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

sigQC: A procedural approach for standardising the evaluation of gene signatures

Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
doi: https://doi.org/10.1101/203729
Andrew Dhawan
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alessandro Barberis
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wei-Chen Cheng
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Enric Domingo
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Catharine West
2University of Manchester, Manchester, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tim Maughan
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jacob G. Scott
3Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Adrian L. Harris
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Francesca M. Buffa
1Department of Oncology, University of Oxford, Oxford, United Kingdom
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

With the increase in next generation sequencing generating large amounts of genomic data, gene expression signatures are becoming critically important tools, poised to make a large impact on the diagnosis, management and prognosis for a number of diseases. Increasingly, it is becoming necessary to determine whether a gene expression signature may apply to a dataset, but no standard quality control methodology exists. In this work, we introduce the first protocol, implemented in an R package sigQC, enabling a streamlined methodological and standardised approach for the quality control validation of gene signatures on independent data sets. The emphasis in this work is in showing the critical quality control steps involved in the generation of a clinically and biologically useful, transportable gene signature, including ensuring sufficient expression, variability, and autocorrelation of a signature. We demonstrate the application of the protocol in this work, showing how the outputs created from sigQC may be used for the evaluation of gene signatures on large-scale gene expression data in cancer.

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 13, 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.
sigQC: A procedural approach for standardising the evaluation of gene signatures
(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
sigQC: A procedural approach for standardising the evaluation of gene signatures
Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
bioRxiv 203729; doi: https://doi.org/10.1101/203729
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
sigQC: A procedural approach for standardising the evaluation of gene signatures
Andrew Dhawan, Alessandro Barberis, Wei-Chen Cheng, Enric Domingo, Catharine West, Tim Maughan, Jacob G. Scott, Adrian L. Harris, Francesca M. Buffa
bioRxiv 203729; doi: https://doi.org/10.1101/203729

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 (3609)
  • Biochemistry (7590)
  • Bioengineering (5533)
  • Bioinformatics (20833)
  • Biophysics (10347)
  • Cancer Biology (7998)
  • Cell Biology (11663)
  • Clinical Trials (138)
  • Developmental Biology (6619)
  • Ecology (10227)
  • Epidemiology (2065)
  • Evolutionary Biology (13647)
  • Genetics (9557)
  • Genomics (12859)
  • Immunology (7931)
  • Microbiology (19575)
  • Molecular Biology (7678)
  • Neuroscience (42192)
  • Paleontology (309)
  • Pathology (1259)
  • Pharmacology and Toxicology (2208)
  • Physiology (3272)
  • Plant Biology (7064)
  • Scientific Communication and Education (1295)
  • Synthetic Biology (1953)
  • Systems Biology (5434)
  • Zoology (1119)