GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes.

BMC Medical Informatics and Decision Making
Aiguo LiHoward A Fine

Abstract

Advances in generating genome-wide gene expression data have accelerated the development of molecular-based tumor classification systems. Tools that allow the translation of such molecular classification schemas from research into clinical applications are still missing in the emerging era of personalized medicine. We developed GliomaPredict as a computational tool that allows the fast and reliable classification of glioma patients into one of six previously published stratified subtypes based on sets of extensively validated classifiers derived from hundreds of glioma transcriptomic profiles. Our tool utilizes a principle component analysis (PCA)-based approach to generate a visual representation of the analyses, quantifies the confidence of the underlying subtype assessment and presents results as a printable PDF file. GliomaPredict tool is implemented as a plugin application for the widely-used GenePattern framework. GliomaPredict provides a user-friendly, clinically applicable novel platform for instantly assigning gene expression-based subtype in patients with gliomas thereby aiding in clinical trial design and therapeutic decision-making. Implemented as a user-friendly diagnostic tool, we expect that in time GliomaPredict...Continue Reading

References

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Feb 27, 2009·Cancer Research·Aiguo LiHoward A Fine

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Citations

Mar 16, 2013·Bioinformatics·Thierry RèmeBernard Klein
Oct 4, 2012·Future Oncology·Maryam RahmanGregory J A Murad
Nov 16, 2013·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Norberto A GandiniAlejandro C Curino
Jun 15, 2014·BMC Medical Informatics and Decision Making·Fabien Subtil, Muriel Rabilloud
Apr 25, 2012·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Pedro R Lowenstein, Maria G Castro
Jan 13, 2015·Clinical Medicine Insights. Oncology·Antti Jekunen
Jul 6, 2011·Nature Reviews. Neurology·Gregory Riddick, Howard A Fine
Aug 4, 2011·Nature Reviews. Neuroscience·Manfred Westphal, Katrin Lamszus
Jun 23, 2011·Expert Review of Vaccines·Alfred P SeeMichael Lim
Mar 4, 2014·Journal of Neuro-oncology·Débora G SalomónMaría M Facchinetti

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Methods Mentioned

BETA
ChIP-ChIP
PCA
pulldown

Software Mentioned

Windows dChip
PCAview
Windows
dChip
Linux
gdChip
PAMR
Perl
GenePattern
MATLAB Statistics Toolbox

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