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Li MM, Cottrell CE, Pullambhatla M, Roy S, Temple-Smolkin RL, Turner SA, Wang K, Zhou Y, Vnencak-Jones CL. Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology. J Mol Diagn 2023; 25:69-86. [PMID: 36503149 DOI: 10.1016/j.jmoldx.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/09/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. A total of 134 participants participated in the variant interpretation challenges, consisting of 11 variants in four cancer cases. Results demonstrate 86% (range, 54% to 94%) of the respondents correctly classified clinically significant variants, variants of uncertain significance, and benign/likely benign variants; however, only 59% (range, 39% to 84%) of responses agreed with the working group's consensus intended responses regarding both tiers and categories of clinical significance. In the implementation survey, 71% (157/220) of respondents have implemented the 2017 guidelines for variant classification and reporting either with or without modifications. Collectively, this study demonstrates that, although they may not yet be optimized, the 2017 guideline recommendations are being adopted for standardized somatic variant classification. The working group identified significant areas for future guideline improvement, including the need for a more granular and comprehensive classification system and education resources to meet the growing needs of both laboratory professionals and medical oncologists.
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Affiliation(s)
- Marilyn M Li
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Catherine E Cottrell
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio
| | | | - Somak Roy
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Scott A Turner
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Kai Wang
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Yunyun Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cindy L Vnencak-Jones
- The Variant Interpretation Testing Across Laboratories (VITAL) Somatic Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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Salehipour D, Farncombe KM, Andric V, Ansar S, Delong S, Li E, Macpherson S, Ridd S, Ritter DI, Thaxton C, Kim RH. Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is. Database (Oxford) 2023; 2023:6972759. [PMID: 36617168 PMCID: PMC9825735 DOI: 10.1093/database/baac109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 11/23/2022] [Accepted: 12/09/2022] [Indexed: 01/09/2023]
Abstract
Von Hippel-Lindau (VHL) disease is a rare, autosomal dominant disorder that predisposes individuals to developing tumors in many organs. There is significant phenotypic variability and genetic variants encountered within this syndrome, posing a considerable challenge to patient care. The lack of VHL variant data sharing paired with the absence of aggregated genotype-phenotype information results in an arduous process, when characterizing genetic variants and predicting patient prognosis. To address these gaps in knowledge, the Clinical Genome Resource (ClinGen) VHL Variant Curation Expert Panel (VCEP) has been resolving a list of variants of uncertain significance within the VHL gene. Through community curation, we crowdsourced the laborious task of variant annotation by modifying the ClinGen Community Curation (C3)-developed Baseline Annotation protocol and annotating all published VHL cases with the reported genotype-phenotype information in Hypothes.is, an open-access web annotation tool. This process, incorporated into the ClinGen VCEP's workflow, will aid in their curation efforts. To facilitate the curation at all levels of genetics expertise, our team developed a 4-day biocuration training protocol and resource guide. To date, 91.3% of annotations have been completed by undergraduate and high-school students without formal academic genetics specialization. Here, we present our VHL-specific annotation protocol utilizing Hypothes.is, which offers a standardized method to present case-resolution data, and our biocuration training protocol, which can be adapted for other rare disease platforms. By facilitating training for community curation of VHL disease, we increased student engagement with clinical genetics while enhancing knowledge translation in the field of hereditary cancer. Database URL: https://hypothes.is/groups/dKymJJpZ/vhl-hypothesis-annotation.
