Biomarkers and Precision Medicine Community (BPMC)

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  • 1.  Question about study sample archives

    Posted 08-06-2024 10:05

    Hello everyone,

    I have a general question about study sample archives. When you generate intermediate/processed samples like DNA, RNA or protein samples which are extracted from the study samples, do you need to archive these processed samples after the study is final?

    Thank you,

    Rachel



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    Rachel Wang, Ph.D.
    Bioanalytical assay development lead
    Spark Therapeutics
    Philadelphia, PA.
    [email protected]

    Disclaimer: Opinions expressed are solely my own and do not express the views or opinions of my employer.
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  • 2.  RE: Question about study sample archives

    Community Leadership
    Posted 08-08-2024 16:34

    My super short answer is no. Now the caveats:

    If the samples are rare, no backup samples are available, processed samples are anticipated to be more stable than study samples, retesting a possibility, then I might want to keep them. If I want to keep them, then you need to prospectively plan a stability program to demonstrate that those intermediate/processed samples are still viable for those analytes.

    An example of this is nasopharyngeal swabs. We'd likely keep the DNA/RNA extracted from those swabs as 1) it's probably more stable after extraction; 2) we don't really expect a lot of "backup" swabs; and 3) the sample type is heterogeneous so wouldn't necessarily expect the same result.

    An example of not keeping is when we extracted samples from dried blood spots. We have other spots, so that is what we archived, not the extract.

    Hope this was at least somewhat helpful



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    Joleen White Ph.D.
    AAPS 2024 Global Health Community Chair
    Bioanalytical 101 Course Development
    Senior Bioassay Development Lead
    Gates Medical Research Institute
    Cambridge MA
    [email protected]

    Disclaimer: Opinions expressed are solely my own and do not express the views or opinions of my employer.
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    Original Message


  • 3.  RE: Question about study sample archives

    Posted 08-10-2024 10:08
    Hi Rui

    The storage of the samples including intermediary is discussed in the relatively fresh FDA guidance
    E18 Genomic Sampling and Management of Genomic Data Guidance for Industry from March 2018.

    Previous guidance had a requirement to store blood samples for pharmacogenomics testing for at least 15 years, However, once DNA was extracted from them the samples were considered used up and purified DNA was destroyed once tested for the target marker, and the report of the analysis for the clinical study was finalized.

    This updated guidance does not have the exact time limit but the wording like this:
    "It is highly recommended that samples are stored long term, i.e., over the course of and beyond a drug development program, to enable re-use and/or future use. The conditions under which specimens or extracted nucleic acids are archived should be suitable for the intended genomic testing application. It is good practice to store samples and extracted nucleic acids as multiple aliquots to avoid repeated freeze/thaw cycles and potential contamination. Storage of aliquots in separate locations avoids simultaneous loss of all samples. If a sample is re-used and undergoes freeze/thaw cycles, then each freeze/thaw cycle, including the temperature and time at each step, should be recorded. "

    My interpretation is that there is no specific limit to store the samples, but if you have a capability to store it until marketing approval of the drug or NDA submission, for example, it will be considered the best case scenario.
    You would need to consider the nature of the samples and their stability. Some samples may expire much earlier so there will be no reason to store them. You may want to incorporate some kind of internal controls you can test from time to time for stability with your samples.
    The safest way would likely be to prepare a sample management plan where you would discuss the nature of the samples before and after extraction and justify the storage times for each type separately, also considering the extraction process and potential value of the samples. This would be a living document to be updated with any new findings from preclinical and clinical testing results including stability.

    If you have discussions with the FDA during your clinical program, you may bring this up as one of the questions. Alternatively, you can keep it as an internal document and if needed present to the FDA or other Agency at some point if requested.

    Best regards,

    Galina Bernstein (AzureDelta Consulting)
     
    Galina Bernstein



    Original Message