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. 

DATA ACCESS REQUEST FORM

 

Approved CBTTC Scientific Projects – Data Only

To contact an investigator or to submit questions related to a CBTTC scientific project, please email research@cbttc.org 

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

Principal Investigator(s): Hideho Okada, PhD, University of California San Francisco
Diagnosis/Classification: DIPG and other primary pediatric brain tumors
Project Summary: We will evaluate the 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 Status: Ongoing

 

Project 2: Proteogenomic Identification of Structural Variations

Principal Investigator(s): Samuel Rivero-Hinojosa, PhD, Children’s National Medical Center
Diagnosis/Classification: Medulloblastoma
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s): Jamie Anastas, PhD, Boston Children’s Hospital
Diagnosis/Classification: High-Grade Glioma
Project Summary: 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 patterns 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 Status: Ongoing

 

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

Principal Investigator(s): Derek Wainwright, PhD, Northwestern University Feinberg School of Medicine
Diagnosis/Classification: Malignant Pediatric Brain Tumors
Project Summary: 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 Status:  Ongoing

 

Project 5:  Telomere Maintenance Across Multiple Brain Tumors

Principal Investigator(s): Gonzalo Lopez Garcia, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Pediatric Brain Tumors (All)
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s): Sri Priya Ponnapalli, Eigengene, Inc.
Diagnosis/Classification: Pediatric Glioma
Project Summary: 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 a patient’s survival and response to treatment.
Project Status: Ongoing

 

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

Principal Investigator(s): Peter Madsen, MD, University of Pennsylvania
Diagnosis/Classification: Pediatric High-Grade Brain Tumors
Project Summary: 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 Status: Ongoing

 

Project 8: Withdrawn Application

 

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

Principal Investigator(s): Birra Taha, MD, Weill Cornell Medicine
Diagnosis/Classification: Gliomatosis Cerebri and other HGG
Project Summary: 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 Status: Ongoing

 

Project 10: Integrative Analysis of Childhood Cancers

Principal Investigator(s): Charles Vaske, PhD, NantOmics
Diagnosis/Classification: All pediatric brain tumors
Project Summary: We will apply the integrative analysis of data types to find potential novel drug targets and matching of therapeutics.
Project Status: Ongoing

 

Project 11: Malignant Cortical Tumors

Principal Investigator(s): Sarah Leary, MD, Seattle Children’s Hospital and Annie Huang, MD, PhD, The Hospital for Sick Children (SickKids)
Diagnosis/Classification: Malignant Cortical Tumors
Project Summary: The goal is to compare CBTTC malignant cortical tumors dataset with a larger international dataset generated by Dr. Huang’s lab to facilitate the 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 Status: Ongoing

 

Project 12: Defining the Mutational Landscape of Pediatric Brain Tumors

Principal Investigator(s): Sharon Diskin, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary: The objective of this study is to perform 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 pleiotropic 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 Status:  Ongoing

 

Project 13: Under Review

 

Project 14: Fusion Analysis in CBTTC RNAseq data

Principal Investigator(s): Rohan Bareja, Weill Cornell Medicine
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s): Thomas De Raedt, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: NF1 brain tumors
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s): Shimin Shuai, Ontario Institute for Cancer Research
Diagnosis/Classification: All Pediatric Brain Tumors
Project Summary: 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 Status: 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, MD, and Sameer Agnihotri, PhD, UPMC Children’s Hospital of Pittsburgh
Diagnosis/Classification: High-Grade Gliomas
Project Summary: 
Project Status: Ongoing

 

Project 18: Withdrawn

 

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

Principal Investigator(s): Pablo Gonzalez Camara, PhD, University of Pennsylvania
Diagnosis/Classification: Ependymomas
Project Summary: 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 Status:  Ongoing

 

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

Principal Investigator(s): Julie Baran, Children’s Hospital of Philadelphia
Diagnosis/Classification: All
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s): David Haussler, PhD, University of California Santa Cruz
Diagnosis/Classification: All
Project Summary: 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 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 Status: 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, MD, Seattle Children’s Hospital
Diagnosis/Classification: All
Project Summary: 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 Status: Ongoing

 

Project 24: Cancer Predisposition in Pediatric Brain Tumors

Principal Investigator(s): Suzanne McFarland, MD, Children’s Hospital of Philadelphia
Diagnosis/Classification: All
Project Summary: 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 Status: Ongoing

 

Project 25: Genomic Landscape of Mixed Glial Neuronal Tumors

Principal Investigator(s): Lea Surrey, MD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Mixed Glial Neuronal Tumors
Project Summary: 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 Status: Ongoing

