CCDI CCDC - sporedata/researchdesigneR GitHub Wiki

General description

The Childhood Cancer Data Catalog (CCDC), part of the Childhood Cancer Data Initiative (CCDI), serves as a comprehensive directory of pediatric oncology data resources. It lists various types of childhood cancer-related resources such as repositories, registries, knowledgebases, and catalogs that manage or reference data. The catalog provides contact information, enabling users to connect with the owners of these resources to learn about accessing the available data. However, the CCDI-CCDC itself does not grant direct access to the data within these resources.

This searchable database encompasses both National Cancer Institute resources and other pediatric cancer-related tools and databases. It allows users to explore and filter a wide array of data resources, or to use specific search terms to locate data relevant to their needs. The catalog includes a variety of resources, from data management systems to analytical tools, all pertaining to pediatric oncology.

CCDI-CCDC comprises nine (09) datasets:

1. Childhood Cancer Data Initiative (CCDI): Molecular Characterization across Pediatric Brain Tumors and Other Solid and Hematologic Malignancies for Research, Diagnostic, and Precision Medicine This research encompasses a wide array of data types, including whole genome sequencing (WGS), RNA sequencing (RNA-Seq), Clinical Panel Sequencing, and other omics and molecular information, focusing on pediatric brain tumors as well as other solid and blood-related cancers in children. The data was compiled from various institutions, notably the multi-institute Children's Brain Tumor Network (CBTN), the Pacific Pediatric Neuro-Oncology Consortium (PNOC), and the Children's Hospital of Philadelphia Division for Genomic Diagnostics (CHOP DGD). In 2019, CBTN introduced the Pediatric Brain Tumor Atlas, now the world's most extensive repository of childhood brain tumor data. This atlas is not only propelling brain tumor research forward but is also enabling discoveries related to other rare childhood conditions. Representing the most extensive, clinically detailed study cohort of pediatric brain tumors to date, this sequencing project aims to elucidate the interaction between inherited (germline) and acquired (somatic) genetic factors in these tumors, set against the broader backdrop of cancer and congenital structural anomalies.

2. Childhood Cancer Data Initiative (CCDI): Comprehensive Genomic Sequencing of Pediatric Cancer Cases (CMRI/KUCC) This research presents genomic sequencing data that is matched between tumor and normal samples from around 200 pediatric cancer patients. The children, suffering from various forms of cancer including both solid tumors and leukemias, were studied under the joint efforts of the Children's Mercy Research Institute (CMRI) and the University of Kansas Cancer Center (KUCC). The data encompasses a comprehensive range, including whole genome sequencing, whole exome sequencing, bulk RNA sequencing, as well as single-cell RNA and ATAC sequencing. Additionally, a rich set of phenotypic, pathological, and genetic information, which was clinically collected for these samples, is also included in the study.

3. Childhood Cancer Data Initiative (CCDI): Molecular Characterization Initiative The Childhood Cancer Data Initiative (CCDI) of the National Cancer Institute (NCI) is dedicated to the vital task of gathering, analyzing, and disseminating data to tackle the impact of cancer on children, adolescents, and young adults (AYAs). Complementing the efforts of CCDI, the Molecular Characterization Initiative (MCI) aims to enhance the availability of improved diagnostic tests for pediatric and AYA patients. The initiative involves molecular characterization of solid tumors, soft tissue sarcomas, and rare diseases, conducted within a CLIA-certified environment. This ensures that the results can be utilized not only for screening and confirming eligibility for clinical trials but also for guiding treatment decisions and contributing to the overall management of the trial.

4. Feasibility and Clinical Utility of Whole Genome Profiling in Pediatric and Young Adult Cancers This dataset encompasses extensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses conducted on 114 pediatric patients at Memorial Sloan Kettering. The data served as the basis for a prospective study focusing on clinical utility and feasibility. Utilizing the Isabl infrastructure designed for precision medicine, a comprehensive 2-week end-to-end pipeline was developed for the analysis of circulating free DNA (cfDNA), Whole Genome Sequencing (WGS), and Whole Transcriptome Sequencing (WTS). This pipeline is referred to as cWGTS.

