Summary

The TCGA Glioma Phenotype Research Group is part of the CIP TCGA Radiology Initiative focused on analyzing images from the TCGA-GBM and TCGA-LGG collections. The group began as an ad hoc multi-institutional research team dedicated to discovering the value of applying controlled terminology to the MR imaging features of patients with gliomas (see: VASARI Research Project). Research trials that incorporate imaging present unique challenges due to nonstandard use of terminologies, absence of uniform data collection and validation. These obstacles traditionally limit the impact of imaging as an effective biomarker in oncology. The original purpose of this project was to assess reliability of tools and terminology developed by the Cancer Bioinformatics Grid (caBIG) initiative when performing a multireader simultaneous assessments of glioblastoma MR imaging features. It has since grown into a number of diverse research initiatives conducted by geographically disparate open science research teams.

Starting or Joining a Research Project

We are currently hosting calls in support of TCGA glioma based research projects (TCGA-GBM or TCGA-LGG) on Mondays at 3pm Eastern. Please contact us at cancerimagingarchive@mail.nih.gov if you would like to inquire about setting up a new research project, discuss potential collaborations with existing groups or be otherwise kept in the loop as this effort moves forward.

Group Projects

This is a listing of ongoing projects. If you are working with the TCGA glioma data hosted on TCIA please let us know and we would be happy to add a section describing your project here.

VASARI Research Project - Multiple readers reviewing TCGA brain cases and evaluating them based on the VASARI feature set and evaluating the results for reader agreement along with possible connection to related clinical/genetic/pathology data collected for the TCGA. This project is being led by Adam Flanders at Thomas Jefferson University.
DSC T2* MR Perfusion Analysis - Survival prediction using molecular classification of glioblastomas using DSC T2* MR perfusion. This project has been accepted/presented at multiple conferences (see below) and is being led by Rajan Jain at Henry Ford Hospital.
Prediction of outcome using clinical, imaging and genetic information - This project seeks to use the VASARI Research Project output in combination with data from the TCGA Data Portal to evaluate survival and time to recurrence. This project is being led by Max Wintermark and Manal Nicolas Jilwan of the University of Virginia.
Mapping of Edema/Cellular Invasion to MR Phenotypes - This project set out to present the first comprehensive radiogenomic analysis using quantitative MRI volumetrics and large-scale gene- and microRNA expression profiling in GBM. This project was led by Pascal Zinn and Rivka Colen of MDACC and BWH respectively.
Growth Kinetics - A collaboration between Andrew Trister at Sage Bionetworks and Kristin Swanson at the University of Washington to make measurements of tumor growth kinetics in two modes (diffusion and proliferation) from pretreatment MRIs.
Man-machine correlation of VASARI features between human and machine observers - This project is being led by Dave Gutman (Emory) and Rivka Colen (BWH).
Analysis of Diffusion-Sensitized MRI for Predicting the Histopathologic, Genomic, and Clinical Features - This is a newer project being initiated and led by Scott Hwang at Emory University
CAD Texture Analysis - Led by Ashlee Byrd and Brad Erickson at Mayo, they are using multispectral features, including intensity, texture, and morphology, to identify imaging features that predict genetic patterns.
Clustering (supervised & unsupervised) of GBM data - Cases are clustered into semantically-distinct categories using image-derived features, followed by examination of genomic correlates from the obtained clusters. Led by Arvind Rao, Jim Chen, and Adam Flanders.
Stanford TCGA radiogenomics project: We are studying computational image features that characterize shape, texture and size of glioblastoma multiforme patients. More specifically, we extract computational image features from MRI images and investigate their clinical relevance and correlation with molecular data. Investigators: Olivier Gevaert, Sylvia Plevritis.
Quantitative imaging features extraction from perfusion imaging - We are extracting perfusion features from different anatomical regions of GBM tumors (enhancing and necrotic regions) to quantify tumor heterogeneity. We are working on correlating perfusion imaging features with molecular characterization as well as defining subtypes of GBM predictive of overall survival using molecular and perfusion imaging features. The investigators of this project are Tiffany Liu and Daniel Rubin at Stanford University.

