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FDA Releases Outline of Guidance for Developing Tests Based on Human Genetic Variants

The FDA is charged with regulating “Next Generation Sequencing (NGS) Tests,” and has just released draft guidance on what needs to be regulated. (A copy of the first draft and second draft can be found at the end of this post.) The strategies involve the generation of reliable diagnostic conclusions for patients based on one or, oftentimes, many many mutations that are compared to those of other patients and to reference databases. Under “Scope,” the FDA has stated:

“[T]his paper discusses factors and principles to identify genetic databases that are of sufficient quality to support a regulatory submission…..[T]his paper discusses data quality and database operations as applied to the clinical interpretation of human genetic variants, i.e., for establishing the link between variants and the risk or diagnosis of disease or other states of health.”

The analysis of the “big data” in publicly available “well-curated” databases can lead to an acceptable source of clinical evidence for genetic variants detected by NGS tests, particularly if the variant is limited in distribution. The FDA may certify the databases and their operation. I am not going to try to summarize the positions outlined in the seven page letter accompanying the announcement except to note that there is not one word about the role of intellectual property and its effect on this ambitious program.

In other words, what is left to patent? The DNA sequences containing the variants cannot be patented post-Myriad, at least not singly, and probably not in association either, if the courts keep on citing Funk Bros. Of course here the sum of the parts (a reliable diagnostic tool) is much greater that any single sequence, but the variants themselves have no clinical value except as pieces of a much larger puzzle. Of course, specific methods of treatment based on these correlations will still  be patentable – unless they are found not to contain an “inventive concept” –  but now we are quite a way down the IP/regulatory road.

I am not aware of any case law in which a specific variant or set of variants that correlate to a germ line dysfunction has been held to be an abstract idea, but things are not going our way, given Judge Lourie’s comments that comparing a patient’s BRCA sequence with a reference sequence to diagnose a predisposition to develop breast cancer is an abstract idea in the Fed. Cir.’s Myriad opinions. Even the patent sympathetic Fed. Cir. panel in CellzDirect stated that “comparing two sequences to detect alterations is an ‘abstract mental process.'”

Can the Court find a difference between (a)”detecting [any] alterations” that indicate breast cancer and (b) determining whether or not the presence of a group of specific alterations in multiple genes that permits or strengthens a diagnosis, so that (b) is a patent-eligible application of a natural phenomenon? Don’t bet the Pharma on it. The normally somnolent FDA’s willingness to develop a regulatory framework for NGS tests while the PTO, the Fed. Cir. and the Supreme Court are demolishing the patent foundation for the same technology is an irony that no IP attorney could have predicted.

first draft guidance

second draft guidance


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