 

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

Principal Investigator(s):  Daphne Li, MD, Ann & Robert H. Lurie Children’s Hospital
Diagnosis/Classification: All
Project Summary:  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 Status: Ongoing

 

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

Principal Investigator(s):  Lihua Zou, PhD, Northwestern University
Diagnosis/Classification: All
Project Summary:  We identified a novel pathway hyperactive in pediatric cancer. We plan to integrate CBTTC data to validate and extend our preliminary results.
Project Status: Ongoing

 

Project 28: Testing/evaluation of cell lines

Principal Investigator(s):  Mateusz Koptyra, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: All
Project Summary:  Evaluating CBTTC cell lines through genomic data analysis.
Project Status: Ongoing

 

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

Principal Investigator(s):  Adam Resnick, PhD, Children’s Hospital of Philadelphia and Brian Rood, MD, Children’s National Medical Center
Diagnosis/Classification: All
Project Summary:  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 Status: Ongoing

 

Project 30: Immunogenomic landscape of pediatric cancers

Principal Investigator(s):  Trevor Pugh, PhD, University Health Network
Diagnosis/Classification: All
Project Summary:  We seek to understand the 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 a wide range of cancers.
Project Status:  Ongoing

 

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

Principal Investigator(s):  Misty Jenkins, PhD, Walter and Eliza Hall of Medical Research
Diagnosis/Classification: All
Project Summary:  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 Status: Ongoing

 

Project 32: Detection of Cooperative and Mutually Exclusive Genetic Alterations in Pediatric Cancer

Principal Investigator(s):  Patrick Kemmeren, PhD, Princess Máxima Center for Pediatric Oncology
Diagnosis/Classification: All
Project Summary:  Cancers arise and progress by acquiring combinations of mutations in the genome, genetic interactions are specific combinations of mutations in gene pairs that have unexpected effects. In this project, we will study genetic interactions in childhood cancer and their relationship with different cancer types. Our goal is to gain more insight into the underlying mechanisms of childhood cancer development and progression, as well as to propose more effective drug treatments.
Project Status: Ongoing

 

Project 33: Characterizing the Prevalence of ETMR by Molecular Signature

Principal Investigator(s):  Derek Hanson, MD, Hackensack University Medical Center
Diagnosis/Classification: Embryonal Tumors with Multilayered Rosettes (ETMR)
Project Summary:  ETMR is a rare and aggressive tumor that occurs in young children. ETMR has only recently been identified as a distinct clinical entity with a unique molecular signature and the prevalence of this tumor is unknown. Through a query of the CBTTC data set, we aim to identify ETMR specimens and characterize the prevalence of these tumors.
Project Status: Ongoing

 

Project 34: Deciphering the Molecular Characteristics of Pediatric Meningiomas

Principal Investigator(s):  Nadia Dahmane, PhD, Weill Cornell Medicine
Diagnosis/Classification: Pediatric Meningioma
Project Summary:  The biology of pediatric meningioma is poorly understood. Our project aims at a better characterization of the molecular underpinnings of these extremely rare tumors and compare them to those underlying adult meningiomas development. This project will lead to a better design of therapies for meningiomas that will be more specific to the pediatric population.
Project Status: Ongoing

 

Project 35: Germline Variants in Pediatric Glioblastoma

Principal Investigator(s):  Adam Resnick, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Pediatric Glioblastoma
Project Summary:  Pediatric glioblastoma is characterized by extensive genetic heterogeneity and undergoes rapid evolution at recurrence.
Project Status: Ongoing

 

 

Project 36: Integrative Functional Genomics of Recurrent Childhood Medulloblastoma

Principal Investigator(s):  Javad Nazarian, PhD, Children’s National Health System
Diagnosis/Classification: Medulloblastoma
Project Summary:  We will assess the conservation and divergence of already generated (CBTTC) genomic and transcriptional landscapes in patient-matched primary/relapse MB pairs.
Project Status: Ongoing

 

Project 37: Comprehensive Genomic and Immune Signature Profiling of Ependymoma and Diffuse Intrinsic Pontine Glioma

Principal Investigator(s):  Katherine Schieffer, PhD, Nationwide Children’s Hospital and Stephanie LaHaye, PhD, Nationwide Children’s Hospital
Diagnosis/Classification: Ependymoma and Diffuse Intrinsic Pontine Gliomas (DIPG)
Project Summary:  Retrospective analysis of ependymoma data to evaluate genomic and transcriptomic profiles and immune signatures. Elucidate the transcriptomic and dynamic epigenomic landscape of DIPG tumors. Comparative analysis of ependymoma and DIPG.
Project Status: Ongoing

