Public availability of de-identified patient data
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3 months ago
dec986 ▴ 340

I'm looking for a published paper where de-identified patient data is available as part of the supporting information.

I myself have gotten a paper accepted for publication, but one of the reviewers is insisting on this data being available, and naturally my employer is hesitant to let me upload such information to a public database. If I were able to show that similar de-identified patient data has been done before, precedent would be shown and I would likely be approved. An American-sourced paper would be best, as the laws/rules would be similar.

Does anyone know of such a paper?

literature • 435 views
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Here is some information about this from DHHS: https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html

https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html#rationale section clearly defines what can be done with such information and a standard https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html#standard.

The Privacy Rule was designed to protect individually identifiable health information through permitting only certain uses and disclosures of PHI provided by the Rule, or as authorized by the individual subject of the information. However, in recognition of the potential utility of health information even when it is not individually identifiable, §164.502(d) of the Privacy Rule permits a covered entity or its business associate to create information that is not individually identifiable by following the de-identification standard and implementation specifications in §164.514(a)-(b). These provisions allow the entity to use and disclose information that neither identifies nor provides a reasonable basis to identify an individual

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Please clarify what kind of data are you are referring to? Many of the posts below are assuming some sort of sequence data (which may not be the case). This is important information that needs to be stated in original post.

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3 months ago

Not a lawyer, but you should never do this unless you have broad consent from the patients. Basic ethics. Also, you're probably then personally liable.

Have a look at controlled access public datasets, like dbgap for example. https://www.ncbi.nlm.nih.gov/gap/

Researchers can then apply to your PI for access. I haven't used this myself though.

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I second colindaven 's suggestion. If the patients did not provide full (and expansive) written consent then you cannot share their raw genomic data without undertaking significant legal liability not to mention academic misconduct etc...

You can however published agglomerated data (gene counts, etc...) which should be sufficient for most purposes.

Otherwise you should submit the data to a controlled database:

US: https://dbgap.ncbi.nlm.nih.gov/ EU: https://ega-archive.org/

It a bit of a slow process and you likely need your uni/institute to put together a data-access committee etc... I think for the revisions you could state that you have initiated the process and that would likely be sufficient.

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We do not know if OP wants to share genomic sequence data. If that is not the case then dbGaP or EGA are not going to be applicable at all.

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3 months ago
Emily 23k

The entire premise for the Genomics England Research Environment is allowing research with de-identified patient data in a controlled research environment. Loads of publications from it.

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While OP has not clearly stated what type of data they need to publish or if it needs to be done at an individual level, does GE allow publishing of deidentified data at the level of an individual? I only looked at one publication and it seemed to have aggregate information in supplementary tables.

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The rules are mostly that aggregate data only can be published. Exceptions can be made for case studies, but these require collaboration with the relevant clinician and extra consent.

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3 months ago
GenoMax 125k

Several papers seems to come up in a google scholar search that contain deidentified data.

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