Scientific Projects- Data

The CBTTC adheres to NIH guidelines for genomic data sharing and follows the longstanding principles of rapid data release as articulated in the Bermuda and Ft. Lauderdale agreements with no pre-established data embargo periods on quality controlled data. As such, access to raw human genomic data will be provided fully to research investigators who, along with their institutions, have certified their agreement with the expectations and terms of access detailed on the website. This process begins with investigators submitting a data access request online. Once received, the CBTTC data access committee reviews the request based on NIH and CBTTC guidelines and approves or asks for further clarification when needed.  For processed data, no data access request is required and can be accessed on PedsCbio portal. 



Approved CBTTC Scientific Projects – Data Only


Project 1: Hideho Okada on DIPG and Other Primary Pediatric Brain Tumors

Principal Investigator(s): Hideho Okada PhD
Affiliation/Contact: UCSF/
Diagnosis/Classification: DIPG and other primary pediatric brain tumors
Project Summary/ Research Use: We will evaluate expression of genes that are deferentially expressed by the effect of specific gene mutations. Especially, as the first step, we will evaluate immune-response related genes that are up-regulated or down-regulated in gliomas with H3K27M mutations. Our goal is to better understand the characteristics of those tumors and develop effective immunotherapy strategies.
Project Date of Approval/ Status: June 28, 2017/ Ongoing


Project 2: Proteogenomic Identification of Structural Variations

Principal Investigator(s): Samuel Rivero-Hinojosa
Affiliation/Contact: CNMC/
Diagnosis/Classification: medulloblastoma
Project Summary/ Research Use: This project aims to discover novel genomic SVs encoding translated cancer specific proteins with the potential for functional effects. We propose here to mine the RNA-seq data generated as a result of the CBTTC/NantOmics collaboration for unique transcripts resulting from tumor specific SVs. We will generate customized protein search databases from RNA-seq data to capture each tumor’s unique set of SNPs, mutations, indels, gene fusions, and alternative splicing
Project Date of Approval/ Status: June 28, 2017/ Ongoing


Project 3: Analysis of Chromatin Pathways as Regulators of High Grade Glioma Gene Expression Patterns

Principal Investigator(s): Jamie Anastas
Affiliation/Contact: Boston Children’s Hospital/
Diagnosis/Classification:high grade glioma
Project Summary/ Research Use: The goal of our research is to identify genes that are up- and down-regulated in brain tumors compared to normal tissue samples and genes that are up- and down-regulated in brain tumors with different mutations. We will compare these patient-derived gene expression profiles to data we have generated using human brain cancer cells grown in the lab that have either been genetically manipulated, or treated with various drugs. By analyzing and comparing patient and laboratory datasets, we hope to identify gene expression patters characteristic of different subsets of pediatric brain tumors, and to investigate the potential consequences of our genetic manipulation and drug treatment studies, which could provide a theoretical basis for the development of new therapies.
Project Date of Approval/ Status: July 19, 2017/ Ongoing


Project 4: Immunotherapeutically – targeting IDO1 in Pediatric High Grade Glioma

Principal Investigator(s):Derek Wainwright
Affiliation/Contact:Northwestern University Feinberg School of Medicine/
Diagnosis/Classification:malignant pediatric brain tumors
Project Summary/ Research Use: We previously showed that increased IDO1 expression is associated with decreased adult glioblastoma patient survival. We are interested in determining its relevance in malignant pediatric brain tumors.
Project Date of Approval/ Status: July 19, 2017/ Ongoing


Project 5:  Telomere Maintenance Across Multiple Brain Tumors

Principal Investigator(s): Gonzalo Lopez Garcia
Affiliation/Contact: CHOP/
Diagnosis/Classification: Pediatric Brain Tumors All
Project Summary/ Research Use: We will apply different algorithms to measure telomere DNA abundance from sequencing data across tumors. We will study the association between tumor mutational background and telomere abundance
Project Date of Approval/ Status: July 28, 2017/ Ongoing


Project 6:  Multi-Tensor Decompositions for Personalized Pediatric Glioma Diagnostics and Prognostics