 

Project 38: Predictive Models for Transcriptome Variations

Principal Investigator(s):  Yoseph Barash, PhD, University of Pennsylvania and Elizabeth Bohj, MD, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: All
Project Summary:  Our study aims to map normal and disease-associated transcriptome variations, then build predictive models for those.
Project Status: Ongoing

 

Project 39: Genomic Correlates with Radiation Injury

Principal Investigator(s):  Oren Becher, MD, Ann & Robert H. Lurie Children’s Hospital of Chicago and Stewart Goldman, MD,  Ann & Robert H. Lurie Children’s Hospital of Chicago
Diagnosis/Classification: All
Project Summary:  We would like to identify genetic alterations that correlate with radiation injury.
Project Status: Ongoing

 

Project 40: Germline mtDNA Variants and Somatic mtDNA Mutations in Pediatric Brain Tumors

Principal Investigator(s): Xiaowu Gai, PhD, Children’s Hospital of Los Angeles
Diagnosis/Classification: All
Project Summary:  The goals of this study is to interrogate the whole-genome sequencing data of the pediatric brain tumor patients for germline mitochondrial DNA (mtDNA) variants and somatic mtDNA mutations, in order to understand their contributory roles, if any, to both the genetic risk for and the cancer development of pediatric brain tumors.
Project Status: Ongoing

 

Project 41: The Study of ATRX, ALT, and Replicative Stress in Pediatric Brain Tumors/Center for Pediatric Tumor Cell Access

Principal Investigator(s): Kristina Cole, MD, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: HGG
Project Summary:  This project aims to create high-grade glioma cell cultures to experimentally test ideas in the laboratory that arise from an examination of the high throughput testing of patient’s tumors.
Project Status: Ongoing

 

Project 42: Hudson Monash Pediatric Precision Medicine Program

Principal Investigator(s): Ron Firestein, MD, PhD, Hudson Institute of Medical Research
Diagnosis/Classification: All
Project Summary:  The program focuses on developing and utilizing individual patients’ tumor cells to identify new therapeutic targets and repurpose existing targets using functional genomics technologies.
Project Status: Ongoing

 

Project 43: Long Non-Coding RNA Signature of Medulloblastoma and AT/RT Subtypes

Principal Investigator(s): Ranjan Perera, PhD, Johns Hopkins All Children’s Hospital
Diagnosis/Classification: AT/RT
Project Summary:  We are investigating the non-coding RNA signature of pediatric CNS tumors, namely medulloblastoma and AT/RT, that could help derive better diagnostic and or prognostic markers. Identifying group-specific and highly expressed non-coding RNAs will help us better understand the role of non-coding RNAs in medulloblastoma subtypes and AT/RT.
Project Status: Ongoing

 

Project 44: Health Disparities of Pediatric Brain Tumors

Principal Investigator(s): Angela Waanders, MD, Ann & Robert H. Lurie Children’s Hospital
Diagnosis/Classification: All
Project Summary:  We aim to look at survival disparity in pediatric research use statement brain tumors among children of different racial/ethnic groups.
Project Status: Ongoing

 

Project 45: Pediatric Brain Tumor Classification and Segmentation using Transfer Learning from Adult Datasets

Principal Investigator(s): Roy Campbell, PhD, University of Chicago at Urbana-Champaign
Diagnosis/Classification: All
Project Summary: Apply ML transfer learning techniques in order to get a better classification and segmentation performance on the pediatric brain tumor dataset using data from the adult brain tumor dataset.
Project Status: Ongoing

 

Project 48: Comprehensive Analysis of Structural Variants in Pediatric Brain Tumors

Principal Investigator(s): Lixing Yang, PhD, University of Chicago
Diagnosis/Classification: All
Project Summary: Strucutral variations (SVs) are large scale changes of DNA typically affecting more nucleotides than other forms of genetic variants. We aim to study how somatic SVs are formed, how they drive disease progression and how they impact treatment in pediatric brain tumors.
Project Status: Ongoing

 

Project 49: Epigenetic Drivers in Medulloblastoma

Principal Investigator(s): Alexandros Tzatsos, MD, PhD, George Washington University
Diagnosis/Classification: Medullo
Project Summary: We will employ next-generation sequencing data to identify alterations in the non-coding genome that may drive the remodeling of enhancer chromatin in Medulloblastoma.
Project Status: Ongoing

 

Project 51: Alternative Splicing in CBTTC Data

Principal Investigator(s): Shihao Shen, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: 
Project Status: Ongoing

