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

CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase

View ORCID ProfileAlex H. Wagner, View ORCID ProfileSusanna Kiwala, View ORCID ProfileAdam C. Coffman, View ORCID ProfileJoshua F. McMichael, View ORCID ProfileKelsy C. Cotto, Thomas B. Mooney, View ORCID ProfileErica K. Barnell, View ORCID ProfileKilannin Krysiak, View ORCID ProfileArpad M. Danos, View ORCID ProfileObi L. Griffith, View ORCID ProfileMalachi Griffith
doi: https://doi.org/10.1101/783134
Alex H. Wagner
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
4Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alex H. Wagner
Susanna Kiwala
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Susanna Kiwala
Adam C. Coffman
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adam C. Coffman
Joshua F. McMichael
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joshua F. McMichael
Kelsy C. Cotto
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kelsy C. Cotto
Thomas B. Mooney
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erica K. Barnell
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Erica K. Barnell
Kilannin Krysiak
5Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kilannin Krysiak
Arpad M. Danos
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Arpad M. Danos
Obi L. Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63130
3Department of Genetics, Washington University School of Medicine, St. Louis, MO 63130
4Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Obi L. Griffith
  • For correspondence: obigriffith@wustl.edu
Malachi Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63130
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63130
3Department of Genetics, Washington University School of Medicine, St. Louis, MO 63130
4Department of Medicine, Washington University School of Medicine, St. Louis, MO 63130
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Malachi Griffith
  • For correspondence: obigriffith@wustl.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

Purpose Precision oncology is dependent upon 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, open-access knowledgebase, providing a structured framework for evaluating genomic variants of various types (e.g., fusions, SNVs) for their therapeutic, prognostic, predisposing, diagnostic, or functional utility. CIViC has a documented API 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 API, 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 (SDK) 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 AACR Project GENIE dataset. 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.

Conclusions 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, an SDK for downstream applications and rapid analysis. CIViCpy (civicpy.org) is fully documented, open-source, and freely available online.

Footnotes

  • http://civicpy.org

Copyright 
The copyright holder has placed this preprint in the Public Domain. It is no longer restricted by copyright. Anyone can legally share, reuse, remix, or adapt this material for any purpose without crediting the original authors.
Back to top
PreviousNext
Posted September 27, 2019.
Download PDF
Data/Code
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.
CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase
Alex H. Wagner, Susanna Kiwala, Adam C. Coffman, Joshua F. McMichael, Kelsy C. Cotto, Thomas B. Mooney, Erica K. Barnell, Kilannin Krysiak, Arpad M. Danos, Obi L. Griffith, Malachi Griffith
bioRxiv 783134; doi: https://doi.org/10.1101/783134
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase
Alex H. Wagner, Susanna Kiwala, Adam C. Coffman, Joshua F. McMichael, Kelsy C. Cotto, Thomas B. Mooney, Erica K. Barnell, Kilannin Krysiak, Arpad M. Danos, Obi L. Griffith, Malachi Griffith
bioRxiv 783134; doi: https://doi.org/10.1101/783134

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 (3479)
  • Biochemistry (7318)
  • Bioengineering (5296)
  • Bioinformatics (20197)
  • Biophysics (9976)
  • Cancer Biology (7703)
  • Cell Biology (11250)
  • Clinical Trials (138)
  • Developmental Biology (6418)
  • Ecology (9916)
  • Epidemiology (2065)
  • Evolutionary Biology (13280)
  • Genetics (9352)
  • Genomics (12554)
  • Immunology (7674)
  • Microbiology (18939)
  • Molecular Biology (7417)
  • Neuroscience (40893)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2126)
  • Physiology (3140)
  • Plant Biology (6838)
  • Scientific Communication and Education (1270)
  • Synthetic Biology (1891)
  • Systems Biology (5296)
  • Zoology (1085)