Brain SPORE Blog

St. Joseph's Hospital to Offer Castle Biosciences Test DecisionDx-GBM

2009-06-26T15:37:58Z

"NEW YORK (GenomeWeb News) - St. Joseph's Hospital and Medical Center in Phoenix, Ariz., said today that it will offer a pharmacogenetic test for a brain cancer drug made by Castle Biosciences.
Under the partnership, the St. Joseph's DNA Diagnostics Lab will perform Castle Biosciences' test to find out if a drug is likely to benefit certain glioblastoma multiforme patients. The DecisionDx-GBM test will tell a doctor if a tumor is likely to be sensitive or resistant to the standard first-line treatment, information that would save doctors time and help them plan their treatment approach.
St. Joseph's said it is the only lab to offer the test, and that doctors from around the US are sending samples to its lab for testing. The test is not yet available for ordering in California and New York, but the lab said it is pursuing licenses for those states.
The agreement was worked out with assistance from the Greater Phoenix Economic Council.
Our offering this test is a prime example of translational genomics closing the loop between the research lab and the clinic," said John Stone, who heads the DNA Diagnostics Lab at St. Joseph's. "While there is currently no cure, this test can certainly help patients understand and plan for the likely course of the disease."

Castle Biosciences is the company behind the DecisionDx-GBM test developed by Drs. Aldape and Colman and their teams - leaders of Project 3 in our Brain Tumor SPORE, where they are continuing to develop this approach.

http://www.genomeweb.com//node/919323?emc=el&m=427776&l=3&v=1b1f28ad9a

Dallas News Article on CPRIT - matching funds?

2009-04-13T00:04:22Z

There was a very interesting article in the Dallas News on the CPRIT: "State cancer funding requires 50% match; scientists unsure how to raise money".

The focus of the article is the uncertainty surrounding the definition of the matching funds requirement. As the article stated: "But scientists say the cancer research initiative may face a major roadblock: Not one penny can be distributed unless researchers can also come up with large sums from a different source."

Apparently the idea was that projects that had been funded by another source, would already have passed muster, and so would present less risk. Of course, the problem is that typically projects funded by one agency are not eligible for funding by another source. This is particularly true of NIH funds, and is scrutinized closely.

Many people in the know are quoted, including our own Dr. DuBois. Worth a read - check it out.

Brain Tumor Center Research Retreat

2009-02-09T01:07:03Z

This past Friday and Saturday the BTC held a research retreat at the Houstonian. A packed program, consisting largely of one-hour sessions with about 5 short presentations and lots of discussion, addressed a broad range of topics.

We started on Friday with one of the most active areas of discussion - the role of cancer stem cells in the growth and treatment of gliomas. The session highlighted shortcomings of current markers and definitions, introduced podoplanin as a contribution in this area and ended with a discussion about mesenchymal stem cells in promoting tumors, and as vehicles for treatment delivery.

The next two sessions highlighted our current clinical trials, both home grown and pharma-sponsored, and explored roadblocks to more rapid and broader clinical translation of other promising approaches - largely these were financial and regulatory, which are tightly connected, as much of the cost of doing clinical trials stems from the burdens imposed by regulations. Follow up is planned to see how we can improve in this critical area, and also how we can overcome some of the barriers to working with other centers.

The morning was rounded off by a discussion of biomarkers in clinical trials, and besides some promising advances that have been made, the question of whether current markers (MGMT, EGFRvIII, PTEN and perhaps a few others) should not be routinely measured for cases in our center - opinions were somewhat divided.

After lunch, we moved to break-out sessions with a Signaling or Epidemiology being followed by Stats or Metastasis and then Epigenetics or Pediatric Tumors. These sessions were more focused on the science and identifying new opportunities to work together and were well attended.

On Saturday we kicked off with a session on some of the multi-investigator efforts in the BTC - SPORE, CERN, TCGA, PO1 and IPCT. Then an interesting session on angiogenesis and microenviroment was followed by two breakouts - one one Drug Development and the other on Autophagy. Then we finished with a discussion on the informatics needs of the BTC.

So how did it go? We are going to send out a survey tomorrow, and I'll come back and post later in the week to tell you.

