On July 29, 2011, a three-judge panel of the Federal Circuit issued its anticipated decision in The Association For Molecular Pathology v. USPTO & Myriad reversing the district court’s opinion that isolated DNA molecules are not patentable subject matter. The Federal Circuit, however, affirmed the district court’s holding that a method for screening a sample for a mutation that only recited a “comparing” step is not within the scope of statutory patentable subject matter. The mixed decision is likely to be appealed to either the full Federal Circuit and/or the United States Supreme Court, which is likely to have the final word.

Isolated DNA Molecules Are Patentable Subject Matter

Examples of the challenged composition claims were as follows:

  1. An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
  2. The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.

5.  An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

The district court had found that “isolated DNA molecules fall within the judicially created ‘products of nature’ exception to § 101 because such isolated DNAs are not ‘markedly different’ from native DNAs.” The district court made this decision, in part, because “unlike other molecules, DNAs are the ‘physical embodiment of information,’ and that this information is not only preserved in the claimed isolated DNA molecules, but also essential to their utility as molecular tools.” The Federal Circuit, relying upon Supreme Court precedent, reversed the district court’s holding.

The Federal Circuit explained that the distinction “between a product of nature and a human-made invention for purposes of § 101 turns on a change in the claimed composition’s identity compared with what exists in nature.” The Federal Circuit continued: “Specifically, the Supreme Court has drawn a line between compositions that, even if combined or altered in a manner not found in nature, have similar characteristics as in nature, and compositions that human intervention has given ‘markedly different,’ or ‘distinctive,’ characteristics.” Applying this standard, the Federal Circuit held that the claims to isolated DNA molecules cover patentable subject matter because “the claims cover molecules that are markedly different—have a distinctive chemical identity and nature—from molecules that exist in nature.” The court explained that DNA molecules exist in nature as part of chromosomes and that “in each chromosome, the DNA molecule is packaged around histone proteins into a structure called chromatin, which in turn is packaged into the chromosomal structure.” In contrast to chromosomal DNA, the Federal Circuit explained, “isolated DNA … is a free-standing portion of a native DNA molecule, frequently a single gene. Isolated DNA has been cleaved (i.e., had covalent bonds in its backbone chemically severed) or synthesized to consist of just a fraction of a naturally occurring DNA molecule.” Therefore, isolated DNA “are not the same molecules as DNA as it exists in the body; human intervention in cleaving or synthesizing a portion of a native chromosomal DNA imparts on that isolated DNA a distinctive chemical identity from that possessed by native DNA.” The court also distinguished isolated from purified because of cases that held that purification is not always sufficient for a claim to cover patentable subject matter. The court emphasized that the isolation produces a molecule that is “markedly different from that which exists in the body.” Purification, in contrast, does not necessarily change what exists in the body. The decision affects both claims to cDNA molecules and fragments of genomic DNA.

Method Claims that Only Recite ‘Comparing’ or ‘Analyzing’ Steps Do Not Recite Patentable Subject Matter

The court then turned to whether a claim reciting only a “comparing” or “analyzing” step covers patentable subject matter. In the instant case, the challenged claim recited a method of screening a tumor sample from a human subject for a somatic alteration [mutation] in a BRCA1 gene in the tumor. The method recited “comparing a first sequence … from said tumor sample … with a second sequence … from a nontumor sample … wherein a difference in the sequence … indicates a somatic alteration.” The Federal Circuit affirmed the district court’s decision and held that “claims to ‘comparing’ or ‘analyzing’ two gene sequences fall outside the scope of § 101 because they claim only abstract mental processes.” The Federal Circuit explained that the claims “do not apply the step of comparing two nucleotide sequences in a process. Rather, the step of comparing two DNA sequences is the entire process claimed.” The court distinguished this type of method claim to the claim at issue in Prometheus Labs., Inc. v. Mayo Collaborative Servs., 628 F.3d 1347(Fed. Cir. 2010, cert. granted 2011 WL 973139 (June 20, 2011)). In Prometheus, the method claims had additional steps outside of mental steps. The Prometheus claims required the administration of a drug and determining the level of the drug’s metabolite and then comparing the level of metabolite to a predetermined level to optimize a drug dosage. In Prometheus, the Federal Circuit held that at least the administration step and the determining steps were transformative and sufficient to satisfy the standards for what is patentable subject matter. In contrast, a claim that only compares one sequence to another has no transformative step. The Federal Circuit explained that the claims, for example, did not have any step isolating the genes from a blood sample or “any other necessary transformative step.” The only step that the claims recited could be accomplished by “mere inspection alone.” Therefore, the court held that the claims do not recite patentable subject matter and “are instead directed to the abstract mental process of comparing two nucleotide sequences.”

The Federal Circuit did find that claims directed to screening for potential cancer therapeutics did recite patentable subject matter because they included the transformative step of culturing and growing cells and measuring what happens to the cells upon the administration of a potential therapeutic. According to the Federal Circuit, the claims recite more than just mental steps, and, therefore, satisfy the standards for patentable subject matter.

Viewing the decision as a whole, diagnostic claims remain patentable so long as they do not solely recite mental steps, such as “comparing” or “analyzing” sequence information. Based upon this decision, a diagnostic claim must have some transformative step, such as isolating gene sequences from a sample or other non-mental step. Under the Federal Circuit standard this should be sufficient for a diagnostic claim to survive a challenge that the claim does not cover patentable subject matter. This distinction, however, raises the issue of distributive infringement when a patentee attempts to enforce a diagnostic claim against a third party. It is very likely that a single entity will not perform all of the steps. For example, a doctor could obtain the sample and isolate the gene sequences and the analysis performed by a different lab. The patentee may then have to sue under an inducement theory rather than a direct infringement theory. In view of recent decisions regarding infringement of method claims and the Federal Circuit’s decision to clarify what constitutes joint infringement (see, Akamai Technologies, Inc. v. Limelight Networks, Inc., (Fed. Cir. 2011) (en banc order) and McKesson Technologies Inc. v. Epic Systems Corp., (Fed. Cir. 2011) (en banc order)), it remains to be seen how diagnostic claims may be enforceable, especially if a patentee does not have a claim to a composition of matter that is necessary to perform the diagnostic method. In such a case, depending upon the outcome of Akamai and McKesson, a patentee may have a method claim that is infringed by a combination of actors, but there is no remedy because of the standards put forward for inducement and/or contributory infringement.

With a likely appeal to the Supreme Court, the standards for what constitutes patentable subject matter could be modified, still leaving the issue open as to whether isolated DNA molecules and diagnostic claims are patentable under U.S. patent law.

The complete description can be found at http://www.cafc.uscourts.gov/images/stories/opinions-orders/10-1406.pdf.