PeCan Knowledge Base: Making sense of complex genomics by St. Jude Children's Research Hospital
PeCan Knowledge Base: Making sense of complex genomics
PeCan Knowledge Base (PeCan) on St. Jude Cloud (part of St. Jude Children’s Research Hospital) is a pioneering resource that began as a collection of curated genomic variants for pediatric cancer. Over time, it has evolved into a robust and comprehensive platform, encompassing interconnected data facets from thousands of hematologic, central nervous system (CNS), and non-CNS solid tumor patient samples worldwide. This expansion includes critical data on gene expression, mutational signatures, and histology, all of which can be explored alongside the enriched variants data facet, inspiring groundbreaking hypothesis generation through integrated analysis.
Collaboration with the Scientific Community
Recognizing the rarity of pediatric cancer subtypes and addressing it through a collaborative approach, PeCan facilitates multi-institutional studies and datasets to amalgamate data from diverse sources into a unified global pediatric cancer knowledgebase. This collaborative effort involves esteemed institutions like St. Jude Children’s Research Hospital, Washington University, NCI-TARGET, German Cancer Research Center (DKFZ), Shanghai Children’s Medical Center, BROAD Institute, UT Southwestern Medical Center and many more. With contributions spanning 37 publications, this collaborative endeavor enriches the knowledge base and underscores its role as a hub for researchers worldwide.
Enhanced Navigation for Precise Diagnosis Subtypes
With PeCan’s sophisticated custom pediatric cancer classification ontology comprising of over 400 subtypes, users gain the ability to tailor their data selection to focus on specific cancer subtypes of interest. The sunburst navigation interface located at the top center of the platform facilitates this process, providing a seamless and intuitive experience. Once a subtype is chosen, a tailored summary of available data within each data facet is presented, enabling researchers to efficiently identify relevant information. For example, a user can select a given subtype and then dive into an exact mutational signature profile of a given sample that may show a novel discovery.
Seamless Data Facet Filtering and Exploration
PeCan Knowledge Base goes a step further by offering customized filtering options through its data facet interfaces. This feature empowers users to precisely access and examine the data they need. The platform employs interactive visualizations, making the exploration of available data an engaging and insightful experience.
Unlocking New Insights with Integrative Analysis
The true power of PeCan lies in its capacity for integrative analysis between diverse data facets. By combining information from each facet, researchers can gain unprecedented insights into pediatric cancer biology. This integration can be exemplified through compelling use cases which show PeCan's ability to unveil potential clinical diagnosis classifications and identify novel therapeutic opportunities.
In summary, PeCan on St. Jude Cloud has transformed from a specialized genomic variants resource to a cutting-edge curated platform for pediatric cancer genomics. With its ever-expanding data facets and intuitive navigation, PeCan empowers researchers around the world to delve into the complexities of hematologic, CNS, and non-CNS solid tumors. Through integrative analysis, PeCan continues to drive innovation, providing invaluable contributions to the fight against pediatric cancer and other catastrophic diseases and offering hope for improved diagnostics and treatments.
CreditsAlex Gout, Lead Bioinformatics Research Scientist Stephanie Sandor, Group Product Manager Jobin Sunny, Staff Software Engineer Delaram Rahbarinia, Mgr Software Engineering Kevin Benton, Mgr Software Engineering Sue Qiu, Senior Software Engineer James Madson, UX Designer