Principal Investigator(s): Sri Priya Ponnapalli
Affiliation/Contact: Eigengene, Inc./
Diagnosis/Classification: Pediatric Glioma
Project Summary/ Research Use: This project aims to create personalized diagnostic and prognostic tests for pediatric gliomas. Eigengene develops and applies algorithms to cancer genomic data in order to find signatures that can predict patient’s survival and response to treatment.
Project Date of Approval/ Status: September 13, 2017/ Ongoing


Project 7:  In Silico Neo-Antigen Detection in High Grade Pediatric Brain Tumors Utilizing RNA-seq and WGS

Principal Investigator(s): Peter Madsen
Affiliation/Contact: UPENN/
Diagnosis/Classification: pediatric high grade brain tumors
Project Summary/ Research Use: Our goal is to identify novel antigens in pediatric high grade brain tumors that can be used for immunotherapy. We will use whole genome sequencing data and RNA-seq data to identify novel antigens with two bioinformatic techniques (one validated and one in production). The results will help to develop new immunotherapy targets and pipelines for the generation of patient-specific immunotherapies.
Project Date of Approval/ Status: August 9, 2017/ Ongoing


Project 8: Withdrawn Application


Project 9: Spatial Evolution and Somatic Mutations Spectrum of Gliomatosis Cerebri

Principal Investigator(s): Birra Taha
Affiliation/Contact:Weill Cornell Medicine/
Diagnosis/Classification: Gliomatosis Cerebri and other HGG
Project Summary/ Research Use: An analysis of the spatial evolution and genetic-epigenetic landscape in Gliomatosis Cerebri and other HGG. Using innovative tools in computational biology to map the spatial differences in glioma progression.
Project Date of Approval/ Status: August 25, 2017/ Ongoing


Project 10: Integrative Analysis of Childhood Cancers

Principal Investigator(s): Charles Vaske
Affiliation/Contact: Nantomics/
Diagnosis/Classification: All pediatric brain tumors
Project Summary/ Research Use: We will apply integrative analysis of data types to find potential novel drug targets and matching of therapeutics.
Project Date of Approval/ Status: November 21, 2017/ Ongoing


Project 11: Malignant Cortical Tumors

Principal Investigator(s): Sarah Leary, Annie Huang
Affiliation/Contact: Seattle Children’s Hospital/; Sick Kids/
Diagnosis/Classification:Malignant Cortical Tumors
Project Summary/ Research Use:  Goal is to compare CBTTC malignant cortical tumors dataset with a larger international dataset generated by Dr. Huang’s lab to facilitate evaluation of biologic and treatment factors related to survival. This is associated with the CBTTC specimen requests, project CBTTC_0003a-d “Genomic evaluation of malignant pediatric cortical tumors”.
Project Date of Approval/ Status: September 27, 2017/ Ongoing


Project 12: Defining the Mutational Landscape of Pediatric Brain Tumors

Principal Investigator(s): Sharon Diskin
Affiliation/Contact: CHOP/
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary/ Research Use: The objective of this study is to perform a primary analysis of recently-generated whole genome sequencing (WGS) of tumor-normal pairs and matched RNA-sequencing within the CBTTC. Our goal is to define the mutational landscape across the diverse cancers sequenced and to identify pleotropic and/or histotypes-specific alterations driving the development and progression of central nervous system cancers in pediatric populations. All variant files will be put into vcf or maf format and placed into a database that will accessible to approved researchers through the consortium.
Project Date of Approval/ Status: November 21, 2017/ Ongoing


Project 13: Under Review


Project 14: Fusion Analysis in CBTTC RNAseq data

Principal Investigator(s): Rohan Bareja
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary/ Research Use: We plan to analyze the pediatric brain tumor RNAseq data for fusions. We have a small cohort of the same tumors at Weill Cornell and we want to compare both the cohorts. This will really strengthen our findings if we find something we already found in our small cohort.
Project Date of Approval/ Status: January 18, 2018/ Ongoing