Mid-Winter Brain SPORE Meeting

2009-01-29T19:32:46Z

We are at the first mid-winter meeting of the Brain Cancer SPORE! This is an annual meeting, where each of the SPOREs in the organ group, present their projects, and progress.

As we are the newbies, we got to go first, and got an extra half hour so that we could present our material in a little more depth. Dr. Yung gave an overview of the BTC program and how the SPORE fits in. Then the projects went in order - Dr. Fueyo with targeted adenovirus Project 1; Dr. Colman with gene-expression biomarkers for glioblastoma prognosis; Dr. Yung with PI3K inhibitors and then, by phone, Drs. Meyers and Bondy on the genetic factors and neuro-cognitive outcomes study. Dr. Bogler closed with a brief overview of the cores, and the Career Development and Developmental Research Projects.

Our talks were well received - everyone presented opportunities for collaboration and interaction - a key aspect of what this meeting is all about.

Now we are seeing the talks from the other Brain SPORE institutions, and are ourselves looking for ways to work together.

M. D. Anderson Neurosurgeon, Amy Heimberger M.D., Receives Presidential Award

2008-12-20T02:36:21Z

MD Anderson made a press release today about Dr. Heimberger's prize:

"Amy Heimberger, M.D., associate professor of neurosurgery at The University of Texas M. D. Anderson Cancer Center has received a Presidential Early Career Award for Scientists and Engineers (PECASE), in recognition for her research on the central nervous system's immune biology, tumor evasion of immune detection and immunotherapeutic approaches for patients with malignant gliomas."

Read the rest of it here.

Congratulations Amy!!!

The Cancer Genome Atlas (TCGA) Steering Committee Meeting December 2008

2008-12-08T02:40:46Z

This is the agenda of the recent TCGA steering committee meeting, with links to the presentations made at that meeting:

National Cancer Institute and National Human Genome Research Institute National Institutes of Health

The Cancer Genome Atlas (TCGA) Steering Committee Meeting

December 3-4, 2008, Bethesda North Marriott Hotel & Conference Center

Bethesda, Maryland

PRESENTATIONS

Wednesday, December 3

8:30 a.m. - 8:40 a.m. Opening Remarks

Anna D. Barker, Ph.D., National Cancer Institute, NIH

Alan E. Guttmacher, M.D., National Human Genome Research Institute, NIH

8:40 a.m. - 10:40 a.m. Center Presentations

Report on data generation and analysis; presenter should include brief comment on status of ovarian project (10 minutes each)

Moderator: Bruce E. Johnson, M.D., Dana-Farber Cancer Institute

a. Cancer Genome Characterization Centers

University of North Carolina at Chapel Hill D. Neil Hayes, M.D.

Memorial Sloan-Kettering Cancer Center Marc Ladanyi, M.D.

Lawrence Berkeley National Laboratory Elizabeth Purdom, Ph.D.

Johns Hopkins/University of Southern California Peter W. Laird, Ph.D.

HudsonAlpha Institute of Biotechnology Devin Absher, Ph.D.

Harvard Medical School Peter J. Park, Ph.D.

Broad Institute of MIT and Harvard Gad Getz, Ph.D.

b. Genome Sequencing Centers

Washington University School of Medicine Li Ding, Ph.D.

Broad Institute of MIT and Harvard Michael S. Lawrence, Ph.D.

Baylor College of Medicine David A. Wheeler, Ph.D.

11:00 a.m. - 12 noon Analysis Working Group Reports

Moderator: D. Neil Hayes, M.D. University of North Carolina at Chapel Hill

Publications Using Integrated Data

Expression Analysis and GBM Subtypes (15 minutes) Roel G.W. Verhaak, Ph.D. Broad Institute of MIT and Harvard

Integrative Copy Number Analysis (15 minutes) Terrence P. Speed, Ph.D. (presented by E. Purdom) University of California, Berkeley

State of Ovarian Cancer Genomics (Literature Review) Paul T. Spellman, Ph.D., Lawrence Berkeley National Laboratory

c. Planning for the Ovarian Analysis Jamboree (15 minutes) Gad Getz, Ph.D., Broad Institute of MIT and Harvard

