Recent patent cases have caused uncertainty about which Life Science inventions are eligible for patenting. This uncertainty arose when the courts interpreted the statute that defines patent-eligible subject matter.   Any new and useful process, machine, manufacture, or composition of matter is patent-eligible. Laws of nature, physical phenomena, and abstract ideas are not. The difficulty, of course, is determining whether a method falls into one camp or the other.
In the landmark 1980 Diamond v. Chakrabarty decision, the Supreme Court found that Pseudomonas strains containing energy-generating plasmids encoding hydrocarbon-degrading pathways are patentable-eligible.  The fact that the claimed invention was directed to living materials did not matter. The invention was not an unknown natural phenomenon. It encompassed a new, non-naturally occurring composition of matter -- a product of human ingenuity. That was enough.
Fast forward to 2010. The Supreme Court issued an opinion in a patent case where the claims were drawn to business methods.  Bernard Bilski applied for a patent directed to methods for buyers and sellers of commodities in the energy market to protect, or hedge, against the risk of price changes. The Court found the claims to be patent-ineligible because the claims were drawn to abstract ideas. Bilski garnered the attention of the biotech patent community for a number of reasons. Importantly, in light of Bilski, the Supreme Court vacated and sent back down to the Court of Appeals for the Federal Circuit the infamous case of Prometheus v. Mayo. 
Prometheus Labs was the exclusive licensee of U.S. Patent Nos. 6,355,623 (the ‘623 Patent) and 6,680,302 (the ‘302 Patent) directed to methods of optimizing the treatment of gastrointestinal disorders such as inflammatory bowl disease with thiopurine drugs. For brevity, the Courts, and I, focus on Claim 1 of the ‘623 Patent:
- A method of optimizing therapeutic efficacy for treatment of an immune-mediated gastrointestinal disorder, comprising:
(a) administering a drug providing 6-thioguanine to a subject having said immune-mediated gastrointestinal disorder; and
(b) determining the level of 6-thioguanine in said subject having said immune-mediated gastrointestinal disorder,
wherein the level of 6-thioguanine less than about 230 pmol per 8x10 8 red blood cells indicates a need to increase the amount of said drug subsequently administered to said subject and wherein the level of 6-thioguanine greater than about 400 pmol per 8x10 8 red blood cells indicates a need to decrease the amount of said drug subsequently administered to said subject.
It is beyond the scope of this discussion to detail the procedural posture of the Prometheus cases. Suffice it to say, however, that the Federal Circuit held Prometheus’ claims to be patent eligible. It said that the "administering" and "determining" steps take the claims outside of the realm of “laws of nature." The Court held that they are drawn to a particular application of naturally occurring correlations, and not simply to correlations between metabolite levels and drug efficacy or toxicity. As many in the biotech patent community breathed a sigh of relief, Mayo again appealed to the Supreme Court.
“Not so fast" said the Supreme Court. When they took the case back up, Prometheus’ claims were held patent-ineligible.  In their view, the claims were directed to laws of nature, i.e., the relationship between the concentrations of certain metabolites in the blood and efficacy/toxicity. The Court reasoned that doctors had been using thiopurine drugs for a long time and the claims were cleverly drafted to ensnare doctors that were making known correlations. Put another way, the Court reasoned that the claimed steps add nothing specific to the laws of nature other than what is well-understood, routine, conventional activity. The Court stated that one must do more than state a law of nature then add the words “apply it." 
Prometheus may be the first of a one-two punch to many biotech patents. The Association for Molecular Pathology had previously appealed its case against Myriad Genetics  to the Supreme Court. They vacated it and sent it back to the Federal Circuit to be decided in light of Prometheus. The Myriad case relates to seven patents disclosing compositions and methods related to the BRCA1 and BRCA2 gene sequences. There are three types of claims: (1) isolated BRCA1/2 nucleic acids, (2) methods of “comparing" or “analyzing" germline or tumor sequences, and (3) cell-based methods of screening for cancer therapeutics. 
