Data Access

TARGET Data Availability Notes

Harmonized TARGET Data Released in the NCI GDC Data Portal

The NCI Genomic Data Commons (GDC) includes the data generated by the TARGET project. GDC harmonizes TARGET data using GDC alignment and variant calling pipelines and makes the harmonized data available in the GDC Data Portal.

For TARGET Rhabdoid Tumor (RT) project, GDC is not analyzing the Bisulfite- Seq or ChIP-Seq data at the moment. The links to the Level 2 ChIP-seq data will be updated on the project’s publication pages (https://gdc.cancer.gov/about-data/publications/TARGET-RT-2016 and https://gdc.cancer.gov/about-data/publications/TARGET-RT-2019) when the data are available at the GDC.

The GDC applies multiple variant calling pipelines for the somatic variant calls in the Variant Call Format (VCF) and aggregates the mutations for each sample in the Mutations Annotation Format (MAF). TARGET genes and mutations can be visualized in GDC Exploration Tools. Additional details on TARGET data are available in the GDC Data Release Notes.

To learn more about the GDC, please visit the GDC Web Site or attend a GDC Webinar.

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CGCI Data Availability Notes

Harmonized CGCI (phs000235) Data Released in the NCI GDC Data Portal

HTMCP - Cervical Cancer (phs000528)

RNA-Seq and miRNA-Seq
WGS
Targeted Sequencing
Methylation Array
ChIP-Seq

BLGSP (phs000527)

RNA-Seq and miRNA-Seq
WGS
Targeted Sequencing

GDC is not analyzing ChIP-Seq data at the moment. The links to the Level 2 BLGSP ChIP-seq data will be updated on the project’s publication page when the data are available at the GDC.

See GDC Data Release Notes for more information on data releases.

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The goal of the Office of Cancer Genomics (OCG) is to accelerate translation of basic science discoveries into the clinic and thereby contribute to precision oncology. OCG collaboratively manages and supports molecular characterization and translational genomics research initiatives: Cancer Genome Characterization Initiative (CGCI); Therapeutically Applicable Research to Generate Effective Treatments (TARGET); Cancer Target Discovery and Development (CTD²) Network; Human Cancer Models Initiative (HCMI); and Next Generation Technologies for Next Generation Cancer Models (NGT). OCG programs produce and share large-scale genomic datasets as “community resource projects”. The data generated by these programs are disseminated to the research community in accordance with National Institute of Health’s data sharing policies via program-specific databases (data matrices, data portals, and dashboard) and through the Genomic Data Commons (GDC).

Access OCG programs’ data and read the accompanying user guides in the table below:

OCG Program	Data Description	Data Links	User Guides
CGCI and TARGET	Genomic profiles (molecular characterization and other sequencing data) and clinical data for rare adult and pediatric cancers. CGCI and TARGET datasets may be open-access or controlled-access (which requires approval by NCI Data Access Committee (DAC)).	CGCI Data Matrix CGCI Data at GDC	CGCI Publication Guidelines
CGCI and TARGET		TARGET Data Matrix TARGET Data at GDC	TARGET Publication Guidelines
CTD²	Raw and analyzed primary data are available through the CTD² Data Portal. CTD² data are mostly open-access.	CTD² Data Portal	Using CTD² Data CTD² Publication Guidelines
CTD²	The CTD² Dashboard is a web interface which assembles Network Center-generated conclusions or “observations” with associated supporting evidence. The Dashboard allows easy navigation to biologists and data scientists.	CTD² Dashboard	Using CTD² Data CTD² Publication Guidelines
HCMI	The quality-controlled and harmonized clinical, biospecimen, and molecular characterization data are available at NCI’s GDC. HCMI datasets may be open-access or controlled-access (which requires approval by NCI Data Access Committee (DAC)).	HCMI Data at GDC	HCMI Publication Guidelines

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Open- vs. Controlled-access Data

OCG and its collaborators comply with National Institutes of Health (NIH) human subjects’ protection for privacy and confidentiality of research participants. Data are shared in accordance with National Cancer Institute’s (NCI) data sharing policies and are available in open- and controlled-access tiers.

Open-access Data

Data within this tier present minimal risk of participant identification. Open-access data are available for users to download, analyze, and reprocess. Researchers may explore these data without restriction.

Examples of open-access data are:

Clinical information that could not be used to identify the patient
Tissue pathology data
Gene expression data (other than 1º exon array data or RNA-seq)
Chromosome-specific (segmented) copy number alterations and loss of heterozygosity
Filtered tumor-associated (somatic) mutations
Sequence of the DNA and RNA of previously established cancer cell lines
Results of high-throughput perturbagen screens
- Validation of the findings

Controlled-access Data

Controlled access protects patient privacy and confidentiality. Data within this tier, while stripped of personal patient identifiers as defined by HIPAA, contain specific patient/tumor information and unverified or raw molecular data (e.g. array-based and sequence files).

Access to these data requires approval by the Data Access Committee (DAC).

