GDportal

GDportal provides access to uniformly processed genomic and clinical data from the Genomic Data Commons (GDC), including The Cancer Genome Atlas (TCGA) and the Therapeutically Applicable Research To Generate Effective Treatments (TARGET) programs, to support comparative cancer genomics and precision medicine.

Key Features:

• Unified Data Repository: Consolidates genomic, epigenomic, proteomic and clinical datasets into a single resource for integrative analyses.
• Data Processing and Harmonization: Standardized pipelines generate aligned reads, somatic mutation calls, gene expression profiles, miRNA expression, DNA methylation data, and copy number variations and harmonize outputs for comparability.
• Reference Genome Utilization: Uses the GRCh38 human genome reference build for data alignment and harmonization.
• Dataset Scale: Contains and has processed over 50,000 raw sequencing inputs and associated data types (as of June 2016).

Scientific Applications:

• Precision Medicine: Enables identification of molecular targets and development of personalized treatment strategies using harmonized genomic and clinical data.
• Collaborative Research: Supports multi-institutional and cross-study analyses by providing a common harmonized dataset resource.
• Genomic Data Exploration: Facilitates exploratory analyses of somatic mutations, gene and miRNA expression, DNA methylation and copy number variation to study cancer biology and progression.

Methodology:

Processing runs on an OpenStack-based private cloud; raw sequencing and other inputs are ingested, processed by standardized pipelines to produce aligned reads, somatic mutation calls, expression (gene and miRNA), DNA methylation and copy-number data, and workflows harmonize outputs by aligning them to the GRCh38 reference genome.