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Gray BRCA Atlas Documentation

website·Indexed 32 days ago

https://docs.graybrcaatlas.org

Documentation for the Gray Foundation Data Coordination Center (GF-DCC), focused on accelerating research into BRCA-associated precancer and early cancerous lesions. It provides guides on data onboarding, uploading to Synapse, clinical metadata templates, data sharing plans, and workflows for cBioPortal integration.

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What's inside Gray BRCA Atlas

  2. Standardize clinical metadata for BRCA pre-cancer research

    The BRCA pre-cancer research initiative utilizes a clinical metadata template to harmonize the collection of patient and biospecimen data (e.g., blood and tissue samples) across diverse project teams and institutions. The standardization focuses on three primary objectives: establishing a consistent data model for patient/sample representation, identifying pragmatically collectable data elements aligned with consortium goals, and determining which clinical phenotypes provide the most value for BRCA-specific pre-cancer analyses.

  3. Understand the Gray Foundation data sharing phases

    Data deposited in the Synapse platform follows a three-phase sharing lifecycle to ensure secure management and controlled release:

    1. Private Phase: The default setting. Data is exclusively accessible to the Contributor and their designated individuals.
    2. Collaborative Sharing Phase: Curated data is made accessible to investigators within the network.
    3. Public Sharing Phase: Data is made available to the broader research community under appropriate controls.

  4. Implement FAIR Data Management Principles

    The Gray Foundation DCC follows the FAIR guiding principles to ensure scientific data is Findable, Accessible, Interoperable, and Reusable. This model is designed to help consortium teams comply with and exceed the NIH Data Management and Sharing Policy (mandated since 2023), which requires data sharing for NIH-supported studies. Adhering to these principles increases collaborative productivity, strengthens future grant proposals (especially for Team Science), and increases research impact and citations.

  5. Use cBioPortal for Cancer Genomics analysis

    cBioPortal is used for sharing and analyzing genomic data, specifically for Copy Number Variation (CNV), Summarized Gene Expression (RNA-seq), and Mutations. The Gray Foundation utilizes a custom instance of cBioPortal. Data transfer to this platform is supported by the Sage and MSK teams.

  6. Visualize molecular and clinical data with cBioportal

    cBioportal is an open-source platform used to visualize molecular and clinical data attributes for specific datasets hosted on Synapse.

  8. Understand File-level Metadata requirements

    File-level metadata is collected for uploaded data files and is assay-specific. Because different data types (e.g., .fastq for sequencing vs. .tiff for imaging) require different information, a unique metadata template is provided for each data type. Additionally, metadata requirements change based on the processing level of the data; for example, raw RNA-seq .fastq data requires different annotations than summarized expression data. The system's data level concepts are derived from the Genomics Data Commons (GDC) data levels.

  10. Join and participate in the Portal Design Working Group

    The Portal Design Working Group focuses on enhancing data discoverability, accessibility, interoperability, and reusability for the Gray Foundation atlas. Objectives include improving the existing portal and developing methods for transferring data to external analysis tools. The group is open to all persons affiliated with the Gray Foundation atlas.

    Meeting Schedule: First Thursday of the month at 3:00 PM EST. Contact: For more information, email gray-foundation-service@sagebase.org.

  11. Access Phase 3 'CONTROLLED ACCESS' datasets

    Controlled Access data (typically raw sequencing data) is available to registered Synapse users who fulfill specific requirements. These requirements may include:

    • Accepting Conditions of Use
    • Submitting a statement
    • Obtaining approval from governance

    Note: Some controls are implemented via a separate data access layer, meaning users on the Access Control List may still need to complete these required actions to download the data.

  12. Upload small files using the Synapse User Interface (UI)

    The Synapse UI is recommended for uploading smaller files (less than 100MB). To upload, navigate to the designated destination folder and use the 'Folder Tools' menu to access upload options.