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TCGA Expedition: A Data Acquisition and Management System for TCGA Data.

Uma R Chandran1,2, Olga P Medvedeva1, M Michael Barmada1,3,4,5

  • 1Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America.

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Summary
This summary is machine-generated.

TCGA Expedition software simplifies accessing and analyzing The Cancer Genome Atlas Project (TCGA) data. This open-source tool facilitates local data management and computational cancer research, making large genomic datasets more usable for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • The Cancer Genome Atlas Project (TCGA) provides extensive genomic and clinical data for cancer research.
  • Navigating and utilizing the large volume (1.2 PB) of TCGA data presents significant challenges for researchers.
  • Existing public portals for TCGA data access have usability limitations.

Purpose of the Study:

  • To develop a software solution, TCGA Expedition, to streamline the acquisition, management, and analysis of TCGA data.
  • To create a robust infrastructure for computational cancer research utilizing TCGA resources.
  • To facilitate the integration of TCGA data with electronic health records for enhanced research capabilities.

Main Methods:

  • Developed TCGA Expedition software using Bash, Python, and Java for data download, harmonization, versioning, and storage.
  • Implemented a participant- and sample-centered data directory with comprehensive metadata.
  • Established the Pittsburgh Genome Resource Repository (PGRR) as a collaborative platform for data access and analysis.

Main Results:

  • TCGA Expedition successfully created a versioned, local data repository with direct references to original and processed data files.
  • The software enables flexible data searching via a web portal and provides user-centric data tracking and provenance tools.
  • Locally accessible Whole Genome Sequencing (WGS) BAM files were made available, addressing critical challenges in data handling and processing.

Conclusions:

  • TCGA Expedition is an open-source, freely available software solution for building local infrastructure to manage and analyze TCGA data.
  • The software supports computational cancer research by simplifying access to large public genomic datasets.
  • The developed repository enhances collaborative research by providing efficient data interrogation tools.