The Survivorship Portal shares high quality genomic and clinical data from large cohorts of survivors of pediatric cancer. This portal currently only contains demo data. For more information or help, please contact us.
The Survivorship Study cohort is comprised of 3006 clinically assessed long-term survivors of childhood cancer and includes whole-genome sequence (WGS) along with detailed demographic, diagnostic, treatment and outcome follow-up clinical information. To accelerate the rate of discovery in survivorship research we have developed this Survivorship Portal, a data-sharing platform on the St. Jude Cloud. The Portal features the Clinical Dictionary Browser and GenomePaint, a genetic variant browser, for visualizing and analyzing clinical and genetic data integratively.
The Clinical Dictionary Browser enables interactive exploration of 1) Cancer-related variables such as diagnosis and treatment; 2) Demographic variables; and 3) Outcomes, including severity-graded chronic health conditions using a modified version of the Common Terminology Classification for Adverse Events, and subsequent cancers. Dictionary terms from these categories are arranged hierarchically from general to specific, allowing a user to traverse the dictionary tree and view patient distributions by user selected terms as customizable barcharts, or perform cross-tabulation between two terms.
The GenomePaint displays germline SNV, indel, and copy number variants computed from WGS, allowing to display and filter variants based on a variety of functional annotations and population allele frequencies. It also supports on-the-fly locus-specific association testing on any coding or non-coding locus to identify variants associated with user’s choice of clinical terms, e.g. 1) leukemia and non-leukemia survivors of a specific ethnic group, or 2) survivors diagnosed within a specific age range (e.g. <=4 years) against gnomAD as a control population.