 

Project 52: Molecular Characterization of Choroid Plexus Tumors

Principal Investigator(s): Christian Thomas, MD, Institute of Neuropathology Münster
Diagnosis/Classification: Choroid Plexus
Project Summary: Choroid Plexus Tumors (CPT) are brain tumors primarily arising in children and adolescents. CPT comprise different histologic and epigenetic subgroups with variable clinical outcome, but despite frequent copy-number alterations and some CPT harboring TP53 mutations, recurrent driver mutations are unknown. The aim of our project is to evaluate the occurrence of fusion transcripts in CPT.
Project Status: Ongoing

 

Project 53: Germline Determinants of Pediatric Brain Tumors

Principal Investigator(s): Sorana Morrissy, PhD, University of Calgary
Diagnosis/Classification: Not specified
Project Summary: We will study the inherited DNA of children with brain tumors to systematically identify differences that may have caused their disease. By comparing their DNA sequence with that of hundreds of thousands of normal adults without cancer, we aim to find new combinations of inherited DNA sequences that may predispose to early onset of cancer.
Project Status: Ongoing

 

Project 54: Discover New Therapeutics for DIPG Using a Systems-Based Approach

Principal Investigator(s): Bin Chen, PhD, Michigan State University
Diagnosis/Classification: Diffuse Intrinsic Pontine Glioma (DIPG)
Project Summary: Novel approaches are urgently needed to treat Diffuse Intrinsic Pontine Glioma (DIPG). We hypothesize that reversing signature gene expression derived from DIPG-RNA-Seq samples will facilitate novel therapeutic discovery for DIPG. We, therefore, request the raw RNA-Seq FASTQ files to build the DIPG gene expression signature which will be fed into our computational pipeline to identify potential candidates, followed by experimental validation.
Project Status: Ongoing

 

Project 55: Relationships Between Genomic, Imaging, and Histopathologic Characteristics in Pediatric Brain Tumors

Principal Investigator(s): Benjamin Hartley, MD, Weill Cornell Brain and Spine Center
Diagnosis/Classification: Not specified
Project Summary: We wish to correlate genomic sequences of pediatric brain tumor samples with radiology and histopathologic text-based reports in the same samples using novel machine learning algorithms.
Project Status: Ongoing

 

Project 56: Evaluating the Landscape of Compound Heterozygous Variants in Pediatric Diseases

Principal Investigator(s): Stephen Piccolo, PhD, Brigham Young University
Diagnosis/Classification: Not specified
Project Summary: Using datasets from the Pediatric Brain Tumor Atlas and the Gabriella Miller Kids First Data Resource Center, we seek to identify inherited mutations in pediatric brain tumors and other pediatric diseases and perform a cross-disease analysis to determine whether certain mutations commonly affect the same genes/pathways across these diseases.
Project Status: Ongoing

 

Project 57: Comparison of CBTTC Patient Data with Molecularly Defined Stem Cell Models of Pediatric Brain Tumors

Principal Investigator(s): Fredrik Swartling, PhD, Uppsala University, Department of Immunology, Genetics, and Pathology
Diagnosis/Classification: Not specified
Project Summary: Our goal is to understand brain tumor development and progression by identifying genes that are differentially regulated in pediatric brain tumors as compared to normal brain samples. We are currently generating animal models for specific malignant childhood brain tumors. By comparing data from our models to global patient datasets, we hope to identify gene expression patterns characteristic of different molecular entities of pediatric brain tumors.
Project Status: Ongoing

 

Project 58: Germline and Somatic Microsatellite Genotypes in Pediatric Brain Tumors

Principal Investigator(s): Brian Rood, MD, Children’s National Health System
Diagnosis/Classification: Not specified
Project Summary: We have used germline sequencing and our innovative microsatellite genotyping software to construct and validate a microsatellite genotype signature with the ability to classify medulloblastoma from control subjects with a high degree of accuracy. We will next expand this effort to identify microsatellite variations specific to other types of pediatric brain tumors.
Project Status: Ongoing

 

Project 59: Clinical, Radiologic, and Molecular Characteristics of Anaplastic Pleomorphic Xanthoastrocytomas

Principal Investigator(s): Alberto Broniscer, MD, Children’s Hospital of Pittsburgh
Diagnosis/Classification: Anaplastic Pleomorphic Xanthoastrocytomas
Project Summary: Anaplastic Pleomorphic Xanthoastrocytomas (PXAs) are rare and poorly understood brain and spinal cord cancers which were not recognized as potentially deadly throughout the world until 2016. We started a multi-institutional study with more than 10 institutions in the US to perform a detailed evaluation of clinical, radiologic, and molecular characteristics in patients with anaplastic PXAs.
Project Status: Ongoing