Project 15: Cooperating Mutations in Bain Tumors of Patients with NF1

Principal Investigator(s): Thomas De Raedt
Affiliation/Contact: CHOP/
Diagnosis/Classification: NF1 brain tumors
Project Summary/ Research Use: To identify cooperating mutations with NF1 in Neurofibromatosis type I patients with brain tumors. This information will help model the tumors these patients develop more accurately.
Project Date of Approval/ Status: January 29, 2018/ Ongoing


Project 16: Identification of Non-coding Drivers from Brain Tumour Genomes

Principal Investigator(s): Shimin Shuai
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary/ Research Use: Cancer somatic mutations and associated RNA-seq and clinical data will be used to identify and validate potential novel coding and non-coding elements that are important for pediatric brain cancer development.
Project Date of Approval/ Status: February 23, 2018/ Ongoing


Project 17: Integrated Genomic Analysis to Elucidate the Role of the PIK3CA and 10q LOH as Unique Drivers and Cooperating Events in Pediatric High Grade Gliomas

Principal Investigator(s): Ian Pollack, Sameer Agnihotri
Affiliation/Contact: Children’s Hospital, Pittsburgh/,
Diagnosis/Classification: High Grade Gliomas
Project Summary/ Research Use: 
Project Date of Approval/ Status: 


Project 18: Withdrawn


Project 19: Molecular Analysis of the Cellular Ecosystem of Childhood Ependymoma

Principal Investigator(s): Pablo Gonzalez Camara
Diagnosis/Classification: Ependymomas 
Project Summary/ Research Use: Ependymomas constitute nearly one-third of the CNS neoplasms among children aged < 3 years and are a significant therapeutic challenge. This project seeks to characterize the composition and dynamics of the cellular ecosystem of childhood ependymoma and its role in tumor progression.
Project Date of Approval/ Status: 4/2/2018/Ongoing


Project 20: Genetic Polymorphisms and Neurocognitive Outcomes in Pediatric Brain Tumor Survivors

Principal Investigator(s): Julie Baran
Affiliation/Contact: CHOP/
Diagnosis/Classification: ALL
Project Summary/ Research Use: This research will evaluate associations between the presence or absence of various polymorphisms from BT biospecimens and neuropsychological functioning. The study will include measures of cognitive, emotional, social and behavioral functioning through the use of direct assessment, self-, and parent- report measures. Overall, we hypothesize that PBTS will have different neurocognitive and behavioral outcomes depending on the presence or absence of genetic polymorphisms.
Project Date of Approval/ Status: Approved/Pending


Project 21: Treehouse Childhood Cancer Initiative: Identification of therapeutic leads for individual pediatric cancer patients via pan-cancer analysis

Principal Investigator(s): David Haussler
Diagnosis/Classification: All
Project Summary/ Research Use: The focal point of this project is comparing genomic data of an individual pediatric patient’s tumor to the genomic data of thousands of pediatric and adult tumors. Although pediatric cancer is rare, by comparing to all the pediatric cancer and adult data possible, similarities can be spotted. These similarities offer information about possible therapeutic directions that can be further researched and validated.
Project Date of Approval/ Status: 05/03/2018/ Ongoing


Project 22: Withdrawn 


Project 23: Comparison of Clinical Targeted Next Generation Sequencing (NGS) in FFPE with whole genome sequencing (WGS) of snap frozen pediatric brain tumors

Principal Investigator(s): Bonnie Cole
Affiliation/Contact: Seattle Children’s/
Diagnosis/Classification: All
Project Summary/ Research Use:Many brain tumor patients at our institution have clinical sequencing of their tumors in addition to having tissue sent to CBTTC and included in the whole bank sequencing project. We want to compare the genetic results of our clinical NGS performed on the Oncoplex platform with the results of WGS performed through the CBTTC. To do this, we need access to the sequencing data from all tumors sent to the CBTTC from Seattle Children’s Hospital
Project Date of Approval/ Status: Approved/ Pending