Examples of controlled-access data are:

HIPAA-regulated demographic and clinical data
Raw whole genome, epigenome, exome, or transcriptome sequences for each case (eg. BAM and FASTQ files)
Analyzed Variant Call Format (VCF) or Mutation Annotation Format (MAF) genomic sequencing data, germline variants or phenotype data for each case

How to Access Controlled Data

1. Obtaining Data Use Certification through dbGaP

Controlled-access data can be used by the research community, but users are required to obtain Data Use Certification (DUC) through National Center for Biotechnology Information’s database of Genotypes and Phenotypes (NCBI’s dbGaP). The proposed research must be consistent with the Data Use Limitations (DULs) for the requested data (i.e. general research use (most CGCI projects and HCMI) or pediatric cancer research (TARGET)). There are data use limitations for some CGCI cases contributed by specific tissue source sites. Researchers must get a separate DUC for each consent group by submitting an electronic Data Access Request (DAR) through dbGaP for each consent group.

Detailed instructions to apply for controlled-access data are provided at NCI’s GDC.
All users must have an eRA Commons account or HHS credentials (for intramural investigators) to submit a Data Access Request (DAR) form through NCBI’s dbGaP authorized access system.

*** The password on the eRA Commons account needs to be updated periodically as required by the eRA Commons. Instructions are distributed when the account is created. ***

The following flowcharts provide an overview of the DAR process in dbGaP:

See dbGaP’s tutorial and “Tips for Preparing a Successful Data Access Request” or contact the NCI Office of Data Sharing for instructions.
Renew the project annually to maintain access. Renewal request include a report of how the data are being used.
Closeout the project if the research is no longer active by providing a summary of how the data was used.

***Failure to submit a renewal or complete the closeout process may result in termination of all current data access.

2. Controlled Data at NCI’s GDC and NCBI’s Sequence Read Archive (SRA)

CGCI and TARGET data can be accessed through CGCI and TARGET data matrices. HCMI data can be accessed through the GDC data portal. The various databases include different types of data. For specifics, see below and read the materials found on the specific project web pages.

The Genomic Data Commons (GDC) is a data repository that accepts and standardizes genomic, clinical and biospecimen data from cancer research programs and enables data sharing. The GDC provides a platform for efficient querying, analyzing, and downloading harmonized clinical, biospecimen, and sequence data across multiple projects.

CGCI (phs 000235)

CGCI data at the GDC include:

Raw and aligned reads from next-generation sequencing; specifics are on the Data Matrix
Analyzed data generated by the GDC’s analysis pipeline

CGCI data at the NCBI SRA include:

Aligned reads from next generation sequencing (BAM files) from Non-Hodgkin lymphoma (Diffuse Large B-Cell Lymphoma and Follicular Lymphoma) project phs000532

TARGET (phs000218)

TARGET data at the GDC include:

Raw and aligned reads from next-generation sequencing; specifics are on the Data Matrix
Some aggregate data (including mutation calls and other associated molecular data)

TARGET data at the NCBI SRA include:

FASTQ/BAM files – next-generation whole genome, whole exome, mRNA-seq, miRNA-seq, targeted capture, bisulfite-seq, ChIP-seq

HCMI (phs001486)

HCMI data at the GDC will be described on the Data Matrix when available.

Raw sequencing data
Harmonized datasets

3. Controlled-access Data at OCG’s Data Coordinating Center (DCC)

The Data Coordinating Center (DCC) is responsible for managing the flow of data generated by the OCG programs. The DCC houses raw, processed, and analyzed data produced by OCG project teams for the projects’ manuscripts. The OCG program data available at the DCC differs from what is at the GDC in that the GDC downloads all the raw CGCI and TARGET next-generation sequencing data and performs their own analysis and harmonization through the GDC analysis pipeline, producing their own L3/analyzed data files.

Data users outside of HHS require eRA Commons account credentials to log on to Globus.org to access controlled data housed at OCG’s Data Coordinating Center (DCC). dbGaP-approved PIs and designated downloaders will receive an email with detailed instructions on how to use Globus.org to access controlled data at the OCG DCC data upon approval.

CGCI

CGCI data stored at the OCG’s DCC include:

Protected clinical information
Raw chip-based molecular characterization data
- Project team processed sequencing data (upper level files e.g. VCF or MAF)
- Epstein-Barr virus BAM files from pediatric Burkitt lymphoma cases

TARGET

TARGET data stored at the OCG’s DCC include:

Protected clinical information
Project team processed sequencing data (upper level files e.g. VCF or MAF)

4. Where to Get Help If You Have Trouble Accessing Data

For GDC data inquiries, visit: https://gdc.cancer.gov/contact-us or email: support@nci-gdc.datacommons.io
For NCBI-stored data – https://dbgap.ncbi.nlm.nih.gov/aa/wga.cgi?page=email&from=login
For OCG’s DCC-stored data – OCG@mail.nih.gov

Navigating Data Matrices

OCG project data matrices were established to provide users easily understood overview of all data obtained for each project.

CGCI and TARGET

The CGCI and TARGET Data Matrices link to both open- and controlled-access data. The data matrices provide information on which molecular characterizations were done for each study and include links to related datasets. New data from ongoing projects are incorporated into the data matrices as they become available. To obtain specific datasets or metadata, including descriptions of each project, users can click on the text within the table and access the appropriate files.

Data Levels

Raw or low-level data files (level 1)
Normalized and integrated data (levels 2 and 3)
Summarized findings (level 4)

Data Access Code

Brown (CGCI), Blue (TARGET) = open-access
Red = controlled-access (NCI & NCBI)
Black = unavailable

Types of Data Found in the Matrix

Names of diseases studied
Clinical information, including outcomes
Types of molecular data generated, and platforms used
Metadata descriptions about each individual project
Multi-level chip-based and sequencing data links