Journal Article

Uniform genomic data analysis in the NCI Genomic Data Commons

Zhang, Zhenyu, Miller, Dan, Grossman, Robert L., Li, Shenglai, Agrawal, Stuti, Savage, Jeremiah, Ortuno, Francisco, Staudt, Louis M., Heath, Allison, Hernandez, Kyle

2021

Overview

The goal of the National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive ( https://gdc.cancer.gov/ ). The Genomic Data Commons repository contains genomic, epigenomic, proteomic and clinical data from the TCGA and TARGET datasets. Here, the authors describe the analysis methods for how these divergent datasets were integrated together.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38 / 45 / 631/1647/48 / 631/67/69 / Base Sequence / Cancer / Cancer research / Copy number / Data Analysis / Data retrieval / Databases, Genetic / Datasets / Deoxyribonucleic acid / DNA / DNA Copy Number Variations - genetics / DNA methylation / DNA Methylation - genetics / Gene expression / Gene Expression Regulation / Genome, Human / Genomes / Genomic analysis / Genomics / Humanities and Social Sciences / Humans / MicroRNAs - genetics / MicroRNAs - metabolism / miRNA / Molecular Sequence Annotation / multidisciplinary / Mutation / Mutation - genetics / National Cancer Institute (U.S.) / Precision medicine / Proteomics / Repositories / Reproducibility of Results / Ribonucleic acid / RNA / RNA-Seq / Science / Science (multidisciplinary) / United States / Viruses - genetics