 

Project 60: Central Nervous System Cancers in Patients with Non-Neurofibromatosis Type 1 RASopathies

Principal Investigator(s): Alberto Broniscer, MD, Children’s Hospital of Pittsburgh
Diagnosis/Classification: Craniopharyngioma
Project Summary: The association of non-neurofibromatosis type 1 (NF-1)-RASopathies (e.g., Noonan Syndrom [NSI]) with the central nervous system (CNS) cancers are uncommon (less than 40 described cases). Based on our experience and the overlapping molecular characteristics of non-NF-1 RASopathies and somatic abnormalities found in some pediatric CNS cancers (e.g. low-grade gliomas), we postulate that this association is more common than currently recognized. We are collecting cases of the association of non-NF-1 RASopathies and CNS cancers at our institution and from other institutions in the US. By using data from cases collected through CBTTC, we are hoping to increase the size of our cohort of research participants.
Project Status: Ongoing

 

Project 61: Body Mass Index Trajectories in Craniopharyngioma

Principal Investigator(s): Shana McCormack, MD, MTR, Children’s Hospital of Philadelphia
Diagnosis/Classification: Craniopharyngioma
Project Summary: The objective of this project is to examine the trajectories of height, weight, and body mass index (BMI) in individuals in the CBTTC with pathological diagnoses of craniopharyngioma. Our overarching research goal is to develop a risk prediction model for the development of hypothalamic obesity-related to craniopharyngioma that will inform the design and testing of individualized prevention strategies.
Project Status: Ongoing

 

Project 62: Descriptive “Pharmacogenomics Analysis” of the CBTTC PBTA Cohort

Principal Investigator(s): Angela Waanders, MD, Ann & Robert H. Lurie Children’s Hospital of Chicago
Diagnosis/Classification: Not specified
Project Summary: Pharmacogenomics is an emerging field, using an individual’s genotype to predict toxicities and/or response to specific drugs. To date, there has been limited information published in pediatric brain tumor patients. This proposal will directly address this gap in knowledge and help to inform clinical care for future patients.
Project Status: Ongoing

 

Project 63: Exploring the Possible Role of Mutations in MTOR Pathway Genes in the Pathogenesis of DNET Tumors

Principal Investigator(s): Anna Maria Buccoliero, MD, Meyer Children’s Hospital, University of Florence
Diagnosis/Classification: Gangliogliomas and DNET
Project Summary: Our study will expand the CBTTC data on the gangliogliomas and DNT (impact of m-tar pathway).
Project Status: Ongoing

 

Project 64: PNOC and SJCRH Collaborative DIPG Radiogenomic Investigation

Principal Investigator(s): John Lucas, MS, MD, St. Jude Children’s Research Hospital
Diagnosis/Classification: DIPG
Project Summary: Semiquantitative imaging parameters extracted from magnetic resonance imaging (radiomics) have been suggested as a means to both identify and better characterize tumor biology and molecular features. We aim to define the relationship between quantitative and qualitative imaging features and molecularly defined subtypes of pediatric brainstem glioma. We also plan to evaluate the relationship between longitudinal changes in tumor and tumor habitat/subregion volumetric changes over time and patient-derived liquid biopsy specimens.
Project Status: Ongoing

 

Project 65: Landscape of Tumor-Infiltrating T-Cell Repertoire of Pediatric Brain Tumors

Principal Investigator(s): Gary Kohanbash, PhD, University of Pittsburgh
Diagnosis/Classification: Not specified
Project Summary: T-cells are immune cells within the body that can fight disease including cancer. Our project will examine similarities and differences in T-cells between patients and tumor types. This will be important information for the development of new immune therapies for these patients.
Project Status: Ongoing

 

Project 66: Molecular and Functional Characterization of Childhood Supratentorial Ependymoma

Principal Investigator(s): Vijay Ramaswamy, MD, PhD, The Hospital for Sick Children
Diagnosis/Classification: Ependymoma
Project Summary: Samples obtained from the CBTTC will be analyzed for the presence of changes in the chromosomes of the tumor that we think are causing ependymomas to form. The samples obtained from CBTTC will be analyzed to find differences, and correlate them with patient outcomes.
Project Status: Ongoing

 

Project 67: Genomic Analysis of Oligodendrogliomas Across the Pediatrics, Adolescents, and Adults