Group Publications

Citation	TCIA Shared Lists	Supporting Materials
Jain R, Poisson L, Narang J, Gutman D, Scarpace L, Hwang SN, Holder C, Wintermark M, Colen RR, Kirby J, Freymann J, Brat DJ, Jaffe C, Mikkelsen T. Genomic Mapping and Survival Prediction in Glioblastoma: Molecular Subclassification Strengthened by Hemodynamic Imaging Biomarkers. <ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="2dd7ec15-72a1-4e6c-8f28-12d0adfe3e43"><ac:plain-text-body><![CDATA[Radiology. 2012 Dec 13. [Epub ahead of print] ([link	http://www.ncbi.nlm.nih.gov/pubmed/23238158])	TCGA-GBM DSC T2* MR Perfusion - contains the raw perfusion image studies]]></ac:plain-text-body></ac:structured-macro> TCGA-GBM DSC T2* nordicICE - contains the post-processed nordiceICE perfusion image studies	Spreadsheet - contains scaling factors, rCBV values, and scanner info Text files – contains text dumps of DICOM elements for nordicICE perfusion image studies
Zinn PO, Sathyan P, Mahajan B, Bruyere J, Hegi M, et al. (2012) A Novel Volume-Age-KPS (VAK) Glioblastoma Classification Identifies a Prognostic Cognate microRNA-Gene Signature. PLoS ONE 7(8): e41522. doi:10.1371/journal.pone.0041522 (link)
Zinn PO, Majadan B, Sathyan P, Singh SK, Majumder S, et al. 2011 Radiogenomic Mapping of Edema/Cellular Invasion MRI-Phenotypes in Glioblastoma Multiforme. PLoS ONE 6(10): e25451. doi:10.1371/journal.pone.0025451 (link)	Radiogenomic Mapping of Edema/Cellular Invasion MRI-Phenotypes

Note: For more information on how Shared Lists are used to cite and share data please view our TCIA Citation Guidelines.

References

This section contains papers, presentations, and videos from the genomics/clinical/pathology perspectives which may be of interest to the glioma imaging group.

2nd Annual TCGA Symposium

The Somatic Genomic Landscape of Glioblastoma Multiforme
- Roel Verhaak, PhD, The University of Texas MD Anderson Cancer Center
- Video | Slides

Selected Publications

Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN; Cancer Genome Atlas Research Network. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010 Jan 19;17(1):98-110. doi: 10.1016/j.ccr.2009.12.020. (Full Text, verhaak-patient-characteristics.xls)
Cooper LAD, Gutman DA, Chisolm C, Appin C, Kong J, Rong Y, Kurc T, Van Meir EG, Saltz JH, Moreno CS, Brat DJ. The Tumor Microenvironment Strongly Impacts Master Transcriptional Regulators and Gene Expression Class of Glioblastoma. American Journal of Pathology 180(5):2108-19, May 2012 (Link)
Cooper LAD, Kong J, Gutman DA, Wang F, Gao J, Appin C, Cholleti S, Pan T, Sharma A, Scarpace L, Mikkelsen T, Kurc T, Moreno CS, Brat DJ, Saltz JH. Integrated Morphologic Analysis for the Identification and Characterization of Disease Subtypes. J Am Med Inform Assoc. 19(2):317-23, Mar-Apr 2012 (Full Text)

Conference Abstracts

RSNA 2012 (Nov 25-Nov 30, 2012, Chicago, IL)

Presentations

Title	Time and Location	Supporting Materials
Predicting Genomic Features of Glioblastomas by Quantitative Analysis of Diffusion-weighted and Diffusion-Tensor Imaging (VSNR21-10) Scott Hwang, Chad Holder, Rajan Jain, Max Wintermark, Rivka Colen, Justin Kirby, Erich Huang, John Freymann, Carl Jaffe, Adam Flanders	Time: Mon, Nov 26, 2012, 11:00-11:10AM Location: E451B
A Novel MRI-based Prognostic Classification Identifies Distinct Molecular Subgroups in GBM (SSG12-04) Rivka Colen, John Bruyere, Prateesh Sathyan, Ashok Kumar, Ferenc Jolesz, Pascal Zinn	Time: Tue, Nov 27, 2012, 11:00-11:10AM Location: N226
The NIH/NCI Cancer Imaging Archive (TCIA): A Comprehensive Source of DICOM Imaging Data for Research – Hands-on (ICIA41) C. Carl Jaffe, John Freymann, Justin Kirby, Fred Prior, Lawrence Tarbox	Time: Wed, Nov 28, 2012, 10:30-12:00PM Location: S401CD

