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NextGen Sequencing in Pathology Setting



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  • NextGen Sequencing in Pathology Setting


    I work in a core facility in South Australia, Australia, running Sanger sequencing on an AB 3130xl. Much of what we do is diagnostic sequencing for breast cancer screening. I'm excited by the possibilities of using NGS sequencing for diagnostic purposes, but am unsure about current standards for accreditation, specifically (but not limited to) Australia. I'd appreciate hearing about other peoples experiences with NGS technologies in a setting.

    Best regards

    Oliver van Wageningen

  • #2
    follow the money

    For some insight into some actual current practice in the US that might be helpful to you, I suggest you check out the link I provided in a previous post here in the news section last month titled:

    Sequencing all for the diagnosis--now it's even covered.

    I refer to a hospital committee obtaining pre-authorization for health insurance payment to conduct diagnostic next-gen sequencing for some patients. You can find some peer reviewed literature that describe the steps taken to found the achievement of this important development in applying next gen technology and contact the authors/hospital mentioned in the article for further information about the role of CLIA certification and other regulatory interfacing in the US.

    I would just also comment here that these successful efforts on behalf of patients revolve around hospital clinical staff rather than any published next-gen industry-wide standards or even any health insurance providers, public or private.


    • #3
      CLIA international laboratory accreditation

      Apparently international labs can apply to the New York Regional Office in New York City to obtain certification according to CLIA standards, (which is necessary for payment approval through Medicare and Medicaid, the US federal health insurance programs).



      • #4
        Many thanks Joann; I'm unaware of any moves by certification bodies in Australia (specifically NPAAC and NATA) to look at NGS technologies, but I'm very interested to see that this appears to be underway with the CLIA certification you mention.

        Thanks again!



        • #5
          Some colleagues of mine have been doing clinical screening of BRCA1/2 with an illumina. http://www.ncbi.nlm.nih.gov/pubmed/20127978 if you want to know the details. They have managed to get the required UK accreditation if you want to contact them.


          • #6
            Thanks for the link Henry. I've many questions, and will be contacting them shortly. It's interesting to note that at the time of writing the paper, at least some bioinformatics knowledge was required by their group to sort barcoded samples, and that third party software was required to look at indels. As you will be aware this can all be done easily now for Sanger sequencing, but it's easy to forget that the software for Sanger analysis required time to develop to its current standard.


            • #7
              the link to Sequencing all for the diagnosis--now it's even covered http://seqanswers.com/forums/showthread.php?t=9840


              • #8
                FDA TELECONFERENCE for Next-Gen Sequencing Tests TODAY July 7, 2016 11 am EST

                FDA TELECONFERENCE ADVISORY Today @ 11 am EST

                Office of Health and Constituent Affairs

                Food and Drug Administration

                U.S. Department of Health and Human Services

                FDA Draft Guidances for Next-Generation Sequencing Tests

                Dear Colleague,

                We are pleased to announce that the FDA has published draft guidances that would streamline submission and review of data supporting the clinical and analytical validity of NGS-based tests. They represent a significant step, working within FDA’s existing regulatory authority, toward the FDA’s long-term goal of establishing a dynamic and flexible regulatory approach for genomic tests. We request that you review the guidances on our website http://www.fda.gov/NewsEvents/Newsro.../ucm509814.htm.

                We incorporated insights from patient and provider groups, test developers, industry coalitions, professional societies, and leading academicians, and from four public meetings. The first draft guidance, entitled “Use of Standards in FDA Regulatory Oversight of Next Generation Sequencing (NGS)-Based In Vitro Diagnostics (IVDs) Used for Diagnosing Germline Diseases” provides recommendations for designing, developing and validating NGS-based tests for hereditary diseases, and addresses the potential for using FDA-recognized standards to demonstrate analytical validity.

                The second draft guidance, entitled “Use of Public Human Genetic Variant Databases to Support Clinical Validity for Next Generation Sequencing (NGS)-Based In Vitro Diagnostics” describes an approach for test developers to use data from public genomic databases that meet certain criteria and gain FDA recognition. Data and assertions from these FDA-recognized databases could help ensure accurate clinical interpretations of genomic test results and support clinical claims in marketing submissions.

                The guidances explain how the FDA would consider, in the future, whether to exempt certain NGS-based tests from premarket review. This system would be efficient and flexible: as technology advances, standards can be updated to help ensure test accuracy. Similarly, as clinical evidence improves, new interpretations could be supported. This adaptive approach would ultimately foster innovation among test developers and improve patients’ access to these new technologies.

                The FDA invites you to participate in our stakeholder call scheduled for July 7, 2016 at 11 a.m. EST. The toll-free number for the call is: 800-369-1193, international callers may call on: 1-415-228-4959, the passcode is: FDA. A replay of the call will be available until August 7, 2016 on: 866-373-1992, international callers may hear the replay on: 1-203-369-0266.

                We look forward to your participation on the stakeholder call scheduled for July 7 at 11 a.m. EST; additionally, FDA will also be hosting informational webinars regarding these draft guidances soon. As they are scheduled we will update you with additional information. Also, if you or your organization plan to issue a statement about FDA’s announcement, would you please forward it to me to the email address below.


                Heidi C. Marchand, Pharm.D.
                Assistant Commissioner

                Office of Health & Constituent Affairs
                Office of External Affairs
                U.S. Food and Drug Administration
                Tel: 301-796-8457 / Main Off: 301-796-8460
                [email protected]

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