1:15 p.m. - 2:45 p.m. Technology Development (10 minutes each + 5-minute discussion)

Moderator: Robert H. Waterston, M.D., Ph.D. University of Washington

TCGA R21 Technology Development Grantees

Cytosine methylation and mammary carcinoma Timothy Bestor, Ph.D. Columbia University

Methylation Profiling of Normal and Cancer Genomes Gerd P. Pfeifer, Ph.D., City of Hope

Allele-Specific DNA Methylation in Normal and Cancer Tissues Benjamin Tycko, M.D., Ph.D., Columbia University

Detecting Structural Mutations in Cancer Genomes by Long-Range End-Tag Profiling

Aleksandar Milosavljevic, Ph.D., Baylor College of Medicine

Microarray Sequence Capture for Large-Scale Targeted Sequencing of Cancer Genomes Thomas Albert, Ph.D., Roche/Nimblegen Systems

Targeted Genomic Circularization for Cancer Genome Resequencing, Hanlee Ji, M.D., Stanford University School of Medicine

3:00 p.m. - 3:30 p.m. Technology Development of the CGCCs (10 minutes each)

RNA Profiling Via High-Throughput DNA SequencingJonathan G. Seidman, Ph.D., Harvard Medical School

Detecting Gene Rearrangement Associated with Intragenic CNA, Cameron W. Brennan, M.D., Memorial Sloan-Kettering Cancer Center

3:30 p.m. - 5:30 p.m. GSC Technology Implementation

Moderator: Mark S. Chee, Ph.D., Prognosys Biosciences, Inc.

Results From Pilots, Planning for 2009, Discussion

Richard A. Gibbs, Ph.D., Baylor College of Medicine

Stacey Gabriel, Ph.D. & Gad Getz, Ph.D., Broad Institute of MIT and Harvard

Elaine R. Mardis, Ph.D., Washington University School of Medicine

Thursday, December 4

8:30 a.m. - 10:00 a.m. Discussion: Cancer Genomics, Biology, and Translation

Moderators: Ronald A. DePinho, M.D. & Geoffrey Duyk, M.D., Ph.D.

What are the predictions for cancer genomics in 2 years? In 5 years?

What are the key challenges in technology? In analysis? In translation?

What are the expectations for diagnostic markers? For therapeutic targets?

How should cancer research communities be preparing for the influx of new findings?

10:10 a.m. - 11:45 a.m. Analyzing and Applying TCGA Data (15 minutes each)

Moderator: Sean Eddy, Ph.D., Janelia Farm Research Campus

caBIG® and TCGA, Kenneth H. Buetow, Ph.D., National Cancer Institute, NIH

Visualizing Cancer Genome Data, Jill P. Mesirov, Ph.D., Broad Institute of MIT and Harvard

UCSC Cancer Genomics Browser for TCGA Data, David Haussler, Ph.D., M.S., University of California, Santa Cruz

TCGA Functional Analysis Protein Mutations & Pathways Chris Sander, Ph.D., Memorial Sloan-Kettering Cancer Center

Analysis of mRNA Expression Data from TCGA and non-TCGA Glioma Samples, Kenneth D. Aldape, M.D., University of Texas M.D. Anderson Cancer Center

11:45 a.m. - 12:30 p.m. Samples Update

Samples Update: A Cautionary Tale (25 minutes), Carolyn C. Compton, M.D., Ph.D., National Cancer Institute, NIH

Breast Cancer Samples from SPORES (5 minutes), Charles M. Perou, Ph.D., University of North Carolina at Chapel Hill

12:30 p.m. Closing Remarks and General Adjournment

Alan E. Guttmacher, M.D.

Anna D. Barker, P

Developmental Research Program awards announced

2008-12-03T23:02:10Z

Each SPORE has a Developmental Research Program, designed to foster new projects that might, in time, become full SPORE projects, as existing ones complete the translational process and go go the clinic.

Like all SPORES, ours holds an annual competition (see here for the Request For Applications from July), and applications are evaluated by our external advisory board. It took us a little longer this year, as we had to complete forming the board, but now the process is complete. We had 18 applications, which were of very high quality. The SPORE has sufficient funds to support 4 projects (at $50,000 per year, for one year at a time). This year we were able to fund two additional projects using some funds raised by the Brain Tumor Center from philanthropy.

