New D3b Research Collaborations – Spring 2019


Project Genie

Project Genomics, Evidence, Neoplasia, Information, Exchange (Project GENIE) is an AACR pilot project that seeks to identify and validate genomic biomarkers relevant to cancer treatment by linking tumor genomic data from clinical sequencing efforts with longitudinal clinical outcomes. AACR Project GENIE will accomplish this by aggregating existing and ongoing next-generation clinical sequencing data and associated pathology reports from multiple cancer centers in the U.S., Canada, and Europe into a single, searchable clinical cancer genomics meta-database. AACR is partnering with Sage Bionetworks to create this database.

 The D³b Center and the CHOP Division of Genomic Diagnostics (DGD) have come together to represent the hospital as the first partnering institution to supply pediatric data, which began January 18.  To view the full list of partnering institutions, including those supplying adult data, visit


Corsica Project

Earlier this year, The ENT team at the University of Pennsylvania (UPenn), including Drs. James Palmer, Nithin Adappa, and Charles Tong, began working to contribute to a broader ENT collaboration group comprising of six institutions, with data collected via the Corsica protocol. The UPenn ENT team’s biospecimen collection protocol is now managed by the D³b team (managing the collection and banking process).   In addition, our D³b laboratory established collaboration with the ENT team in data generation efforts. 

The D³b generated data from inverted papilloma samples obtained from Dr. Tong. In addition, the D³b’s Molecular Diagnostic Research Unit (MDRU) generated gene expression data from close to 20 samples including rare but aggressive type of inverted papilloma, the squamous carcinoma.


Kentucky Cancer Registry: Factors Associated with High Incidence of Pediatric Brain and Central Nervous System Tumors in Kentucky  

Kentucky children suffer from a particularly high burden of brain and central nervous system tumors. To better understand the higher incidence of tumors occurring within Kentucky, The Kentucky Cancer Registry (KCR), lead by Dr. Eric Dubrin, will perform a comprehensive environmental scan and molecular testing on existing tumor samples in collaboration with national partners including D³b and the Gabriella Miller Kids First Data Resource Center. KCR believes this information will provide important clues about why an increased number of Kentucky children are afflicted with these diseases and to identify potential opportunities for interventions and additional research.

D³b Director, Dr. Adam Resnick is a co-investigator on this project.  The collaboration will involve supporting the sample processing and data generation of pediatric brain tumor specimens collected by KCR. We are currently discussing details regarding logistics and processing pipelines.


Pacific Pediatric NeuroOncology Consortium (PNOC) 008 Enrolls First Two Study Participants

PNOC 008 is a clinical trial for pediatric midline gliomas where Whole Genome Sequencing (WGS) and RNAseq analysis is used to identify therapies. Enrolling its first study participant in May 2019 and the second participant in June, PNOC 008 is expected to enroll 1-2 subjects per month across any PNOC site that is IRB approved. These subjects will have tumor collected for clinical genomics to determine treatments. At the time of surgery, collection sites will preserve the extracted tissue sample in FFPE or flash freeze depending on the tissue amount. A clinical genomic panel will be conducted by the University of California, San Francisco (UCSF) and any flash frozen tissue will come to CHOP to have extractions done via the Division of Genomic Diagnostics, led by Dr. Marilyn Li.

Samples will then be sent to Nantomics for Whole Genome Sequencing. Nantomics will provide a clinical report that will be reviewed during the PNOC tumor board. Concurrently, D³b will also receive the raw data from Nantomics, load the data into the data service, do harmonization on the data following the Kids First DRC pipeline, and run analysis against the Pediatric Brain Tumor Atlas (PBTA) and also provide a clinical report to the PNOC tumor board. Both reports will be reviewed and will aid in deciding treatment for the subject.