Educational Exhibits

Title	Time and Location	Supporting Materials
The Cancer Genome Atlas (TCGA) Radiology Initiative for Image Genomic Mapping in Glioblastoma Multiforme: The TCGA Glioma Phenotype Research Group Rivka Colen, Pascal Zinn, John Freymann, Scott Hwang,David Gutman,Rajan Jain, Manal Nicolas-Jilwan, Chad Holder, Max Wintermark, Justin Kirby, Daniel Rubin, Adam Flanders	LL-INE2519

ASNR 2012 (April 21-26, 2012, New York, NY)

Presentations

Title	Time and Location	Supporting Materials
Imaging Genomic Mapping in Glioblastoma Multiforme: A Novel Quantitative Merge between Imaging and Genomics. The Creation of a Signature for Tumor Necrosis Using Image Genomic Analysis in 12, 764 genes and 555 microRNAs Colen, R. R. Mahajan, B. * Bruyere, J. * Jolesz, F. A. * Sathyan, P. * Zinn, P. O.*	Mon, Apr 23, 3:08 - 3:16 PM: Grand Ballroom Suite, Session 15a - Adult Brain: Neoplasms I	Abstract
Quantitative Histogram Analysis of Diffusion and Diffusion Tensor Imaging of Glioblastomas for the Prediction of Clinical Outcome: A TCGA Glioma Phenotype Research Group Project Desai, H. Hwang, S. N. * Holder, C. A. * Flanders, A. * Jilwan-Nicolas, M. * Kirby, J. * Saltz, J. * Gutman, D. A. * Raghavan, P. * Buetow, K. H. * TCGA Glioma Phenotype Research Group*	Mon, Apr 23, 3:40 - 3:48 PM: Grand Ballroom Suite, Session 15a - Adult Brain: Neoplasms I	Abstract
Survival Prediction in Glioblastoma: Role of Tumor Blood Volume versus Molecular Subclassification Using Genomic Mapping -- A TCGA Glioma Phenotype Research Group Project Jain, R. Poisson, L. * Narang, J. * Gutman, D. * Flanders, A. * Daniel, B. * Jaffe, C. * Mikkelsen, T. * TCGA Glioma Phenotype Research Group*	Tue, Apr 24, 3:00 - 3:08 PM: Grand Ballroom Suite, Session 34a - Adult Brain Neoplasms III	Abstract PPT
Associations between Genomic Features and Quantitative Histogram Analysis of Diffusion and Diffusion Tensor Imaging of Glioblastomas: A TCGA Glioma Phenotype Research Group Project Hwang, S. N. Holder, C. A. * Desai, H. * Clifford, R. * Huang, E. * Hammoud, D. * Wintermark, M. * Colen, R. R. * Jain, R. * Freymann, J. * Flanders, A. * TCGA Glioma Phenotype Research Group*	Tue, Apr 24, 3:32 - 3:40 PM: Grand Ballroom Suite, Session 34a - Adult Brain Neoplasms III.	Abstract