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Affiliation(s)
- Dena Salehipour
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, 200 Elizabeth St, Toronto, ON M5G 2C4, Canada
| | - Veronica Andric
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Safa Ansar
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Sean Delong
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Eric Li
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Samantha Macpherson
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Sarah Ridd
- Department of Medicine, Division of Medical Oncology, University Health Network, 620 University Ave, Toronto, ON M5G 2C1, Canada
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, 1102 Bates Ave, Houston, TX 77030, USA
| | - Courtney Thaxton
- Department of Genetics, University of North Carolina, 120 Mason Farm Rd, Chapel Hill, Chapel Hill, NC 27514, USA
| | - Raymond H Kim
- *Corresponding author: Tel: +416-946-2270; Fax: +416-946-6528;
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Wilhelm K, Edick MJ, Berry SA, Hartnett M, Brower A. Using Long-Term Follow-Up Data to Classify Genetic Variants in Newborn Screened Conditions. Front Genet 2022; 13:859837. [PMID: 35692825 PMCID: PMC9178101 DOI: 10.3389/fgene.2022.859837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022] Open
Abstract
With the rapid increase in publicly available sequencing data, healthcare professionals are tasked with understanding how genetic variation informs diagnosis and affects patient health outcomes. Understanding the impact of a genetic variant in disease could be used to predict susceptibility/protection and to help build a personalized medicine profile. In the United States, over 3.8 million newborns are screened for several rare genetic diseases each year, and the follow-up testing of screen-positive newborns often involves sequencing and the identification of variants. This presents the opportunity to use longitudinal health information from these newborns to inform the impact of variants identified in the course of diagnosis. To test this, we performed secondary analysis of a 10-year natural history study of individuals diagnosed with metabolic disorders included in newborn screening (NBS). We found 564 genetic variants with accompanying phenotypic data and identified that 161 of the 564 variants (29%) were not included in ClinVar. We were able to classify 139 of the 161 variants (86%) as pathogenic or likely pathogenic. This work demonstrates that secondary analysis of longitudinal data collected as part of NBS finds unreported genetic variants and the accompanying clinical information can inform the relationship between genotype and phenotype.
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Affiliation(s)
- Kevin Wilhelm
- Newborn Screening Translational Research Network, American College of Medical Genetics and Genomics, Bethesda, MD, United States
- Graduate Program in Genetics and Genomics, Graduate School of Biological Sciences, Baylor College of Medicine, Houston, TX, United States
| | | | - Susan A. Berry
- Department of Pediatrics, Division of Genetics and Metabolism, University of Minnesota, Minneapolis, MN, United States
| | - Michael Hartnett
- Newborn Screening Translational Research Network, American College of Medical Genetics and Genomics, Bethesda, MD, United States
| | - Amy Brower
- Newborn Screening Translational Research Network, American College of Medical Genetics and Genomics, Bethesda, MD, United States
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Krysiak K, Danos AM, Kiwala S, McMichael JF, Coffman AC, Barnell EK, Sheta L, Saliba J, Grisdale CJ, Kujan L, Pema S, Lever J, Spies NC, Chiorean A, Rieke DT, Clark KA, Jani P, Takahashi H, Horak P, Ritter DI, Zhou X, Ainscough BJ, Delong S, Lamping M, Marr AR, Li BV, Lin WH, Terraf P, Salama Y, Campbell KM, Farncombe KM, Ji J, Zhao X, Xu X, Kanagal-Shamanna R, Cotto KC, Skidmore ZL, Walker JR, Zhang J, Milosavljevic A, Patel RY, Giles RH, Kim RH, Schriml LM, Mardis ER, Jones SJM, Raca G, Rao S, Madhavan S, Wagner AH, Griffith OL, Griffith M. A community approach to the cancer-variant-interpretation bottleneck. NATURE CANCER 2022; 3:522-525. [PMID: 35624339 PMCID: PMC9872366 DOI: 10.1038/s43018-022-00379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As guidelines, therapies, and literature on cancer variants expand, the lack of consensus variant interpretations impedes clinical applications. CIViC is a public domain, crowd-sourced, and adaptable knowledgebase of evidence for the Clinical Interpretation of Variants in Cancer, designed to reduce barriers to knowledge sharing and alleviate the variant interpretation bottleneck.