5. Childhood Cancer Data Initiative (CCDI): Clonal Evolution During Metastatic Spread in High-Risk Neuroblastoma This study aims to provide an in-depth analysis of the patterns of disease spread in high-risk neuroblastoma at various stages: at diagnosis, during disease progression, and in response to treatment. It involves the collection of tumors from different locations and at different times from patients. The gathered clinical data encompasses details of diagnosis and treatment, while the biospecimen data includes comprehensive assessments through whole genome sequencing (WGS) and whole transcriptome sequencing (WTS).

6. National Childhood Cancer Registry Explorer NCCR-Explorer offers detailed statistics on cancer incidence and survival among children, adolescents, and young adults aged 0-39, utilizing data sourced from the National Childhood Cancer Registry (NCCR). This tool provides comprehensive statistics for various cancer types, delineated by gender, race/ethnicity, and age group, and enables comparisons between different cancer types and their subtypes. The data includes information from Cancer in North America (CiNA) compiled by the North American Association of Central Cancer Registries (NAACCR) for the years 1995-2018 and the National Cancer Institute's (NCI) Surveillance, Epidemiology, and End Results (SEER) Registries, with the latest submission in December 2020.

7. NCI CCSG CCDI Supplement Additional Genomic Submission The application of specific treatments for acute myeloid leukemia (AML) has faced obstacles due to the intricate and varied mutation patterns observed among patients and the limited availability of drugs targeting most of these mutations. The additional data from the Beat AML program offers new insights into Adolescent and Young Adult (AYA) and pediatric tumor samples that were not previously available. This new information encompasses detailed exome and RNA profiling, along with studies on drug sensitivity conducted ex vivo. Altogether, this dataset enables a comprehensive exploration of clinical, genomic, transcriptomic, and functional aspects of leukemia in pediatric and AYA groups, providing valuable resources for understanding and treating the disease.

8. UCSF Database for the Advancement of JMML - Integration of Metadata with "Omic" Data Juvenile myelomonocytic leukemia (JMML) is a rare, often fatal myelodysplastic and myeloproliferative disease that primarily affects young children, with an estimated occurrence of 1.2 cases per million. This condition exhibits a wide range of outcomes, from the uncommon spontaneous resolution in some patients to the progression to acute myeloid leukemia in others. A significant proportion of JMML patients, approximately 95%, present mutations in key Ras pathway genes such as NF1, NRAS, KRAS, PTPN11, and CBL. Since Ras proteins are involved in over 30% of human cancers, research on JMML has shed light on Ras signaling in cancer, as well as a collection of congenital conditions predisposed to tumors, known as "Rasopathies." Despite the prevalence of oncogenic Ras mutations in many human cancers, developing effective treatments for these mutations remains a challenging task.

9. Childhood Cancer Data Initiative (CCDI): OncoKids - NGS Panel for Pediatric Malignancies The focus of this study was to comprehensively gather and analyze clinical, registry, and genomic information on children with cancer, aiming to contribute significantly to the CCDI Pediatric Data Ecosystem. The study involved the collection and harmonization of clinical, treatment, and outcome information from 1,039 pediatric cancer patients at Children's Hospital Los Angeles. These patients had undergone molecular profiling using the OncoKids gene panel, and the data was prepared for submission to the NCI's Cancer Data Service.

   The OncoKids panel is specifically designed to identify DNA mutations, gene amplifications, and a range of gene fusions at the RNA level. It targets nearly 200 oncogenes and tumor suppressor genes, some pharmacogenomic targets, and about 1,700 disease-related gene fusions. This panel covers a broad spectrum of the FDA's pediatric molecular targets and includes genes related to extremely rare pediatric cancers. The comprehensive data set compiled includes DNA and RNA sequencing data, OncoKids test outcomes, and detailed clinical information encompassing patient demographics, diagnosis, comorbidities, adverse events, and treatment specifics.

Data access

More information about CCDI-CCDC can be found at https://datacatalog.ccdi.cancer.gov/

To access CCDI-CCDC data, visit https://datacatalog.ccdi.cancer.gov/resource/CCDI