Principal Investigator(s): Adam Resnick, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Oligodendrogliomas
Project Summary: This project will generate WGS and RNAseq data to perform genomic analysis of oligodendrogliomas across pediatric, adolescents, and adults.
Project Status: Ongoing

 

Project 68: Cancer Stemness of Pediatric Tumors

Principal Investigator(s): Maciej Wiznerowicz, MD, PhD, International Institute for Molecular Oncology
Diagnosis/Classification: Not specified
Project Summary: We aim to draw parallels between epigenetic, molecular circuits, and phenotype between normal pluripotent stem cells and cells with the stem cell like phenotype that propel tumor growth.
Project Status: Ongoing

 

Project 69: Targeting Immunosuppressive Macrophage in Pediatric Brain Tumors

Principal Investigator(s): Erin Crotty, MD, Seattle Children’s Hospital
Diagnosis/Classification: Not specified
Project Summary: We hypothesize that macrophages within pediatric brain tumors (PBT) may enable local tumor regrowth and spinal metastasis. To determine the burden of infiltrating macrophage in human PBT tissue samples, we plan to correlate gene expression of macrophage signature genes with patterns of clinical progression and outcome.
Project Status: Ongoing

 

Project 70: Detecting Gene Fusions and Subtype Discovery in Pediatric Solid Tumors RNA-Seq Using CICERO

Principal Investigator(s): Scott Newman, PhD, St. Jude Children’s Research Hospital
Diagnosis/Classification: Pediatric tumors including neuroblastoma, low and high grade glioblastoma, medulloblastoma, choroid plexus carcinoma, ependymoma, and other rare diagnoses
Project Summary: Find new childhood brain tumor gene fusions and sub-groups by analyzing the CBTTC data in tandem with St. Jude Cloud data.
Project Status: Ongoing

 

Project 72: Cross Disease Variant Lookup in CBTTC

Principal Investigator(s): Yiran Guo, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Not specified
Project Summary: This project aims at identifying variants in the CBTTC gremlin DNA whole genome sequencing data that are reported and/or found in other diseases, especially birth defects and rare Mendelian disorders, hoping to explain/reveal shared genetics between pediatric cancer and rare diseases.
Project Status: Ongoing

 

Project 73: Genomics of Radiation-Induced Cavernomas in Pediatric Tumor Patients

Principal Investigator(s): YouRong Sophie Su, MD, University of Pennsylvania
Diagnosis/Classification: Tumor (unspecified) and cavernoma
Project Summary: Many pediatric patients with tumors receive subsequent radiation therapy. A select cohort of these patients develop cavernous. We went to analyze and compare the genetic data of these patients to genetic data of patients with familial and sporadic cavernomas.
Project Status: Ongoing

 

Project 74: NF Hackathon

Principal Investigator(s): Adam Resnick, PhD, Children’s Hospital of Philadelphia
Diagnosis/Classification: Neurofibromatosis (NF)
Project Summary: Over 120 researchers, data scientists, and engineers will come together on September 13-15 at the Google Launchpad in San Francisco to explore and analyze data from the NF Data Portal, the leading open-source collection of genomic and clinical data dedicated to the genetic disorder neurofibromatosis. This intensive 3-day event will merge together the fields of genomic medicine, computer science and vision, statistics, and bioinformatics in the quest for innovative new insights into rare diseases like NF.
Project Status: Ongoing

 

Project 37: Comprehensive Molecular Profiling of Pediatric Meningioma

Principal Investigator(s): Kathleen Schieffer, PhD, MLS(ASCP), Nationwide Children’s Hospital
Diagnosis/Classification: Meningioma
Project Summary: Meningioma is an exceedingly rare brain tumor in the pediatric population. Patients with the genetic disorder, neurofibromatosis type 2, are predisposed to meningioma due to their underlying genetic variation in the gene NF2. A better understanding of tumor development in patients without NF2 variation is needed.
Project Status: Ongoing

 

Project 76: Multi-scale Model of Children with Brain Tumors

Principal Investigator(s): Olivier Gevaert, PhD, Stanford University
Diagnosis/Classification: Not specified
Project Summary: We will test a multi-scale model that was developed in adult brain tumor patients and test this model on pediatric brain tumor data. We will evaluate whether existing models can be used, or if the model needs to be fine-tuned to pediatric brain tumor data.
Project Status: Ongoing

 

Project 77: The Australian Bioinformatics Commons Pediatric Cancer Pathfinder Project