The Myriad Court held that the isolated nucleic acid claims are patent eligible because isolated nucleic acids are distinctive chemical entities that do not exist in nature. The Court rejected the argument that they are not patent-eligible because the sequences are found in nature. Similarly, the Court held the methods of screening for cancer therapeutics to be patent eligible. The cells recited in the screening claims have been transformed with exogenous DNA and grown in the presence or absence of drug candidates. Thus, the claims recite non-naturally occurring materials and methods. Additionally, the claims are not drawn to mere abstract ideas or scientific principles.
In contrast, the Myriad Court held the methods of “comparing" or “analyzing" sequences to be patent-ineligible. The Court found that these claims are directed to only abstract mental processes. The claims do not apply the comparison of two sequences to a process that includes DNA extraction, sequencing, or any other real-world steps. They only require a comparison of two sequences. This was not enough.
At the time of this writing, the parties, and interested third parties, have filed briefs in the case supporting their various positions as a matter of patent law or public policy. The Federal Circuit will again hear arguments in this case on July 20. No matter how the case is decided, Myriad will likely be going back to the Supreme Court. At stake may be the fundamental ability of biotechnology, bioinformatics, and personalized medicine companies to patent their important technologies.
Will the courts knock out the ability to claim methods for personalized medicine, diagnostics, and drug screening? Will they go nuclear (pardon the pun) and take out isolated nucleic acid and protein claims? The status of such claims is up in the air, however, I have a hard time believing that the Courts would wipe out such a large class of IP assets and seriously undermine an entire industry. Under the existing precedents, biotechnology claims, including isolated nucleic acid and protein claims, should be held to be patent-eligible. What is clear, however, is that the pendulum is swinging back in the direction of more restrictive subject matter eligibility.
I counsel my clients that strong composition of matter claims are an important part of an effective patent portfolio – even if the core technologies are methods. Composition claims typically avoid questions of patent eligibility. Diagnostic and drug screening methods may require probes, isolated cDNAs, engineered cells, antibodies, or other compounds. They may require gene chips or other solid media. Claims to these components of the new methods can greatly enhance the patent estate. While any individual component may be known in the art, new combinations of known components may be patentable. Additionally, composition claims are better when it is time to assert patent rights.
In the new regime, claiming new methods requires significant forethought going back to the original drafting of the patent specifications. A patent specification should be thought of as a reservoir of language from which to draw during the many years of subsequent patent prosecution. There should be many examples, both prophetic and actual, of real, tangible tools and materials that are used to carry out the claimed methods. Applicants should not rely on broad claim language directed to the principles of the claimed method. Rather, Applicants should be prepared to pursue claims that recite many tools and materials in order to get broad coverage for their inventions.
Where Prometheus and Myriad may create obstacles to patentability, they may create opportunities to expand businesses into areas that were previously considered unavailable. Companies that focus, for example, on diagnostics, personalized medicine, and drug screening may wish to reconsider the relevance of certain 3rd party patent portfolios. A careful analysis of issued patents in light of these cases may show that they have significant invalidity problems. Alternatively, one may reassess the likelihood that broad claims will issue in published patent applications that are being monitored. These analyses will likely change the risks of moving forward with new products and services. They might also provide ammunition for negotiating lower royalty rates on those portfolios.
Hopefully, the Courts will provide further clarity on what are patent-eligible biotechnology inventions. Check back here for updates as the laws progress. If anybody would like to further discuss this with me, please do not hesitate to contact me by telephone or email.
 35 U.S.C. §101
 Patent eligibility should be viewed independently of novelty and non-obviousness.
 Diamond, Comm’r of Patents and Tradmarks v. Chakrabarty, 447 U.S. 303 (1980)
 Bilski v. Kappos, 130 S. Ct. 3218 (2010)
 Prometheus Labs., Inc. v. Mayo Collaborative Servs. & Mayo Clinic Rochester, 628 F.3d 1347, 1354 (Fed. Cir. 2010)
 Mayo Collaborative Servs. v. Prometheus Labs., Inc., 132 S. Ct. 1289 (U.S. 2012)
In my view, the Federal Circuit got it right and the Supreme Court got it wrong.
 Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 653 F.3d 1329 (Fed. Cir. 2011)
 See, e.g., U.S. Patent Nos. 5,747,282 (Claims 1, 2, 5, and 20), 5,710,001 (Claim 1) and 5,709,999 (Claim 1)