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Affiliation(s)
- Kilannin Krysiak
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Arpad M Danos
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Lana Sheta
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason Saliba
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Lynzey Kujan
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Shahil Pema
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jake Lever
- School of Computer Science, University of Glasgow, Glasgow, UK
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Andreea Chiorean
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Damian T Rieke
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kaitlin A Clark
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Payal Jani
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Hideaki Takahashi
- Department of Experimental Therapeutics/Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Peter Horak
- Department of Translational Medical Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Deborah I Ritter
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Benjamin J Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sean Delong
- Lassonde School of Engineering, York University, Toronto, Ontario, Canada
| | - Mario Lamping
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alex R Marr
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian V Li
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Panieh Terraf
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasser Salama
- Department of Medicine, Division of Medical Oncology, University Health Network, Toronto, Ontario, Canada
| | - Katie M Campbell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Jianling Ji
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelsy C Cotto
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Ronak Y Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rachel H Giles
- International Kidney Cancer Coalition, Amsterdam, the Netherlands
| | - Raymond H Kim
- Fred A. Litwin Family Centre in Genetic Medicine, Familial Cancer Clinic, Princess Margaret Cancer Centre, University Health Network, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Neurosurgery, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Gordana Raca
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Saliba J, Church AJ, Rao S, Danos A, Furtado LV, Laetsch T, Zhang L, Nardi V, Lin WH, Ritter D, Madhavan S, Li MM, Griffith OL, Griffith M, Raca G, Roy A. Standardized Evidence-Based Approach for Assessment of Oncogenic and Clinical Significance of NTRK Fusions. Cancer Genet 2022; 264-265:50-59. [DOI: 10.1016/j.cancergen.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/13/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
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Cree IA, Indave Ruiz BI, Zavadil J, McKay J, Olivier M, Kozlakidis Z, Lazar AJ, Hyde C, Holdenrieder S, Hastings R, Rajpoot N, de la Fouchardiere A, Rous B, Zenklusen JC, Normanno N, Schilsky RL. The International Collaboration for Cancer Classification and Research. Int J Cancer 2021; 148:560-571. [PMID: 32818326 PMCID: PMC7756795 DOI: 10.1002/ijc.33260] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/21/2022]
Abstract
Gaps in the translation of research findings to clinical management have been recognized for decades. They exist for the diagnosis as well as the management of cancer. The international standards for cancer diagnosis are contained within the World Health Organization (WHO) Classification of Tumours, published by the International Agency for Research on Cancer (IARC) and known worldwide as the WHO Blue Books. In addition to their relevance to individual patients, these volumes provide a valuable contribution to cancer research and surveillance, fulfilling an important role in scientific evidence synthesis and international standard setting. However, the multidimensional nature of cancer classification, the way in which the WHO Classification of Tumours is constructed, and the scientific information overload in the field pose important challenges for the translation of research findings to tumour classification and hence cancer diagnosis. To help address these challenges, we have established the International Collaboration for Cancer Classification and Research (IC3 R) to provide a forum for the coordination of efforts in evidence generation, standard setting and best practice recommendations in the field of tumour classification. The first IC3 R meeting, held in Lyon, France, in February 2019, gathered representatives of major institutions involved in tumour classification and related fields to identify and discuss translational challenges in data comparability, standard setting, quality management, evidence evaluation and copyright, as well as to develop a collaborative plan for addressing these challenges.
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Affiliation(s)
- Ian A. Cree
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | | | - Jiri Zavadil
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - James McKay
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Magali Olivier
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Zisis Kozlakidis
- International Agency for Research on Cancer (IARC), World Health Organization (WHO)LyonFrance
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular PathologyThe University of Texas, MD Anderson Cancer CenterHoustonTexasUSA
| | - Chris Hyde
- Exeter Test GroupCollege of Medicine and Health, University of ExeterExeterUK
| | | | - Ros Hastings
- GenQA (Genomics External Quality Assessment)Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation TrustOxfordUK
| | - Nasir Rajpoot
- Department of Computer ScienceUniversity of WarwickCoventryUK
- Alan Turing InstituteLondonUK
- Department of PathologyUniversity Hospitals Coventry & Warwickshire NHS TrustCoventryUK
| | | | - Brian Rous
- National Cancer Registration Service (Eastern Office), Public Health England, Victoria HouseCambridgeUK
| | - Jean Claude Zenklusen
- Center for Cancer GenomicsNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Nicola Normanno
- Cell Biology and Biotherapy UnitIstituto Nazionale Tumori—IRCCS—“Fondazione G. Pascale,” Via M. SemmolaNaplesItaly
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7