Principal Investigator(s): Mark Cowley, PhD, Children’s Cancer Institute
Diagnosis/Classification: Not specified
Project Summary: In partnership with investigators from CAVATICA, we are developing The Australian Bioinformatics Commons, which is the largest genomic data sharing initiative undertaken in Australia. This platform will be able to link data in Australia, with data in CAVATICA in the United States, allowing seamless data analysis and integration across geographical borders. We thus request access to brain tumor data from the CBTTC cohort to demonstrate the utility of this approach.
Project Status: Ongoing

 

Project 78: Decoding the Dark Matter of the High-Risk Pediatric Cancer Genome

Principal Investigator(s): Mark Cowley, PhD, Children’s Cancer Institute
Diagnosis/Classification: Not specified
Project Summary: High-risk pediatric cancers have dismal survival rates, and despite best efforts using advanced DNA sequencing, we find very few mutations to explain this aggressiveness. We reasoned that whole classes of under-explored mutations in the “noncoding genome” may explain their poor outcomes, and we propose innovative ways to study these in the largest study of patients with these cancers to date.
Project Status: Ongoing

 

Project 79: Developing Summative Measures of Pediatric Cancer Risk

Principal Investigator(s): Mark Cowley, PhD, Children’s Cancer Institute
Diagnosis/Classification: Not specified
Project Summary: Understanding the genetic reasons why some families develop cancer at a young age is critical for effective screening and identifying at-risk individuals. Currently, we mostly look at the effect of individual mutations in well-known cancer genes to determine a patient’s likely cancer risk. Here, we propose to develop new methods that look at far more genes and alternative signals in the data which we believe will lead to better ways of predicting cancer risk.
Project Status: Ongoing

 

Project 80: Stand Up 2 Cancer

Principal Investigator(s): Mi-Youn Brusniak, PhD, Fred Hutchinson Cancer Research Center
Diagnosis/Classification: HGG, DIPG, Rhabdoid, and others
Project Summary: Investigating biomarker for treatment responders and non-responders in PDX model experiment.
Project Status: Ongoing

 

Project 81: Comparison of Fusion Calling Platforms in Pediatric DIPG and High-Grade Glioma

Principal Investigator(s): Carl Koschmann, MD, University of Michigan
Diagnosis/Classification: Pediatric HGG (including DIPG)
Project Summary: In this proposal, we will collaborate with the Children’s Brain Tumor Tissue Consortium (CBTTC) to compare the CODAC tool against other established computational tools on the RNA-sequencing data of over 100 DIPG tumors. To confirm that fusions called by the CODAC pipeline are tumor driving (not false positives), we will model them in various in vitro and in vivo (mouse) genetically engineered models. For confirmed tumorigenic fusions, we will treat these models with pathway relevant therapies.
Project Status: Ongoing

 

Project 37B: Comprehensive Molecular Profiling of Pediatric Diffuse Astrocytomas: Independent Validation of Proteomic Analysis

Principal Investigator(s): Kathleen Schieffer, PhD, MLS(ASCP), Nationwide Children’s Hospital
Diagnosis/Classification: Diffuse astrocytoma
Project Summary: Molecular characterization of pediatric brain tumors helps to improve prognostication and identify targeted therapies. In children with diffuse astrocytomas, these tumors rarely transform into high-grade malignancies but rather keep growing and require multiple interventions. We aim to identify molecular targets that are associated with time to progression that may help to inform treatment strategies and determine prognosis.
Project Status: Ongoing

 

Project 75: A Highly Usable and Fully Comprehensive Proteogenomic Method Leveraging the Breadth of Genetic Variation for Oncogenic and/or Therapeutic Novel Protein Discovery

Principal Investigator(s): Alex Kentsis, MD, PhD, Memorial Sloan-Kettering Cancer Center
Diagnosis/Classification: Not specified
Project Summary: Proteogenomics, as a concept, utilizes patient or sample-specific genetic data to streamline the chemical identification of proteins occurring in a real cell or tumor sample. Our software handles certain genetic peculiarities of tumors more accurately than its predecessors. We anticipate that the analysis of the CBTTC (+CPTAC) dataset using our method will enable the discovery of tumor-associated protein signatures at the genome-scale.
Project Status: Ongoing

 

Project 82: Novel Neoantigen Detection from Complex Transcriptomic Structures in Pediatric Brain Tumors

Principal Investigator(s): Tamer Ahmed Mansour, PhD, University of California-Davis
Diagnosis/Classification: Not specific
Project Summary: We are proposing a new pipeline that can predict novel and more accurate neoantigens for pediatric brain tumors using an approach independent from the assembled genomes. This project helps support current efforts being made to implement immunotherapy for this type of childhood tumors.
Project Status: Ongoing

 

