Children's Brain Tumor Tissue Consortium Data Set Now Available in the Proteomic Data Commons
The NCI Proteomic Data Commons (PDC) just released the proteomic data set from the Children’s Brain Tumor Tissue Consortium (CBTTC).
The CBTTC and the Pacific Pediatric Neuro-Oncology Consortia (PNOC) are collaborative research consortia focused on identifying therapies for children with brain tumors. The consortia have contributed a Pediatric Brain Tumor Atlas (PBTA) data set, a cohort of 991 brain tumor subject clinical data, with associated whole genome sequencing and RNAseq hosted by the Data for Driving Innovation at Children's Hospital of Philadelphia.
The Office of Cancer Clinical Proteomics Research (CPTAC) and CBTTC have collaborated to examine seven brain tumor subtypes in children to aid in the identification of therapies for pediatric patients. Data included in this release are proteomic and phosphoproteomic analyses of brain tumor samples included in the PBTA cohort and represent the first 199 patients analyzed, integrating the proteomic and genomic molecular characterization across seven pediatric and AYA (adolescent and young adult) histologies: Low Grade Glioma, High Grade Glioma, Ependymoma, Ganglioglioma, Craniopharyngioma, Atypical Teratoid Rhabdoid Tumor (ATRT), and Medulloblastoma. Mass Spectrometry raw data generation along with preliminary analyses were performed at the Thermo Fisher Scientific Center for Multiplexed Proteomics, Harvard Medical School, under the direction of Professor Steven Gygi. Samples were prepared using the streamline (SL)-TMT protocol and MS analysis was performed using the SPS-MS3 strategy developed in the Gygi lab. Additional data analyses from the CPTAC Common Data Analysis Pipeline and from the University of Michigan Proteomics and Integrative Bioinformatics Laboratory are also provided. All raw and processed genomic data, as well as pathology reports, radiology reports, MRIs, and histology slide images are accessible via the Kids First Data Resource Portal.