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Pediatric Preclinical Genomic Characterization Project

Julie Gastier-Foster, David Wheeler, Malcolm Smith, John Maris
Grant Type: 
Catalyst Grants
Year Awarded: 
Type of Childhood Cancer: 
General Pediatric Cancer
Project Description: 

Overseen by the National Cancer Institute’s Pediatric Preclinical Testing Consortium (PPTC), the Pediatric Preclinical Genomic Characterization Project is an effort to characterize the vast number of pediatric cancers that lack full genomic data and then make that available to scientists to use when searching for potential drugs and compounds that might be effective in treating childhood cancer.

The project was initiated once Alex’s Lemonade Stand Foundation learned that the PPTC only had a limited number of characterized childhood cancer models to test potential drugs against; but had access to over 400 stored tumor samples. With the support of ALSF, the PPTC was able to rectify this problem by characterizing and developing reliable genomic data for over 270 samples in 25 different childhood cancers; a critical step in the acceleration of research into effective, safe treatments.

The PPTC completed the characterization of the samples in patient-derived xenograft (PDX) childhood cancer models (samples taken directly from patients) with advanced genomic technology and released that data on July 9, 2018. All academically qualified petitioners can access the data through the PedcBioPortal for Childhood Cancer Genomics (pedcBio portal). Raw characterization data will be available on the database of Genotypes and Phenotypes (dbGaP) in the coming months. Tissue samples will be available by request.

Modeling molecular image
Above, this map shows the RNA clustering of childhood cancer PDX models.

The completion of this project is a landmark for the oncology community and even more, it represents hope for children waiting for cures.

John Marris“This is momentous because the deep genetic profiling that happened as a result of ALSF’s funding for the PPTC overcomes some major problems we have when treating childhood cancer. The data allows us to treat a genetic target, rather than the disease name,” said Dr. John Maris, MD, from Children’s Hospital of Philadelphia, ALSF’s Scientific Advisory Board and the PPTC’s neuroblastoma member. “This data will help us design effective and successful clinical trials, much more rapidly than ever before, accelerating breakthroughs and pushing us closer to cures."

The PDX models were derived from 25 different types of childhood cancer. Process data available includes:

  • Somatic mutations
  • mRNA expression
  • RNA fusions (translocations)
  • Gene copy number (amplifications and deletions)
  • Chromosomal segments (for broad and focal chromosomal gains/amplifications/losses)

Read more about the PPTC project and the hope it represents to science and children waiting for cures, on the ALSF blog.