Project 83: The Role of Genetic Factors in Ependymoma Susceptibility

Principal Investigator(s): Maral Adel Fahmideh, PhD, Baylor College of Medicine
Diagnosis/Classification: Ependymoma
Project Summary: In this study, we aim to identify genetic markers that play an important role in the increased risk of childhood brain tumors.
Project Status: Ongoing

 

Project 84: Genetic Susceptibility to Medulloblastoma

Principal Investigator(s): Maral Adel Fahmideh, PhD, Baylor College of Medicine
Diagnosis/Classification: Medulloblastoma
Project Summary: In this study, we aim to identify genetic markers that play an important role in the increased risk of childhood brain tumors.
Project Status: Ongoing

 

Project 85: Defining Molecular Neighborhoods for Pediatric HGG

Principal Investigator(s): Kenneth Cohen, MD, MBA, Johns Hopkins Medicine
Diagnosis/Classification: HGG
Project Summary: We want to see if we can take NGS and associated data for children with HGG and define a finite series of groupings that reflect the range of variability of genetic data for this diagnosis. If this is possible, we should then be able to determine the recommended treatment for each group identified and use these results to predefine treatment recommendations for future cases.
Project Status: Ongoing

 

Project 86: Therapeutic Targeting of the Blood-Brain Barrier in Pediatric Malignant Brain Tumors

Principal Investigator(s): Sadhana Jackson, MD, National Institute of Health
Diagnosis/Classification: Malignant glioma including diffuse midline glioma and diffuse intrinsic pontine glioma
Project Summary: Our studies are focused on understanding why drugs have a hard time getting to brain tumor cells. The wall known as the blood-brain barrier, allows drugs to pass in certain areas but not in other areas. We want to understand more about the restricted areas.
Project Status: Ongoing

 

Project 87: Mitochondrial Mutations in Pediatric Brain Cancer

Principal Investigator(s): Tsumugi Gebo, University of California, Los Angeles and Paul Boutros, PhD, MBA, University of California, Los Angeles
Diagnosis/Classification: Not specified
Project Summary: We will be looking for mutations in the mitochondrial DNA and compare the presence of these to mutations in nuclear DNA to try to understand the biology of mutations in these cancer types.
Project Status: Ongoing

 

Project 88: iPC EU Horizon 2020—Individualized Pediatric Cure: Cloud-Based Virtual-Patient Models for Precision Pediatric Oncology

Principal Investigator(s): Dejan Štepec, XLAB University of Ljubljana
Diagnosis/Classification: Not specified
Project Summary: Unsupervised visual anomaly detection methods will be developed on available imagery data (histology images, MR images, radiology images) to detect anomalies (e.g. tumors metastases) without the need for expertly labeled lesion level data. The research will be performed as part of the iPC EU Horizon 2020 project and PIs Ph.D. study.
Project Status: Ongoing

 

Project 89: Splicing Analysis in Ependymoma

Principal Investigator(s): Marcel Kool, PhD, DFKZ, KiTZ (Hopp-Children’s Cancer Center, Heidelberg, Germany)
Diagnosis/Classification: Ependymoma
Project Summary: RNA-Seq data of ependymoma (and other brain tumors) will be analyzed to identify differential splicing between tumor types. Ideally, we would like to link results to clinical data, such as age, gender, tumor location, and outcome. If necessary, we would also like to link potential isoforms to mutations in the DNA.
Project Status: Ongoing

 

Project 90: The Role of Mutational Signatures in the Development of Childhood Cancer

Principal Investigator(s): Michael Scheurer, PhD, MPH, Baylor College of Medicine
Diagnosis/Classification: Not specified
Project Summary: In this study, we aim to identify genetic aberrations across different histological types of childhood cancer. And to evaluate the importance of these aberrations in the development of childhood cancers.
Project Status: Ongoing

 

Project 91: Exploring the Somatic Landscape of Adult and Pediatric Chordoma

Principal Investigator(s): Adrienne Flanagan, University College London Cancer Institute
Diagnosis/Classification: Chordoma
Project Summary: Our research seeks to uncover more about adult and pediatric chordoma by studying genetic patterns. By understanding these patterns, we hope to identify new treatments.
Project Status: Ongoing

 

Project 92: Mechanistic Modeling of High-Grade Glioma

Principal Investigator(s): Christoph Wierling, PhD, Alacris Thernostics GmbH
Diagnosis/Classification: HGG
Project Summary: We will use a computer model to find potential drug treatments for high-grade glioma patients. We will use the expression and mutation data of glioma patients as a basis for personalized in silico modeling of drug responses.
Project Status: Ongoing