A data processing pipeline for the AACR project GENIE biopharma collaborative data with the {genieBPC} R package.

Area of Science:

• Oncology
• Bioinformatics
• Genomics

Background:

• The American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange Biopharma Collaborative (GENIE BPC) is a multi-institution, pan-cancer data repository.
• It provides comprehensive clinical and high-throughput sequencing data for cancer patients, enabling health outcomes and precision medicine research.
• The complexity of GENIE BPC data necessitates robust data integration and preparation for analytical modeling.

Purpose of the Study:

• To introduce the {genieBPC} R package, a user-friendly pipeline for processing GENIE BPC data.
• To facilitate the creation of analytic cohorts ready for clinico-genomic modeling and analyses.
• To enhance accessibility and usability of the GENIE BPC dataset for oncology research.

Main Methods:

• Development of the {genieBPC} R package as a data processing pipeline.
• Implementation of user-friendly functions for data integration and preparation.
• Leveraging existing data structures from the GENIE BPC repository.

Main Results:

• The {genieBPC} package provides a streamlined approach to preparing GENIE BPC data.
• It enables researchers to readily build analytic cohorts for clinico-genomic studies.
• The package simplifies the complex process of integrating phenomic and genomic datasets.

Conclusions:

• The {genieBPC} package significantly lowers the barrier to entry for utilizing the GENIE BPC dataset.
• It supports advanced clinico-genomic research and precision medicine initiatives in oncology.
• The package promotes wider adoption and analysis of this valuable cancer data resource.