We are pleased to announce the following applications were funded:

William G. Bornmann, Ph.D. (MDACC) Imaging PI3K Activity in Glioma

Candelaria Gomez-Manzano, M.D. (MDACC) Significance of the Tyrosine Kinase Receptor Tie-2 in the Brain Tumor Stem Cell Population

Suyun Huang, M.D., Ph.D. (MDACC) Targeting FoxM1 for Inhibition of Angiogenesis and Tumor Growth of Glioblastoma

Christopher Pelloski, M.D. (MDACC) The Investigation of Methylome Expression Signatures in Glioblastoma : Prognostic Biomarker Discovery and Clinical Applications

Vinay K. Puduvalli, M.D. (MDACC) Targeting Gliomas Through Histone Deacetylase Inhbition

Michael E. Scheurer, PhD, MPH (BCM) Neuropsychological Outcomes in Pediatric Brain Tumor Survivors: The Influence of Polymorphisms in Cytokine Genes

Congratulations to the investigators, and we look forward to their active participation in the SPORE community.

RSS - explained with moving pictures and sound

2008-10-21T22:24:50Z

I am following up on the "how to" post from a little while ago, which explained how to get the RSS feed from this blog into your favorite reader. It turns out, that many folks are not aware of the amazing benefits of RSS. Here is a little video to help explain it (don't take my word for it):

A big "Thanks" to Jennifer Texada, social media guru at MDACC, for alerting me to this vid!

I hear you saying - "OK, so I am going to all this trouble just to read YOUR blog. You must be kidding - that's not worth the effort..."

Wrong. There are literally thousands of useful RSS feeds out there, and it is increasingly dominating the way information is served. Most major journals put our their electronic table of contents out by RSS. So instead of these piling up in your email, and quickly getting lost, you can find them in your RSS reader - when you want to look them over. New items can be distinguished here, just like in your email.

But there is something even cooler about RSS - you can use it to easily set up search robots. A simple example is any News search on Google, which can be turned into an RSS feed. Once you have an RSS reader, you will discover many things that you can track.

CPRIT Website up

2008-10-17T13:31:49Z

I wanted to share the State of Texas Cancer Prevention and Research Institute (CPRIT) website with all of you for reference purposes. It includes information and news about CPRIT, the board, meeting agendas, meeting minutes, laws, rules and guidelines, Texas Cancer Plan, funded projects, publications, reports and statistics, useful links and funding opportunities.

The next CPRIT Oversight Committee meeting is scheduled for Wednesday, November 19, 2008. The State of Texas tentatively plans to begin awarding grant funds in Fall 2009.

Link to State of Texas CPRIT website:
http://www.cprit.state.tx.us/

Making Cancer History: Disease and Discovery at the University of Texas M. D. Anderson Cancer Center

2008-10-16T20:53:52Z

A history of MDACC is schedule to appear by the end of the year. You can pre-order it now at Amazon. It will be available in our gift shops at a discount to employees.

From the description on the Amazon page: "The history of the M. D. Anderson Cancer Center vividly reveals how cancer treatment in America -- and our attitudes toward the disease -- has changed since the middle of the twentieth century.

One of the preeminent cancer centers in the world, M. D. Anderson is also one of the first medical institutions devoted exclusively to caring for people with cancer and researching treatments and cures for the disease. Historian James S. Olson's narrative relates the story of the center's founding and of the surgeons, radiologists, radiotherapists, nurses, medical oncologists, scientists, administrators, and patients who built M. D. Anderson into the world-class institution it is today.

Through interviews with M. D. Anderson's leaders and patients, Olson brings to life the struggle to understand and treat cancer in America. A cancer survivor who has himself been treated at the center, Olson imbues this history with humor, passion, and humanity."

Splice Center @ NCI Genomics and Bioinformatics Group

2008-10-10T20:59:34Z

Dr. Weinstein presented a useful tool to use at today's TCGA meeting, called Splice Center.

VisitGenomics and Bioinformatics Group and look under tools at left, or use this link to Splice Center.

You can see the splice variants from GenBank and RefSeq, and see Affy probes superimposed. Links to NCBI allow you to look at the genes.

