Summary

The TCGA Glioma Phenotype Research Group is part of the CIP TCGA Radiology Initiative focused on analyzing images from the TCGA-GBM collection. Images which correlate to the Glioblastoma Multiforme tissue data in the TCGA Data Portal are continuing to be gathered for submission to TCIA.

According to the TCGA page on Glioblastoma Multiforme, researchers have already made the following types of discoveries with this data:

Identified a new subtype of GBM that affects younger adults and has an increased survival rate. A subset of GBM tumors had specific chemical changes or 'marks' called methylation of a large group of genes. The methylation of these genes may account for the improved survival of these patients when compared to patients with other subtypes of GBM. These findings could aid in development of new treatment options for these patients.
Recognized four distinct molecular subtypes of GBM that respond differently to aggressive therapies. Patients with one subtype survive about 50 percent longer than those with other GBM subtypes. Knowing a tumor's subtype could help match each patient to the most effective therapies. See more information about TCGA brain tumor subtype studies.
Identified possible mechanisms that can cause some GBM tumors to become resistant to therapy after treatment with the standard chemotherapy called temozolomide. Treatment with temozolomide can cause gene mutations that help tumor cells become resistant. If GBM tumors return after successful treatment with temozolomide, the new gene mutations make the tumor resistant to further treatment with the drug. This finding could be used to develop new drugs that will not activate this drug resistance mechanism.
Pinpointed four gene mutations in GBM tumors that may provide new insights into the biology of this disease.
- NF1, a gene identified as the cause of neurofibromatosis 1, a rare, inherited disorder characterized by uncontrolled tissue growth along nerves
- ERBB2 , a gene involved in breast cancer
- TP53, a gene involved in many types of cancers
- PIK3R1 , a gene that controls an enzyme that is found in many cancers

Research and Publications

Per TCGA and TCIA Guidelines there are no outstanding limitations from the freedom-to-publish criteria for these data sets:

Data Source	Status
TCGA Data Portal Publication Guidelines	No restrictions; all data available without limitations
TCIA Data Usage Policies and Restrictions	No restrictions; image data available without limitations

We are currently hosting open t-cons for discussion of TCGA glioma based research projects (TCGA-GBM) on Wednesdays at 3pm Eastern. Please contact us at cancerimagingarchive@mail.nih.gov if you would like to join the calls or our mailing list to be otherwise kept in the loop on these topics.

TCGA-GBM Marker Paper and Image Source Sites (ISS)

Imaging Source Site (ISS) Groups are populated and governed by participants from institutions that have provided imaging data to the archive for a given cancer type. Modeled after TCGA analysis groups, these groups are given the opportunity to publish a marker paper for a given cancer type per the aforementioned publication policy. The TCGA Glioma Phenotype Research Group's formation pre-dated current TCIA policies on TCGA related publications and therefore there is no ISS marker paper for TCGA-GBM imaging data. However several publications and numerous conference presentations utilizing this data have been generated by the research group, which are outlined below in the References section. Current TCGA-GBM source sites include:

Thomas Jefferson University
Henry Ford Hospital
University of California, San Francisco
MD Anderson Cancer Center
Emory University
Mayo Clinic
CWRU School of Medicine

Upcoming Events

03/13 - Dr. David Gutman will present on 3-D based quantitative analysis of brain tumors, covering his work in segmenting both T1 Post-GD lesions as well as the Flair envelope, and development of a computational pipeline to both register and extract imaging features from the MRI images included in the TCGA GBM data set.
03/20 - Dr. Dan Bratt will present an introduction to large scale analysis of the TCGA lower grade gliomas and a discussion of preliminary data coming from these tumors.
04/10 - RSNA 2013 Abstract deadline is 12pm CST
05/18 - ASNR meeting begins in San Diego (multiple abstracts from group members were accepted to this meeting)

References

The following links contain publications from the main TCGA project, as well as their posted publication guidelines.

Publications utilizing TCGA-GBM imaging data from TCIA:

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="58b89e67-63b6-4fe6-855d-225cf22bdffc"><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.

Conference abstracts utilizing TCGA-GBM imaging data from TCIA:

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

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