RT Journal Article
T1 Uniform genomic data analysis in the NCI Genomic Data Commons.
A1 Zhang, Zhenyu
A1 Hernandez, Kyle
A1 Savage, Jeremiah
A1 Li, Shenglai
A1 Miller, Dan
A1 Agrawal, Stuti
A1 Ortuno, Francisco
A1 Staudt, Louis M
A1 Heath, Allison
A1 Grossman, Robert L
AB 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/ ).
YR 2021
FD 2021-02-22
LK http://hdl.handle.net/10668/17217
UL http://hdl.handle.net/10668/17217
LA en
DS RISalud
RD Apr 7, 2025