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CBTTC Launches Cavatica

CBTCC-logopnoc logo

May 31, 2016


The Children’s Brain Tumor Tissue Consortium (CBTTC) and the Pacific Pediatric
NeuroOncology Consortium (PNOC) conclude Brain Cancer Awareness Month of May
with the announcement of the Beta launch of Cavatica, a new cloud-based environment
for securely storing, sharing and analyzing large volumes of pediatric brain tumor
genomics data.


Cavatica will, for the first time, allow doctors, researchers and data scientists
unparalleled access to pediatric brain tumor genomic data paired with a suite of analysis
tools in a cloud computing environment that enables scalable, faster and more robust
research. Upon its full release, Cavatica will host the largest standardized, integrated,
and quality-controlled genomic database of pediatric brain cancer genomic data.


Working with Seven Bridges, a biomedical data analysis company, the eight CBTTC site
members and 15 member hospitals of PNOC are further fulfilling their commitment
earlier this year to the White House Precision Medicine Initiative (PMI) with the launch
of the Beta version of Cavatica being announced today. The Beta release will be open
for subscribed end-user input and will be iteratively enhanced by ongoing
implementation of advanced platform features and deposition of additional data sets
over the coming months. These datasets will include additional pediatric cancer
supporting pan-cancer pediatric data analysis in partnership with additional consortia
including the SU2C-St. Baldrick's Pediatric Cancer Dream Team.


Sign up for access to the Beta release of Cavatica is available for researchers and data
scientists by going to cavatica.org.


For more information or to schedule an interview, please contact the CBTTC at
This email address is being protected from spambots. You need JavaScript enabled to view it.

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National Pediatric Brain Cancer Awareness Day

September 26th Is designated National Pediatric Brain Cancer Awareness Day

In this video you will meet Dr Jay Storm, attending Neurosugeon at CHOP.

 

 

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CHOP Presentation 2013

On April 24th 2013 we were delighted to present CHOP with a check for $24,000.   This represented the funds raised by the 2013 Tsunami Karate Kick-a-Thon, the sale of "Christopher's Miracle Marigolds"  and donations from the SAFR Spring Dinner event.  The money will be used to support the Childhood Brain Tumor Tissue Consortium.  Kyra Sathra also delivered cards for the children on the wards that were made by children attending the Kick-a-Thon and by the students of one of the members of the dojo.

Check Presentation 2013

In this picture are, from left to right, Kyra Sathra, Betsy Sathra, Tim Court, Caroline Court, Dr. Peter Phillips, Dr. Adam Resnick.

Doctors Phillips and Resnick provided an update on the progress of the CBTTC and of the brain tumor research being undertaken at CHOP.  

In adult brain tumors, over 100 different genetic mutations have been identified, however, in childhood brain tumors they have only seen five.  This is good news because investigating the causes of five mutations is a more manageable task than investigating over one hundred.  The doctors believe the reasons that there are fewer mutations in childhood tumors are that the brain is still developing and children have not yet had time to be affected by other cancer causing agents such as smoking.

Dr. Resnick explained that their research into tumors categorized as Astrocytomas has revealed that mutation is related to the way DNA coils and uncoils within cells.  DNA uncoils certain sections to "express" particular genes that affect the behavior of the cell.  In mutated cells they can see that the uncoiling either doesn't happen or happens in the wrong part of the DNA strand which results in expressing the wrong gene.

Dr. Phillips explained the work being done at a higher level to make it easy for other hospitals to submit tumor samples to the CBTTC.  This includes information on how to harvest and prepare the samples in order to keep them as viable as possible.  They are also continuing to work on software that will record the clinical data associated with each sample.  This will ensure that the same information is recorded for each sample no matter which institution it comes from.

The Foundation members were taken on a tour of the CBTTC and the research labs.  The CBTTC is housed in a large room in the basement of the Colket Translation Research building. 

Freezers

 

 

The room contains large freezers that maintain tumor samples at -80C (-112F).  These samples are able to be grown either in a dish or by implanting the cells into mice.

 

Nitrogen Storage Tanks

 

 

Other samples are stored in Liquid Nitrogen at a temperature  around -200C (-328F).

 

 

Robot

 

 

Prepared tumor samples for examination under a microscope are stored in a large refrigerated room which will ultimately be capable of storing two million samples.  Each sample is bar-coded and can be retrieved quickly by the robot shown in this picture.

 

 

The CBTTC has a battery backup system and diesel generators to power the freezers in case of a power failure.

Gene Sequencers

 

Another key part of the CBTTC is the genetic mapping of the tumors.  Gene mapping used to take years and many millions of dollars.  Today, it can be done in hours for a few thousand dollars.  CHOP is collaborating with a company that specializes in gene mapping.  This company has a lab at CHOP with several gene mapping machines like the ones in this picture.

 

 

The gene mapping is producing many terabytes of data (a terabyte is 1,000,000,000,000 bytes) and one of the challenges is to find ways to efficiently make this vast amount of data available to those that want it.  To this end they are investigating cloud computing solutions.

Doctor Resnick explained how philanthropic funding by groups such as ours is changing the way research is done.  With philanthropic donations, the donors insist on openness and collaboration.  With government funding, institutions are forced to compete against one another.

