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I am working in a improved diagnostic tool with an innovation in sample handling and in time reducing modifications of an existing PCR protocol. I would like to know whether is it commandatory to design new primers for the detection of such pathogens (not published) in order to patent such diagnostic kit. Thanks in advance

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To answer this question requires some specialized knowledge. Fortunately I know a bit about this field. If you are trying to get a patent in order to make money licensing to other companies, there is an incentive to make the patent as universal as possible. If your innovation applies across a range of assays then it could be very valuable to others. In this case, I would clearly recommend trying to pursue a patent that is not specific to a single pathogen and thus doesn't necessitate the design of new primers. Even if the innovation applied to a single assay, I'd try to get the patent without needing new primer design. If you specify new primers as a requirement of the claims, then it would be easy to circumvent your patent by simply using existing primers or primers of a different sequence. Thus, you may get a patent, but it wouldn't provide much protection.

In any case, I highly recommend you work with a patent attorney or agent with experience in molecular diagnostics. Going it alone may seem like it will save you money, but you are much more likely to either find your patent application rejected or a patent so narrow as to be of little value.

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