PCAT

PCAT provides an integrated bioinformatics portal aggregating genomic, clinical, and preclinical testing data for pediatric cancer patient-derived xenograft (PDX) models to support biomarker discovery and therapeutic prioritization.

Key Features:

• Pediatric cancer PDX collection: Contains data for 324 pediatric cancer patient-derived xenograft (PDX) models.
• Genomic data types: Includes gene expression profiles, somatic mutations, and copy number alterations for PDX models.
• Preclinical testing results: Curates preclinical testing outcomes for 68 PDX models across 79 therapeutic agents, manually collected from individual agent testing studies published since 2008.
• TARGET project integration: Integrates clinical and molecular data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) project and provides access to gene fusions identified in nearly 1,000 TARGET samples.
• Implementation technologies: Implemented using R-shiny for the application layer and MySQL for database management.

Scientific Applications:

• Molecular driver identification: Enables analysis of gene expression, mutations, and copy number alterations to investigate molecular drivers in pediatric cancers.
• Biomarker discovery: Supports identification and evaluation of genomic biomarkers linked to preclinical drug responses in PDX models.
• Therapeutic prioritization: Facilitates comparison of preclinical testing outcomes across 79 agents to prioritize therapeutic candidates for pediatric tumors.
• Comparative analyses with patient data: Allows comparison between PDX models and TARGET patient tumors, including analysis of gene fusions from nearly 1,000 TARGET samples.

Methodology:

Manual curation of preclinical testing results from studies published since 2008; integration of clinical and molecular datasets from the TARGET project; cataloguing of gene fusions from nearly 1,000 TARGET samples; implementation using R-shiny and MySQL.