Uniform genomic data analysis in the NCI Genomic Data Commons.

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• The National Cancer Institute (NCI) established the Genomic Data Commons (GDC) to address the need for standardized cancer data.
• Existing data repositories lacked uniform processing, hindering collaborative research and precision medicine initiatives.

Purpose of the Study:

• To describe the pipelines and workflows for processing and harmonizing genomic and clinical data within the GDC.
• To provide a comprehensive data repository supporting precision medicine research through data sharing and collaborative analysis.

Main Methods:

• Utilized an OpenStack-based private cloud for data production starting in June 2015.
• Processed over 50,000 raw sequencing data inputs and multiple other data types by June 2016.
• Employed the latest human genome reference build (GRCh38) for data generation, including aligned reads, somatic mutations, gene expression, miRNA expression, DNA methylation, and copy number variation.

Main Results:

• The GDC now houses uniformly processed genomic, epigenomic, proteomic, and clinical data from NCI TCGA and TARGET programs.
• A variety of data types have been generated, ranging from raw sequencing data to processed analytical outputs.
• Data is accessible via the GDC Data Portal and Legacy Archive for download and analysis.

Conclusions:

• The GDC provides a robust platform for accessing and analyzing large-scale cancer genomic and clinical data.
• The implemented pipelines ensure data uniformity, facilitating reproducible research and advancing precision medicine.
• The GDC promotes collaborative cancer research by making diverse datasets readily available to the scientific community.