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Standard operating procedure for curation and clinical interpretation of variants in cancer.

ABSTRACT: Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of evidence obtained from peer-reviewed publications and meeting abstracts, and currently holds over 6300 Evidence Items for over 2300 variants derived from over 400 genes. CIViC has seen increased adoption by, and also undertaken collaboration with, a wide range of users and organizations involved in research. To enhance CIViC's clinical value, regular submission to the ClinVar database and pursuit of other regulatory approvals is necessary. For this reason, a formal peer reviewed curation guideline and discussion of the underlying principles of curation is needed. We present here the CIViC knowledge model, standard operating procedures (SOP) for variant curation, and detailed examples to support community-driven curation of cancer variants.

SUBMITTER: Danos AM

PROVIDER: S-EPMC6883603 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Standard operating procedure for curation and clinical interpretation of variants in cancer.

Danos Arpad M AM Krysiak Kilannin K Barnell Erica K EK Coffman Adam C AC McMichael Joshua F JF Kiwala Susanna S Spies Nicholas C NC Sheta Lana M LM Pema Shahil P SP Kujan Lynzey L Clark Kaitlin A KA Wollam Amber Z AZ Rao Shruti S Ritter Deborah I DI Sonkin Dmitriy D Raca Gordana G Lin Wan-Hsin WH Grisdale Cameron J CJ Kim Raymond H RH Wagner Alex H AH Madhavan Subha S Griffith Malachi M Griffith Obi L OL

Genome medicine 20191129 1

Manually curated variant knowledgebases and their associated knowledge models are serving an increasingly important role in distributing and interpreting variants in cancer. These knowledgebases vary in their level of public accessibility, and the complexity of the models used to capture clinical knowledge. CIViC (Clinical Interpretation of Variants in Cancer - www.civicdb.org) is a fully open, free-to-use cancer variant interpretation knowledgebase that incorporates highly detailed curation of ...[more]

PMID: 31779674

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Project description:INTRODUCTION: The ability of standard operating procedures to improve pre-hospital critical care by changing pre-hospital physician behaviour is uncertain. We report data from a prospective quality control study of the effect on pre-hospital critical care anaesthesiologists' behaviour of implementing a standard operating procedure for pre-hospital controlled ventilation. MATERIALS AND METHODS: Anaesthesiologists from eight pre-hospital critical care teams in the Central Denmark Region prospectively registered pre-hospital advanced airway-management data according to the Utstein-style template. We collected pre-intervention data from February 1st 2011 to January 31st 2012, implemented the standard operating procedure on February 1st 2012 and collected post intervention data from February 1st 2012 until October 31st 2012. We included transported patients of all ages in need of controlled ventilation treated with pre-hospital endotracheal intubation or the insertion of a supraglottic airways device. The objective was to evaluate whether the development and implementation of a standard operating procedure for controlled ventilation during transport could change pre-hospital critical care anaesthesiologists' behaviour and thereby increase the use of automated ventilators in these patients. RESULTS: The implementation of a standard operating procedure increased the overall prevalence of automated ventilator use in transported patients in need of controlled ventilation from 0.40 (0.34-0.47) to 0.74 (0.69-0.80) with a prevalence ratio of 1.85 (1.57-2.19) (p?=?0.00). The prevalence of automated ventilator use in transported traumatic brain injury patients in need of controlled ventilation increased from 0.44 (0.26-0.62) to 0.85 (0.62-0.97) with a prevalence ratio of 1.94 (1.26-3.0) (p?=?0.0039). The prevalence of automated ventilator use in patients transported after return of spontaneous circulation following pre-hospital cardiac arrest increased from 0.39 (0.26-0.48) to 0.69 (0.58-0.78) with a prevalence ratio of 1.79 (1.36-2.35) (p?=?0.00). CONCLUSION: We have shown that the implementation of a standard operating procedure for pre-hospital controlled ventilation can significantly change pre-hospital critical care anaesthesiologists' behaviour.

Project description:Clinical interpretation of DNA sequence variants is a critical step in reporting clinical genetic testing results. Application of next-generation sequencing technology in molecular genetic testing has facilitated diagnoses of genetic disorders in clinical practice. However, the large number of DNA sequence variants detected in clinical specimens, many of which have never been seen before, make clinical interpretation challenging. Recommendations by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) have been widely adopted by clinical laboratories around the world to guide clinical interpretation of sequence variants. The ClinGen Sequence Variant Interpretation Working Group and various disease-specific variant curation expert panels have also developed specifications for the ACMG/AMP recommendations. Despite these efforts to standardize variant interpretation in clinical practice, different laboratories may subjectively use professional judgment to determine which criteria are applicable when classifying a variant. In addition, clinicians and researchers who are not familiar with the variant interpretation process may have difficulty understanding clinical genetic reports and communicating the clinical significance of genetic testing results. Here we provide a step-by-step protocol for clinical interpretation of sequence variants, including practical examples. By following this protocol, clinical laboratory geneticists can interpret the clinical significance of sequence variants according to the ACMG/AMP recommendations and ClinGen framework. Furthermore, this article will help clinicians and researchers to understand variant classification in clinical genetic testing reports and evaluate the quality of the reports. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Interpreting the clinical significance of sequence variants Support Protocol: Reevaluating the clinical significance of sequence variants.

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Standard operating procedure for curation and clinical interpretation of variants in cancer.

Publications

Standard operating procedure for curation and clinical interpretation of variants in cancer.

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