Project 24: Cancer Predisposition in Pediatric Brain Tumors

Principal Investigator(s): Suzanne McFarland
Affiliation/Contact: CHOP/
Diagnosis/Classification: All
Project Summary/ Research Use: Some children with brain tumors have changes in genes leading to an increased likelihood of tumor development. These are changes that are either inherited, or new to the child. We would like to query the CBTTC germline (blood) and somatic (tumor) DNA data to identify cancer predisposing variants, and compare these findings to clinical data, in order to better understand the reason that these tumors develop
Project Date of Approval/ Status: Approved/Pending


Project 25: Genomic Landscape of Mixed Glial Neuronal Tumors

Principal Investigator(s): Lea Surrey
Affiliation/Contact: CHOP/
Diagnosis/Classification:Mixed Glial Neuronal Tumors
Project Summary/ Research Use: This study aims to examine the genomic landscape research use statement (3 sentences MAX) of mixed neuronal-glial tumors in pediatric patients. We are examining molecular/genomic signatures and correlating them with patient features (seizures, survival, etc).
Project Date of Approval/ Status: 7/18/2018/ Ongoing


Project 26: Cracking the Histone Code: Characterizing Pediatric Brain Tumor Epigenetics using Cerebrospinal Fluid

Principal Investigator(s):  Daphne Li
Affiliation/Contact:  Ann & Robert H. Lurie Children’s Hospital
Diagnosis/Classification: All
Project Summary/ Research Use:  To characterize the tumor and cerebrospinal fluid tumor protein profile and combine this information with gene expression profiling of tumors. This will allow us to explore potential targets for future diagnosis and therapeutic treatment of pediatric central nervous system tumors
Project Date of Approval/ Status: 08/01/2018 – Ongoing


Project 27: Identify novel therapeutic targets and biomarkers in non-coding genome of pediatric cancers

Principal Investigator(s):  Lihua Zou
Affiliation/Contact:  Northwestern University
Diagnosis/Classification: All
Project Summary/ Research Use:  We identified a novel pathway hyperactive in pediatric cancer. We plan to integrate CBTTC data to validate and extend our preliminary result.
Project Date of Approval/ Status: 10/01/2018 – Ongoing


Project 28: Testing/evaluation of cell lines

Principal Investigator(s):  Mateusz Koptyra
Affiliation/Contact:  Children’s Hospital of Philadelphia
Diagnosis/Classification: All
Project Summary/ Research Use:  Evaluating CBTTC cell lines through genomic data analysis.
Project Date of Approval/ Status: N/A – Ongoing


Project 29: Children’s Brain Tumor Tissue Consortium Pediatric Brain Tumor Proteomics Pilot

Principal Investigator(s):  Adam Resnick and Brian Rood
Affiliation/Contact:  Children’s Hospital of Philadelphia and Children’s National Medical Center
Diagnosis/Classification: All
Project Summary/ Research Use:  The analysis of proteomics data with whole genome and transcriptomic data will provide new insights into the classification of tumors, prognosis, as well as provide for novel therapeutic strategies targeting actionable activity protein targets.
Project Date of Approval/ Status: 10/2/2018 – Ongoing


Project 30: Immunogenomic landscape of pediatric cancers

Principal Investigator(s):  Trevor Pugh
Affiliation/Contact:  University Health Network
Diagnosis/Classification: All
Project Summary/ Research Use:  We seek to understand immune composition of childhood cancers. CBTTC datasets plus data from our collaborator will allow us to outline the role of immune cells in children with wide range of cancers.
Project Date of Approval/ Status: 10/1/2018 – Ongoing


Project 31: Identifying New Cell Surface Targets for Immunotherapy treatment of Poor Prognosis Pediatric Brain Tumors

Principal Investigator(s):  Misty Jenkins
Affiliation/Contact:  Walter and Eliza Hall of Medical Research
Diagnosis/Classification: All
Project Summary/ Research Use:  We aim to screen the established CBTTC database of pediatric brain tumor tissue to identify a list of proteins. We then aim to use an established protocol to compare this list to normal tissue expression lists, to potentially compile a list of proteins expressed in pediatric brain tumors
Project Date of Approval/ Status: 9/27/2018 – Ongoing