Center for Cancer Genomics |Genomic Data Commons portal.gdc.cancer.gov | @NCIGDC_Updates | support@nci-gdc.datacommons.io

The Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. Access Data & Tools • Harmonized genomic data uniformly processedand aligned to latest reference genome.• Mutation calls, expression levels, and otherhigh-level data generated via best-in-class pipelines. • Web-based tools to search, download and analyze data from over 33,000 cancer cases. • Visualize biological & clinical relationships inreal-time, then download publication-ready figures.• Consume data efficiently with GDC’s API or DataTransfer Tool

Projects Available Clinical Proteomic Tumor Analysis Consortium (CPTAC), Foundation Medicine (FMI), The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and other cancer studies

Examples of Supported Data Types

Data type File Format

Clinical & Biospecimen TSV, XML, JSON

Sequencing (e.g., WGS, WXS, RNA)

BAM, FASTQ

Array (e.g., SNP, Methylation)

TXT, IDAT

High-level Data TSV (expression, splice junctions), TXT (CNV, methylation), MAF & VCF (mutations)

Analyze with DAVE Data Analysis, Visualization & Exploration (DAVE) tools are web-based and open-access, helping make genomic data accessible for anyone.

Mut CNV

OncoGrid Visualize

combinations of gene mutations &

copy number variants for a project or custom cohort

Gen

esCl

inic

al

Alteration Frequencies

mutation copy number

Cases

Survival Analysis

Compare overall survival of any two

cohorts, such as patients with &

without a mutated gene of interest

U.S. Department of Health & Human Services | National Institutes of Health

Analyze with DAVE

Protein Viewer

Visualize gene mutations mapped

to their protein functional domains

Visualize Frequent

Alterations View the most

frequently mutated genes

for any cohort

30

% o

f Cas

es A

ffect

ed

Distribution of Most Frequently Mutated Genes

0

10

20

TP53

PIK3CA

CDH1

GATA3

KMT2C

MAP3K1

PTEN

NCOR1NF1

RUNX1

ARID1A

PIK3R1

MAP2K4

RNF213

SPEN

KMT2D

AKAP9FA

T1MYH9

TBX3

Plot frequencies of cases with

mutations and copy number variants for a selected gene

80

% o

f Cas

es A

ffect

ed

TP53 Cancer Distribution

0

20

40

60

TCGA-UCS

TCGA-OV

CGA-LUSC

GA-ESCA

GA-READ

GA-HNSC

GA-PAAD

GA-COAD

GA-LUAD

GA-BLCA

CGA-STAD

CGA-LGG

GA-UCEC

GA-SARC

GA-BRCA

CGA-KICH

CGA-LIHC

CGA-GBM

CGA-ACC

GA-MESO

T TC TC TC TC TC TC TC T T TC TC TC T T T T TC

ESC

GA-C

TC

% o

f Cas

es A

ffect

ed

TP53 CNV Distribution

TCGA-SARC

TCGA-PRAD

TCGA-UCS

TCGA-OV

TCGA-LIHC

TCGA-DLBC

TCGA-CHOL

TCGA-UCEC

TCGA-ACC

TCGA-BRCA

TCGA-BLCA

TCGA-LUAD

TCGA-ESCA

TCGA-GBM

TCGA-STAD

TCGA-HNSC

TCGA-LUSC

TCGA-MESO

TCGA-SKCM

0

10

20

30

AnalyzeCustom Sets

Create custom sets of cases, genes,

or mutations Compare survival and

clinical features of case sets

portal.gdc.cancer.gov | @NCIGDC_Updates | support@nci-gdc.datacommons.io