentioning

confidence: 99%

“…In order to create consistency and transparency in somatic variant interpretation, the Association of Molecular Pathology (AMP) has recently published a set of guidelines for somatic variant interpretation in cancer, which is seeing steady adoption across multiple platforms (Li et al., 2017). However, currently the field of somatic cancer variant classification is still in development, especially when compared to variant interpretation for germline or Mendelian disorders (Richards et al., 2008; Richards et al., 2015).…”

Section: Introductionmentioning

confidence: 99%

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Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards

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Harmonization of cancer variant representation, efficient communication, and free distribution of clinical variant‐associated knowledge are central problems that arise with increased usage of clinical next‐generation sequencing. The Clinical Genome Resource (ClinGen) Somatic Working Group (WG) developed a minimal variant level data (MVLD) representation of cancer variants, and has an ongoing collaboration with Clinical Interpretations of Variants in Cancer (CIViC), an open‐source platform supporting crowdsourced and expert‐moderated cancer variant curation. Harmonization between MVLD and CIViC variant formats was assessed by formal field‐by‐field analysis. Adjustments to the CIViC format were made to harmonize with MVLD and support ClinGen Somatic WG curation activities, including four new features in CIViC: (1) introduction of an assertions feature for clinical variant assessment following the Association of Molecular Pathologists (AMP) guidelines, (2) group‐level curation tracking for organizations, enabling member transparency, and curation effort summaries, (3) introduction of ClinGen Allele Registry IDs to CIViC, and (4) mapping of CIViC assertions into ClinVar submission with automated submissions. A generalizable workflow utilizing MVLD and new CIViC features is outlined for use by ClinGen Somatic WG task teams for curation and submission to ClinVar, and provides a model for promoting harmonization of cancer variant representation and efficient distribution of this information.

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“…Additional DNA sequence and copy number variants of clinical significance were also identified by targeted next-generation sequence panel [suppl. Tables 2, 3, 4 (Online Resource 1)] [7]. FGFR2, a receptor kinase, regulates several growth-related signaling pathways implicated in cancer progression, including RAS-RAF-MAPK and PI3K/AKT/mTOR [3].…”

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confidence: 99%

Novel FGFR2-INA fusion identified in two low-grade mixed neuronal-glial tumors drives oncogenesis via MAPK and PI3K/mTOR pathway activation

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Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

Cited by 1,314 publications

References 113 publications

Clinical practice guidance for next‐generation sequencing in cancer diagnosis and treatment (Edition 1.0)

Clinical practice guidance for next‐generation sequencing in cancer diagnosis and treatment (Edition 1.0)

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community‐driven standards

Novel FGFR2-INA fusion identified in two low-grade mixed neuronal-glial tumors drives oncogenesis via MAPK and PI3K/mTOR pathway activation

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