Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
Confirmatory Results

Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L. Griffith, Peter McGarvey, Shashikant Kulkarni, The Clingen Somatic Working Group
doi: https://doi.org/10.1101/212225
Subha Madhavan
Innovation Center for Biomedical Informatics, Georgetown University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: sm696@georgetown.edu
Deborah Ritter
Baylor College of Medicine and Texas Children's Hospital;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christine Micheel
Vanderbilt University School of Medicine;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shruti Rao
Innovation Center for Biomedical Informatics, Georgetown University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Angshumoy Roy
Baylor College of Medicine and Texas Children's Hospital;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dmitriy Sonkin
National Cancer Institute;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Matthew McCoy
Innovation Center for Biomedical Informatics, Georgetown University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Malachi Griffith
The McDonnell Genome Institute, Washington University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Obi L. Griffith
The McDonnell Genome Institute, Washington University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Peter McGarvey
Innovation Center for Biomedical Informatics, Georgetown University;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shashikant Kulkarni
Baylor College of Medicine and Texas Children's Hospital;
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
-
  • Abstract
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

A growing number of academic and community clinics are conducting genomic testing to inform treatment decisions for cancer patients. In the last 3-5 years, there has been a rapid increase in clinical use of next generation sequencing (NGS) based cancer molecular diagnostic (MolDx) testing. The increasing availability and decreasing cost of tumor genomic profiling means that physicians can now make treatment decisions armed with patient-specific genetic information. Accumulating research in the cancer biology field indicates that there is significant potential to improve cancer patient outcomes by effectively leveraging this rich source of genomic data in treatment planning. To achieve truly personalized medicine in oncology, it is critical to catalog cancer sequence variants from MolDx testing for their clinical relevance along with treatment information and patient outcomes, and to do so in a way that supports large-scale data aggregation and new hypothesis generation. One critical challenge to encoding variant data is adopting a standard of annotation of those variants that are clinically actionable. Through the NIH-funded Clinical Genome Resource (ClinGen), in collaboration with NLM ClinVar database and >50 academic and industry based cancer research organizations, we developed the Minimal Variant Level Data (MVLD) framework to standardize reporting and interpretation of drug associated alterations. We are currently involved in collaborative efforts to align the MVLD framework with parallel, complementary sequence variants interpretation clinical guidelines from the Association of Molecular Pathologists (AMP) for clinical labs. In order to truly democratize access to MolDx data for care and research needs, these standards must be harmonized to support sharing of clinical cancer variants. Here we describe the processes and methods developed within the ClinGen Somatic WG in collaboration with over 60 cancer care and research organizations as well as CLIA-certified, CAP-accredited clinical testing labs to develop standards for cancer variant interpretation and sharing.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted November 01, 2017.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research
Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L. Griffith, Peter McGarvey, Shashikant Kulkarni, The Clingen Somatic Working Group
bioRxiv 212225; doi: https://doi.org/10.1101/212225
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Clingen Cancer Somatic Working Group: standardizing and democratizing access to cancer molecular diagnostic data to drive translational research
Subha Madhavan, Deborah Ritter, Christine Micheel, Shruti Rao, Angshumoy Roy, Dmitriy Sonkin, Matthew McCoy, Malachi Griffith, Obi L. Griffith, Peter McGarvey, Shashikant Kulkarni, The Clingen Somatic Working Group
bioRxiv 212225; doi: https://doi.org/10.1101/212225

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (999)
  • Biochemistry (1492)
  • Bioengineering (946)
  • Bioinformatics (6832)
  • Biophysics (2429)
  • Cancer Biology (1791)
  • Cell Biology (2530)
  • Clinical Trials (106)
  • Developmental Biology (1700)
  • Ecology (2575)
  • Epidemiology (1495)
  • Evolutionary Biology (5030)
  • Genetics (3623)
  • Genomics (4636)
  • Immunology (1171)
  • Microbiology (4252)
  • Molecular Biology (1629)
  • Neuroscience (10799)
  • Paleontology (83)
  • Pathology (240)
  • Pharmacology and Toxicology (409)
  • Physiology (555)
  • Plant Biology (1457)
  • Scientific Communication and Education (412)
  • Synthetic Biology (542)
  • Systems Biology (1878)
  • Zoology (259)