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Wagner AH, Kiwala S, Coffman AC, McMichael JF, Cotto KC, Mooney TB, Barnell EK, Krysiak K, Danos AM, Walker J, Griffith OL, Griffith M. CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase. JCO Clin Cancer Inform 2020; 4:245-253. [PMID: 32191543 PMCID: PMC7113080 DOI: 10.1200/cci.19.00127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Precision oncology depends on the matching of tumor variants to relevant knowledge describing the clinical significance of those variants. We recently developed the Clinical Interpretations for Variants in Cancer (CIViC; civicdb.org) crowd-sourced, expert-moderated, and open-access knowledgebase. CIViC provides a structured framework for evaluating genomic variants of various types (eg, fusions, single-nucleotide variants) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented application programming interface for accessing CIViC records: assertions, evidence, variants, and genes. Third-party tools that analyze or access the contents of this knowledgebase programmatically must leverage this application programming interface, often reimplementing redundant functionality in the pursuit of common analysis tasks that are beyond the scope of the CIViC Web application. METHODS To address this limitation, we developed CIViCpy (civicpy.org), a software development kit for extracting and analyzing the contents of the CIViC knowledgebase. CIViCpy enables users to query CIViC content as dynamic objects in Python. We assess the viability of CIViCpy as a tool for advancing individualized patient care by using it to systematically match CIViC evidence to observed variants in patient cancer samples. RESULTS We used CIViCpy to evaluate variants from 59,437 sequenced tumors of the American Association for Cancer Research Project GENIE data set. We demonstrate that CIViCpy enables annotation of > 1,200 variants per second, resulting in precise variant matches to CIViC level A (professional guideline) or B (clinical trial) evidence for 38.6% of tumors. CONCLUSION The clinical interpretation of genomic variants in cancers requires high-throughput tools for interoperability and analysis of variant interpretation knowledge. These needs are met by CIViCpy, a software development kit for downstream applications and rapid analysis. CIViCpy is fully documented, open-source, and available free online.
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Affiliation(s)
- Alex H. Wagner
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
- Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Adam C. Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Joshua F. McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Kelsy C. Cotto
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Thomas B. Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Erica K. Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Kilannin Krysiak
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - Arpad M. Danos
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Jason Walker
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
| | - Obi L. Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
- Department of Medicine, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
- Department of Genetics, Washington University School of Medicine, St Louis, MO
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO
- Department of Medicine, Washington University School of Medicine, St Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St Louis, MO
- Department of Genetics, Washington University School of Medicine, St Louis, MO
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8
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Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, Raca G, Lin WH, Grisdale CJ, Kim RH, Wagner AH, Madhavan S, Griffith M, Griffith OL. Standard operating procedure for curation and clinical interpretation of variants in cancer. Genome Med 2019; 11:76. [PMID: 31779674 PMCID: PMC6883603 DOI: 10.1186/s13073-019-0687-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/07/2019] [Indexed: 02/04/2023] Open
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.
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Affiliation(s)
- Arpad M Danos
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Erica K Barnell
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Adam C Coffman
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua F McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas C Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lana M Sheta
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Shahil P Pema
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lynzey Kujan
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Kaitlin A Clark
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Amber Z Wollam
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, USA
| | - Deborah I Ritter
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA
| | - Gordana Raca
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Wan-Hsin Lin
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Cameron J Grisdale
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Raymond H Kim
- Fred A. Litwin Family Center in Genetic Medicine, University Health Network, Toronto, ON, Canada
| | - Alex H Wagner
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington DC, USA.,Georgetown Lombardi Comprehensive Cancer Center, Washington DC, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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9
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Ritter DI, Rao S, Kulkarni S, Madhavan S, Offit K, Plon SE. A case for expert curation: an overview of cancer curation in the Clinical Genome Resource (ClinGen). Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004739. [PMID: 31645350 PMCID: PMC6824250 DOI: 10.1101/mcs.a004739] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We describe the Clinical Genome Resource (ClinGen) cancer-related curation activities and the importance of curation to the evolving state of variant interpretation in a clinical context for both pediatric and adult cancer patients. We highlight specific examples from the CDH1 and PTEN Variant Curation Expert Panels (VCEPs) of the FDA-recognized process by which ClinGen VCEPs specify the American College of Medical Genetics and Genomics/Association of Molecular Pathology evidence code to develop variant classifications. We also review gene curations performed within the Hereditary Cancer Clinical Domain. We describe the parallel efforts for curation of somatic cancer variants from the Somatic Cancer Working Group. The ClinGen Germline/Somatic Committee is working to improve incorporation of both hereditary and somatic variant data to aid clinical interpretation. These ClinGen efforts rely on broad data sharing and detailed phenotypic and molecular information from published case studies to provide expert-curated variant interpretation to the cancer community.