Educational Exhibits

Title	Time and Location	Supporting Materials
Genomic Imaging: Creation of a Uniformed Terminology to Describe the Morphologic MR Imaging Features of Gliomas to Augment Clinical Research in the Genomics of Cancer: A TCGA Glioma Phenotype Research Group Project Flanders, A. E. * Hwang, S. * Nicolas-Jilwan, M. * Raghavan, P. * Colen, R. R. * Gutman, D. * Jain, R. * Holder, C. A. * Wintermark, M. * Kirby, J. * Rubin, D. L. * TCGA Glioma Phenotype Research Group	Mon, Apr 23, 6:30 AM - 9:00 PM: Rhinelander, Session eEdE1 - Adult Brain (Electronic Education Exhibit)	Abstract PPT
Genomic Imaging: Gliomas and Perfusion Imaging: a TCGA Glioma Phenotype Research Group Project Jain, R. TCGA Glioma Phenotype Research Group*	Mon, Apr 23, 6:30 AM - 9:00 PM: Rhinelander, Session eEdE1 - Adult Brain (Electronic Education Exhibit)	Abstract PPT
Imaging Genomics: Correlation of Invasive Genomic Composition and Patient Survival Using Qualitative and Quantitative MR Imaging Parameters Colen, R. R. * Mahajan, B. Flanders, A. * Huang, E. * Jain, R. * Gutman, D. * Hwang, S. * Kirby, J. * Freyman, J. * TCGA Glioma Phenotype Research Group * Jolesz, F. * Zinn, P. O.*	Mon, Apr 23, 6:30 AM - 9:00 PM: Rhinelander, Session eEdE1 - Adult Brain (Electronic Education Exhibit)	Abstract PPT
Methodology for Imaging Genomics of Gliomas Colen, R. R. Mahajan, B. * Sathyan, P. * Kovacs, A. * Zinn, P. O. * Jolesz, F. A.*	Mon, Apr 23, 6:30 AM - 9:00 PM: Rhinelander, Session eEdE1 - Adult Brain (Electronic Education Exhibit)	Abstract PPT

Posters

Title	Time and Location	Supporting Materials
Man vs Machine - Validation of the Qualitative Imaging Feature Set VASARI Using Volumetric Analysis by 3 D Slicer of the TCGA GBM Dataset: A TCGA Glioma Phenotype Research Group Project Gutman, D. A. Huang, E. * Flanders, A. * Mikkelsen, T. * Scarpace, L. * Holder, C. * Hwang, S. * Aurora, T. * Jolesz, F. A. * Saltz, J. * Colen, R. * TCGA Glioma Phenotype Research Group*	Monday, Apr 23, 2012, 6:30 AM - 3:00 PM: Americas Hall II, Session P1 - Adult Brain (Printed Poster)	Abstract
Imaging Genomic Mapping of Edema/Cellular Invasion MR Imaging-Phenotypes in Glioblastoma Multiforme Zinn, P. O. Mahajan, B. * Sathyan, P. * Singh, S.* Majumder, S. * Flanders, A.* Huang, E. * Jain, R.* Gutman, D. * Hwang, S.* Kirby, J. * Freyman, J.* * Holder, C. * Wintermark, M. * TCGA Glioma Phenotype Research Group * Jolesz, F. A. * Colen, R. R.	Monday, Apr 23, 2012, 6:30 AM - 3:00 PM: Americas Hall II, Session eP1 - Adult Brain (Electronic Poster)	Abstract PPT
Introduction into Imaging Genomic Mapping in Brain Tumors Colen, R. R. Mahajan, B. * Jolesz, F. A.* * Zinn, P. O.	Monday, Apr 23, 2012, 6:30 AM - 3:00 PM: Americas Hall II, Session eP1 - Adult Brain (Electronic Poster)	Abstract PPT
Radiogenogram: MR Imaging as a Screening Tool for Uncovering Novel Genomic Drug Targets Colen, R. R. * Sathyan, P. * Jolesz, F. A. * Zinn, P. O.	Monday, Apr 23, 2012, 6:30 AM - 3:00 PM: Americas Hall II, Session eP1 - Adult Brain (Electronic Poster)	Abstract PPT

RSNA 2011 (Nov 27-Dec 2, 2011, Chicago, IL)

