In the largest academic collaboration of its kind, The Broad Institute of MIT and Harvard, Dana-Farber Cancer Institute and St. Jude Children’s Research Hospital launched the Pediatric Cancer Dependencies Accelerator (PedDep), a research initiative to accelerate understanding of pediatric cancer biology. Drawing on the expertise and resources of all three institutions, the collaboration seeks to identify genetic and chemical pediatric cancer vulnerabilities in order to improve existing treatments and develop new ones.
The Department of Computational Biology contributes to this initiative through innovative approaches in data mining, integrating and sharing.
“Through data sharing and tool development, we are committed to creating a resource that the scientific community can leverage to make a real impact on childhood cancers. I am excited to see the impact this project will have on the pace of therapeutic discovery.”
- Francisca Vazquez, PhD, Broad Institute Cancer Dependency Map Project director
St. Jude Cloud is the largest cloud-based genomic resource for pediatric cancer. By sharing data and analytic resources with the global research community, St. Jude Cloud facilitates knowledge sharing to advance cures for pediatric cancer and other catastrophic diseases.
By partnering with Microsoft and DNANexus, St. Jude Cloud offers apps that provide comprehensive data on research domains for pediatric cancer, cancer survivorship, and non-cancerous diseases.
The solid tumor Comprehensive METhylation (COMET) database is the largest, most comprehensive pediatric solid tumor epigenetic reference dataset in the world. The tool accelerates the understanding on the origins of pediatric solid tumors by advancing clinical trial research and the ability to classify difficult cases.
As part of a suite of research collaboratives led by St. Jude, the collaborative research consortium on 3D Genomic Architecture of Pediatric Cancer examines dysregulated genome structure and gene expression to identify promising therapeutic targets and understand gene regulation in cancers.
The collaborative uses large-scale, integrative computational analysis to study complex biological processes that leads to a greater understanding of chromatin characteristics in cancer. Leveraging these insights, the collaborative aims to unravel the nuclear and chromatin architecture that drives malignant characteristics in pediatric cancers.
As major contributions to survivorship research, St. Jude leads the St. Jude Lifetime Study (SJLIFE) and the Childhood Cancer Survivorship Study (CCSS). SJ LIFE and the CCSS are large longitudinal studies of pediatric cancer survivors that aim to advance knowledge about survivorship outcomes.
Both studies consist of retrospectively constructed cohorts who are assessed via prospective follow-up. Studies of these cohorts have generated comprehensive and diverse datasets that include deeply assessed clinical data and germline DNA whole-genome sequencing. Such a robust dataset provides a complete profile of the diagnosis, treatment and health of pediatric cancer survivors.
Sequencing datasets and research-access management for both the SJLIFE and CCSS cohorts are stored on St. Jude Cloud. The Survivorship Portal, also stored on St. Jude Cloud, offers real-time visualization and analysis of both datasets, with support for secure access to controlled data.
In a first-of-its-kind initiative, St. Jude routinely releases prospective, high-quality clinical genome sequencing data. The data, available on the St. Jude Cloud, allows all researchers in a relevant field to access whole-genome, whole-exome and transcriptome data from consenting St. Jude patients. Data is uploaded to the St. Jude Cloud via a secure, private environment on a regular basis, and is available at no cost.
By sharing clinical genetic data on an ongoing basis, St. Jude advances research efforts for pediatric cancer and other catastrophic diseases.