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Affiliation(s)
- Deborah I Ritter
- Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
| | - Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, D.C. 20007, USA
| | - Shashikant Kulkarni
- Baylor College of Medicine, Houston, Texas 77030, USA.,Baylor Genetics, Houston, Texas 77021, USA
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, D.C. 20007, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Sloan Kettering Institute, New York, New York 10065, USA
| | - Sharon E Plon
- Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Cancer Center, Texas Children's Hospital, Houston, Texas 77030, USA
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10
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Takeuchi S, Okuda S. Knowledge base toward understanding actionable alterations and realizing precision oncology. Int J Clin Oncol 2019; 24:123-130. [PMID: 30542800 PMCID: PMC6373253 DOI: 10.1007/s10147-018-1378-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 02/08/2023]
Abstract
In Japan, the National Cancer Center and university hospitals have initiated next-generation sequencing-based in vitro diagnostic testing for cancer patients as a method of clinical sequencing. Based on the molecular alterations detected, physicians can provide approved targeted therapy and access to investigational drugs for cancer patients. However, interpretation of the clinical significance of genomic alterations remains the most severe bottleneck of precision medicine in cancer. Although many research institutes in the United States are developing knowledge bases for interpretation of the tumor alterations and clinical decisions, these knowledge bases are unsuited as sources of reference in Japan due to differences in the information on approved drugs and implementation of clinical trials. In this review, we introduce knowledge bases for clinical decision-making based on genomic events in cancer, and discuss the resources of additional information necessary for implementing precision medicine in Japan.
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Affiliation(s)
- Shiho Takeuchi
- Division of Cancer Genome Informatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Shujiro Okuda
- Division of Cancer Genome Informatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.
- Division of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.
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11
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Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, Kujan L, Kulkarni S, Griffith M, Madhavan S, Griffith OL. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Hum Mutat 2018; 39:1721-1732. [PMID: 30311370 PMCID: PMC6282863 DOI: 10.1002/humu.23651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/02/2018] [Accepted: 08/28/2018] [Indexed: 12/19/2022]
Abstract
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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Affiliation(s)
- Arpad M. Danos
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | | | - Alex H. Wagner
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Kilannin Krysiak
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and DiagnosisNational Cancer InstituteRockvilleMaryland
| | | | - Matthew McCoy
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Shruti Rao
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Gordana Raca
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Simina M. Boca
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | | | - Erica K. Barnell
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Joshua F. McMichael
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Susanna Kiwala
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Adam C. Coffman
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Lynzey Kujan
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Shashikant Kulkarni
- Baylor College of MedicineHoustonTexas
- Baylor GeneticsHoustonTexas
- Dan L. Duncan Cancer CenterHoustonTexas
| | - Malachi Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
| | - Subha Madhavan
- Georgetown Lombardi Comprehensive Cancer CenterWashingtonDistrict of Columbia
| | - Obi L. Griffith
- McDonnell Genome InstituteWashington University School of MedicineSaint LouisMissouri
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12
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Rehm HL, Berg JS, Plon SE. ClinGen and ClinVar – Enabling Genomics in Precision Medicine. Hum Mutat 2018. [DOI: 10.1002/humu.23654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Heidi L. Rehm
- Medical and Population Genetics ProgramThe Broad Institute of MIT and Harvard Cambridge Massachusetts
- Center for Genomic MedicineMassachusetts General Hospital Boston Massachusetts
| | - Jonathan S. Berg
- Department of GeneticsUniversity of North Carolina at Chapel Hill Chapel Hill North Carolina
| | - Sharon E. Plon
- Departments of Molecular and Human Genetics and PediatricsBaylor College of Medicine Houston Texas
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