Another tool, GoMiner, is an interpretation tool for 'omics' data. You can upload gene IDs and look at gene ontologies. According to the website: "Addresses the question, "Now that I've done the gene expression experiment and identified a set of 'interesting' genes, what do those genes mean biologically?" GoMiner batch-processes and organizes lists of thousands or tens of thousands of genes and provides two fluent, robust visualizations of the genes in the framework of the Gene Ontology hierarchy. (Zeeberg, et al., Genome Biology 2003; 4:R28)".

Contact Dr. Weinstein if you would like to be referred to someone who can help.

Systems Biology - coming to MD Anderson

2008-10-10T20:21:36Z

Systems Biology, the counterpoint to reductionist science, is a coming thing. With the ever increasing availability of high-throughput technology it is becoming accessible. With the realization that defects in single genes, or even pathways, can not explain complex diseases, it is becoming a necessity. And with the advent of this year's Annual Symposium on Cancer Research, it is coming to MD Anderson!

At the end of October, on R11, there will be a fantastic, 3-day meeting on Systems Biology - everyone in the BTC interested in the analysis of more than one gene at a time, is strongly encouraged to attend. You can see more information on the meeting here: www.mdanderson.org/ascr.

See you there!

Methylation levels key to glioblastoma survival - Dr. Pelloski

2008-09-23T21:28:01Z

Dr. Chris Pelloski presented his analysis of methylation status in glioblastoma at the American Association for Cancer Research "Molecular Diagnostics in Cancer Therapeutic Development" meeting being held at the moment. AACR made a press release that you can see here:

Methylation levels key to glioblastoma survival

Quote:
"This study shows that the methylation status of CpG islands may serve a robust, and previously unexplored, source of biomarkers for this disease," said lead author Christopher E. Pelloski, M.D., an assistant professor of radiation oncology and pathology at M. D. Anderson. "It also indicates that there seems to be a common theme to glioblastoma that the more closely the tumor cells resemble cells of neural development, the less aggressive the clinical course; whereas if they more resemble mesenchymal cells, which are poorly differentiated and invasive, the worse the clinical outcome will be.

TCGA Study highlighted on web

2008-09-23T19:52:16Z

A nice comprehensive blog post on the TCGA brain study can be seen here:
http://www.highlighthealth.com/diseases-and-conditions/the-cancer-genome-atlas-reports-molecular-characterization-of-brain-tumors/trackback/

It is interesting how the perception of TCGA has changed - it is hard to remember that there was a time when some people were very concerned about whether it would yield anything of value. The blogger at highlighthealth.com says:

"This is an excellent example of how current genome characterization technologies can systematically explore the universe of genomic changes involved in cancer. The TCGA is also studying lung and ovarian cancer."

TCGA Data: Local Update by Pablo Freire

2008-09-08T18:45:47Z

Pablo Freire, working with Dr. Jonas Almeida on the TCGA data, has posted new data to our (secure) TCGA intranet site. If you are part of our MDACC TCGA group and wish to have access to these data, please send an email to Oliver Bogler.

Pablo writes:

The data is presented as tab-delimited files and can be imported to excel. For the expression and copy number data, those values are calculated for every affymetrix probe position. Sequence data are the exact tab-delimited files from the TCGA portal.

For the expression and copy number files, I did the following:

Expression platform: Affymetrix U133A plate set, performed by Broad Inst.
Copy number platoform: Agilent 244A aCGH, performed by Harvard Medical School.

For expression, the raw data (CEL files) were retieved from the TCGA portal. For the copy number, the normalized data was used.

Expression data normalized with RMA.
Copy number data segmented with CBS.

For every affymetrix probe position, I eliminated genes that were not annotated at the RefSeq or probes that either don't match anywhere or match in more than one location in the genome.
Also, for every affymetrix probe position, I calculated the copy numeber associated by getting the mean values of the copy number probes within the span of the gene.

Just one sample per patient was used. In the cases where there were multiple samples per patient, the first one was used, yielding a total of 207 patients.

Links to the data are (access & password required):

TCGA sequence data

TCGA Agilent copy number

TCGA Affymetrix Expression