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Protocols

GDC specifications

Information


Unique identifier OMICS_16627
Name GDC
Alternative name Genomic Data Commons
Restrictions to use None
Community driven No
Data access Browse, Application programming interface
User data submission Allowed
Maintained Yes

Documentation


Maintainers


  • person_outline Sean Davis
  • person_outline Martin Morgan

Publication for Genomic Data Commons

GDC citations

 (50)
call_split

Systematic pan cancer analysis of somatic allele frequency

2018
Sci Rep
PMCID: 5956099
PMID: 29769535
DOI: 10.1038/s41598-018-25462-0
call_split See protocol

[…] Seq platform. The human genome reference (hg38)-aligned sequencing reads (Binary Alignment Maps, .bams) and the Simple Nucleotide Variation mutation annotation file (SNV.maf) were downloaded from the Genomic Data Commons Data Portal (https://portal.gdc.cancer.gov/) and processed downstream through an in-house pipeline. The RNA and DNA alignments, together with the variant lists were processed thro […]

library_books

Mutation hotspots at CTCF binding sites coupled to chromosomal instability in gastrointestinal cancers

2018
Nat Commun
PMCID: 5906695
PMID: 29670109
DOI: 10.1038/s41467-018-03828-2

[…] ibrary-type fr-firststrand). Transcript abundances at the gene level were estimated by Cufflinks. The normalized counts of RNA sequencing data of 35 tumors from the TCGA cohort were obtained from the Genomic Data Commons Portal. […]

call_split

Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment

2018
Hum Genomics
PMCID: 5896091
PMID: 29642934
DOI: 10.1186/s40246-018-0150-x
call_split See protocol

[…] unprocessed WES BAM files, which were available for 325 CCLE cell lines (Fig. ), from the CCLE project at the National Cancer Institute (NCI) Cancer Genomics Hub; these data are available at the NCI Genomic Data Commons (GDC) data portal []. All CCLE WES data had been reported to be sequenced at the Broad Institute using the same version of the Agilent Exome Bait kit, and the same sequencing prot […]

library_books

Discovery of physiological and cancer related regulators of 3′ UTR processing with KAPAC

2018
Genome Biol
PMCID: 5875010
PMID: 29592812
DOI: 10.1186/s13059-018-1415-3

[…] BAM files for matching normal and tumor RNA-seq samples (the number which is listed in Table S5 of Additional file ) were obtained from the Genomic Data Commons (GDC) Data Portal [] along with gene expression values counted with HTSeq and reported in fragments per kilobase per million (FPKM). […]

library_books

Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

2018
Genome Biol
PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] s GSE17312 [] and GSE16368 []. Level 3 DNA methylation Infinium 450 K array data, mRNA expression (RNA-seq data V2 RSEM), and clinical information for glioblastoma primary tumor are acquired from the Genomic Data Commons (https://portal.gdc.cancer.gov/) via the GDC client tool (https://gdc.cancer.gov/access-data/gdc-data-transfer-tool). […]

library_books

Identification of potential regulatory mutations using multi omics analysis and haplotyping of lung adenocarcinoma cell lines

2018
Sci Rep
PMCID: 5862974
PMID: 29563587
DOI: 10.1038/s41598-018-23342-1

[…] The RNA-Seq v2 data and clinical information of TCGA lung adenocarcinoma (TCGA-LUAD) was downloaded from the NCI Genomic Data Commons using TCGA-Assembler v2.0.1 (the data were downloaded on 2017/03/09). The normalized counts of genes expression (assayPlatform = gene.normalized_RNAseq) were used. Expression leve […]


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GDC institution(s)
Roswell Park Cancer Institute, Buffalo, NY, USA; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA

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