Title	Presentation Time (CST) and Location	Supporting Materials
A Coordinated Method for Clinical Trials Research: Multireader Assessment of MR Imaging Features of Human Gliomas A E Flanders, MD, Philadelphia, PA; E Huang, PhD; M Wintermark, MD; M Nicolas-Jilwan, MD; P Raghavan, MD; C A Holder, MD; et al.	Tue Nov 29 2011 9:25AM - 9:35AM ROOM E451B	Abstract
Computer-aided Visual Image Analysis of Glioblastomas and Genomic Features S N Hwang, PhD,MD, Atlanta, GA; C A Holder, MD; E Huang, PhD; R A Clifford; D Hammoud, MD; P Raghavan, MD; et al.	Sun Nov 27 2011 12:30PM - 1:00PM ROOM Lakeside Learning Center (poster) Mon Nov 28 2011 11:10AM - 11:20AM ROOM N226 (oral)	Abstract
A Novel Statistical Method for Lossless Compression of Diagnostic Imaging Features E Huang, PhD, Rockville, MD; J B Freymann, BS; J Kirby; R A Clifford; C Jaffe, MD; A E Flanders, MD	Wed Nov 30 2011 12:15PM - 12:45PM ROOM Lakeside Learning Center	Abstract
Prediction of Glioblastoma Multiforme (GBM) Time to Recurrence Using MRI Image Features and Gene Expression M Nicolasjilwan, MD, Charlottesville, VA; R A Clifford; A E Flanders, MD; L Scarpace; P Raghavan, MD; D Hammoud, MD; et al.	Thu Dec 01 2011 11:50AM - 12:00PM ROOM N229	Abstract
Radiogenomic Mapping in GBM: A Novel Quantitative Merge between Imaging and Genomics - The Creation of a Signature for Tumor Necrosis Using Image Genomic Analysis in 12, 764 genes and 555 microRNAs R R Colen, MD, Boston, MA; P O Zinn, MD; J R Bruyere, BS,MA; B Mahajan, MBBS; F A Jolesz, MD	Tue Nov 29 2011 11:00 AM - 11:10 AM ROOM E451B	Abstract

SNO 2011 (Nov 17-20, 2011, Orange County, CA)

Title	Supporting Materials
Radiogenomic Mapping in GBM in Patients with High versus Low Edema/Tumor Infiltration using An Image- Genomic Analysis of 12, 764 genes and 555 microRNAs Rivka R. Colen, Bhanu Mahajan, Ferenc A. Jolesz, Pascal O. Zinn	Abstract
*Survival prediction using molecular classification of glioblastomas: Role of tumor blood volume estimation using DSC T2 MR perfusion** Rajan Jain, Laila Poisson, Jayant Narang, Lisa Scarpace, David Gutman, Carl Jaffe, Joel Saltz, Adam Flanders, Brat Daniel, Tom Mikkelsen	Abstract

The Cancer Genome Atlas Network Symposium (Nov 17-18, 2011, Washington, DC)

Title	Supporting Materials
Neuroimaging Predictors of Survival, Pathology, and Molecular Profiles in TCGA Glioblastomas David A Gutman, Lee A.D. Cooper, Joel Saltz, Adam Flanders, Dan Brat and the TCGA Glioma Phenotype Research Group	Slides Presentation Video

ASNR 2011 (June 4-9, 2011, Seattle, WA)

Title	Supporting Materials
Relationship between MR Imaging Features, Gene Expression Subtype, and Histopathologic Features of Glioblastomas Hwang SN, Clifford R, Huang E, Hammoud D, Jilwan M, Raghavan P, Wintermark M, Gutman DA, Moreno C, Cooper L, Freymann J, Kirby J, Krishnan A, Dehkharghani S, Jaffe C, Saltz JH, Flanders A, Brat DJ, Holder CA	Abstract Presentation
Associations Between MR Imaging and Genomic Features of Glioblastomas Hwang SN, Holder CA Huang E, Clifford R, Hammoud D, Raghavan P, Jilwan M, Wintermark M, Gutman DA, Cooper L, Moreno C, Kirby J, Freymann J, Dehkharghani S, Krishnan A, Jaffe C, Flanders A, Saltz JH, Brat DJ	Abstract Presentation
A Methodology for Multi-reader Assessment of MR Imaging Features of Gliomas in Clinical Trials Flanders, A. Huang E, Wintermark M, Hammoud D, Jilwan, M. Raghaven, Holder C, Hwang S, Clifford R, Freymann J, Kirby J, Jaffe C C	Abstract Presentation VASARI Features visual training guide
Prediction of Glioblastoma Multiforme (GBM) Patient Survival Using MRI Image Features and Gene Expression Nicolasjilwan M, Clifford R, Raghavan P, Wintermark M, Hammoud D, Huang E, Jaffe C, Freymann J, Kirby J, Buetow K, Huang S, Holder C	Abstract Presentation