As you can see, your donations are helping to produce tangible results. The enthusiasm and excitement of the team is infectious and it really feels that this work is going to play a key role in finding a cure for childhood brain  tumors.

Thank you.

 

 

 

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Meet the team

On Thursday, April 18th, we were invited to CBS studios in New York to meet members of the team responsible for Brain Tumor Research at the Children's Hospital of Philadelphia (CHOP) and to receive an update on their progress to date. We thought you might like to meet them also.

Phillip B. Storm Jr. M.D. Adam C. Resnick Ph.D Peter C. Phillips M.D. Tom Curren Ph.D

Phillip B. Storm Jr. M.D.

Adam C. Resnick Ph.D

Peter C. Phillips M.D.

Tom Curren Ph.D

Incoming Chief of Neurosurgery

Research scientist in Neuro-Onchology

Director, Pediatric Neuro-Onchology Program

Deputy Scientific Director

In addition to meeting the doctors, we were introduced to representatives of other fund raising groups who support this important work.

Dr. Phillips, who incidentally was Christopher's Neuro-Onchologist, explained that treatment for pediatric brain tumors has made very little progress in the last 30 years. Brain tumors are now the leading cause of pediatric cancer deaths largely due to advances made in the treatment of other pediatric cancers. The treatment for brain tumors is basically surgery, radiation and chemotherapy. Chemotherapy regimes are essentially trial and error based on results in adults and the results are unpredictable in children. Children that survive their tumors often suffer side effects from the treatment such as muscle weakness/paralysis, learning disabilities, hearing/vision loss and growth problems. It is clearly time to look at brain tumor treatment in a different way.

In order to develop effective treatments it is vital to understand what happens in cancer cells at the genetic level. This is where the Childhood Brain Tumor Tissue Consortium (CBTTC) comes in. It is a collaborative effort between multiple world renowned children's hospitals to collect tumor samples, gene map them, combine them with clinical treatment data and provide the results openly to any researcher that wants them. At the time of writing, the CBTTC has amassed approximately 1,000 samples which includes Christopher's tumor.

Dr. Resnick described advances that are already being made as a result of the CBTTC. One particular discovery is centered around a mutation in a gene called BRAF which occurs in a type of tumor called an astrocytoma. This gene also mutates in a form of melanoma in adults and an effective drug has been developed for it. However, when the drug was used on brain tumor tissue it caused the tumor to grow more quickly. The researchers worked with the drug company to discover why this occurred and together they came up with a new variant of the drug that can actually slow down and reverse tumor growth in this specific type of tumor. They are now moving toward a clinical trial. They were very fortunate to identify a gene for which there is already a treatment; many of the genes involved in brain tumors do not yet have effective treatments and so there is still much work to be done.

Dr. Storm is one of the leading pediatric brain surgeons in the world, who incidentally performed Christopher's tumor biopsy. He said  "This is the future of brain tumor treatment, not surgery, much as it pains me to say it!"

The doctors explained our role in this work. This kind of research is expensive. Worse, it is difficult to fund because there are so many other diseases that aflict much larger numbers of patients. It is the job of foundations like ours to not only raise funds, but to make people aware of the important work being done here. The doctors stressed that every penny we send them is used entirely for research, it does not get used for admin or for paying for events such as this one. We ARE making a difference and maybe in the not too distant future, brain tumors will be preventable or at least curable.

For more information on the work being done with the BRAF gene in astrocytomas, see this article on the CHOP web site http://www.research.chop.edu/blog/genetic-study-suggests-fine-tuning-drugs-for-pediatric-brain-tumors/

 

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Decoding Cancer: Scientists Release 520 Tumor Genomes from Pediatric Patients

By ALICE PARK | @aliceparkny |  

 
Child receiving chemo treatmentCould the answer to cancer lie within our own DNA?

Childhood cancer experts are hoping that at least some of what drives pediatric cancers can be gleaned from the genomes of patients and their tumors. That’s the thinking behind the Pediatric Cancer Genome Project (PCGP), a three-year, $65 million effort to sequence major pediatric cancers.

The latest release of data from the PCGP, published in the journal Nature Genetics, includes 520 genome sequences from childhood cancer patients; half of the genetic material comes from their tumors, and half from their healthy tissues. By matching the tumor genomes to those of normal cells from the same patients, researchers hope to pinpoint the differences and get a better idea of where the cancer cells went awry. These discrepancies in the genetic code are also likely to be the richest targets yet for potential new therapies.

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Philly CureSearch Walk

Philadelphia CureSearch Walk

 

Date: May 20th, 2012

Location: Franklin Square, Philadelphia

Pictures from the event

The first annual CureSearch walk in Philadelphia took place on May 20th, 2012 in Franklin Square, Philadelphia.  The walk was a largely symbolic stroll twice around the park covering approximately 1 mile with over 600 walkers participating.  The event was attended by teams supporting cancer survivors, current patients and those that have lost children to cancer.   Each survivor and patient received a medal at a ceremony held before the walk.  For those that had lost a child, there was a balloon release and a moment of silence.  

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