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Upload of "non-shareable" human exomes to the FireCloud for GATK?

I have access to a few human whole exomes (.bam) from a legacy project where patient consenting has been interpreted by IRB as OK for research data analysis, but NOT OK for individual data sharing.
I would like to run GATK variant calling on these exomes, can I use the Firecloud infrastructure? Or do I need to run my analysis on a local instance to avoid "sharing" of the data via upload?
No metadata or identifiable info needs to accompany the samples besides their numerically coded sample ID, so I believe it qualifies as "de-identified", but don't want to accidentally breach if anyone has more confident insight into the question. I'm a geneticist, not a lawyer!

Best Answer

  • jberghoutjberghout
    Accepted Answer
    Received helpful response from twitter. Copied exchange below:

    @joanneberghout
    @gatk_dev - having a hard time finding definitive answer in docs... Can I upload a human #exome .bam to @BroadFireCloud for GATK #variantCalling if it is consented for research data analysis, but not sharing? Or do I need to run on local #GATK? #bioinformatics #Genetics

    @gatk_dev
    Will defer to our @BroadFireCloud colleagues who know the relevant infosec/compliance rules back to front for definitive answer, but fwiw we do a ton of work in FireCloud on research-consented human data that has been cleared appropriately.

    @BroadFireCloud
    Right, many of our users work on human data under research consents. It depends what the consent protocol specifies wrt data access and security. The platform meets FISMA moderate compliance and the permissions system allows you to control exactly who can have access to the data.

    @dbernick
    Replying to @BroadFireCloud @joanneberghout @gatk_dev
    Use the Authorization Domains feature to make sure data is not-reshareable by the people you share it with.

Answers

  • jberghoutjberghout Member
    Accepted Answer
    Received helpful response from twitter. Copied exchange below:

    @joanneberghout
    @gatk_dev - having a hard time finding definitive answer in docs... Can I upload a human #exome .bam to @BroadFireCloud for GATK #variantCalling if it is consented for research data analysis, but not sharing? Or do I need to run on local #GATK? #bioinformatics #Genetics

    @gatk_dev
    Will defer to our @BroadFireCloud colleagues who know the relevant infosec/compliance rules back to front for definitive answer, but fwiw we do a ton of work in FireCloud on research-consented human data that has been cleared appropriately.

    @BroadFireCloud
    Right, many of our users work on human data under research consents. It depends what the consent protocol specifies wrt data access and security. The platform meets FISMA moderate compliance and the permissions system allows you to control exactly who can have access to the data.

    @dbernick
    Replying to @BroadFireCloud @joanneberghout @gatk_dev
    Use the Authorization Domains feature to make sure data is not-reshareable by the people you share it with.
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