The Software Impact of Myriad Genetics

My thanks to Justin McCarthy for this guest post:

On July 29, 2011, The Federal Circuit decided The Association for Molecular Pathology v. Myriad Genetics, 2010-1406 (Fed. Cir. July 29, 2011).  While this case deals with the patentability of gene fragments and methods of use, the case does present interesting questions surrounding the patentability of software.   Myriad was brought by a number of medical organizations, researchers, genetic counselors, and patients as a declatory judgment proceeding against a number of patents that Myriad had secured which protect both the isolated gene fragment BRCA1 and BRCA2 as well as methods for using those gene fragments to detect certain breast and ovarian cancers.  Myriad, at 8-9.   The court’s decision has two parts, both having implications for the software patent landscape.

Part I – The method claims:

The patent included claims drawn both to the gene fragments themselves as well as methods for using the gene fragments.  The court’s decision on the method claims was the only part of the decision that was unanimous.  The decision on the patentability of the gene fragments was split 2-1.

The challenged method claims recite:

1. (‘999 patent) A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 12A, 14, 18 or 19 in a human which comprises analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample or analyzing a sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1.

1. (‘001 patent) A method for screening a tumor sample from a human subject for a somatic alteration in a BRCA1 gene in said tumor which comprises [] comparing a first sequence selected from the group consisting of a BRCA1 gene from said tumor sample, BRCA1 RNA from said tumor sample and BRCA1 cDNA made from mRNA from said tumor sample with a second sequence selected from the group consisting of BRCA1 gene from a nontumor sample of said subject, BRCA1 RNA from said nontumor sample and BRCA1 cDNA made from mRNA from said nontumor sample, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said tumor sample from the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said nontumor sample indicates a somatic alteration in the BRCA1 gene in said tumor sample.

20. (‘282 patent) A method for screening potential cancer therapeutics which comprises: growing a trans-formed eukaryotic host cell containing an altered BRCA1 gene causing cancer in the presence of a compound suspected of being a cancer therapeutic, growing said transformed eukaryotic host cell in the absence of said compound, determining the rate of growth of said host cell in the presence of said compound and the rate of growth of said host cell in the absence of said compound and comparing the growth rate of said host cells, wherein a slower rate of growth of said host cell in the presence of said compound is indicative of a cancer therapeutic.

The court held all but claim 20 invalid under 35 U.S.C. 101 as directed to abstract ideas and therefore not patent eligible.  The court found that claims 1 and 2 recited nothing more than abstract mental steps necessary to compare two different nucleotide sequences.  The court summarized the claims as “look at the first position in a first sequence; determine the nucleotide sequence at that first position; look at the first position in a second sequence; determine the nucleotide sequence at that first position; determine if the nucleotide at the first position in the first sequence and the first position in the second sequence are the same or different, wherein the latter indicates an alteration; and repeat for the next position.” Myriad, at 50.

The court stated that while the application of a formula or abstract idea in a process may describe patentable subject matter, the claims at issue did not describe applying the step of comparing two nucleotide sequences in a process, rather the comparison was the process.

The court also briefly distinguished Prometheus Labs., Inc. v. Mayo Collaborative Servs., 628 F.3d 1347, 1350 (Fed. Cir. 2010), cert. granted 2011 WL 973139 (June 20, 2011), which upheld a claim including the steps of  “(a) “administering” a thiopurine drug to a subject, and/or (b) “determining” the drug’s metabolites levels in the subject, wherein the measured metabolite levels are compared with predetermined levels to optimize drug dosage.” Myriad, at 52.  The court stated that in addition to the “administering” step being transformative, that the “determining step” was both transformative and central to the purpose of the claims.  Because the determining step could not be determined merely by inspection, the determining step required a transformation, i.e. the metabolites must be extracted and analyzed from a bodily sample.  The court held that the method claims in the instant case were capable of being performed by mere inspection and thus were not transformative. Id.

The court did hold that claim 20 was valid stating: “the claim recites a method that comprises the steps of (1) ‘growing’ host cells transformed with an altered BRCA1 gene in the presence or absence of a potential cancer therapeutic, (2) ‘determining’ the growth rate of the host cells with or without the potential therapeutic, and (3) ‘comparing’ the growth rate of the host cells. The claim thus includes more than the abstract mental step of looking at two numbers and ‘comparing’ two host cells’ growth rates. The claim includes the steps of ‘growing’ transformed cells in the presence or absence of a potential cancer therapeutic, an inherently transformative step involving the manipulation of the cells and their growth medium. The claim also includes the step of ‘determining’ the cells’ growth rates, a step that also necessarily involves physical manipulation of the cells.” Id. at 53.

The impact of this case is likely to be important to software patents as many such patents commonly contain method claims which rely on analyzing and comparing data.  To avoid invalidation after Myriad, practitioners’ should consider adding transformative limitations which attempt to remove the method from physically being able to be performed by a human mind.  For example, practitioners’ may consider adding limitations relating to the computer system as a whole, such as using calculated information to control a peripheral device or another computing device; transforming data from one form to another using a processor; receiving input (preferably reciting the source of the input – e.g. a network, a keyboard, or the like); or any other tangible connection that ties into the software method.  This will leave an argument that the method cannot be performed simply by a human mind and that some tangible step (such as physically sending electrons to a device) is necessary.  Such a connection should be as substantial as practically possible as a court may find such connections to be merely post-solution activity or data gathering steps which will not save the claim.  However, at least it leaves the litigators an argument for why the claim is not so abstract as to be unpatentable.

Bottom line, practitioners’ may be better off with a slightly narrower claim with more specific limitations that concretely tie the method to a particular machine, rather than a broad method claim which could literally be performed by a human mind.

Part II the Gene Fragment Claims

The gene fragment claims are only applicable to computer software patents in the sense that the arguments used by the Federal Circuit to uphold the validity of Myriad’s gene fragment claims undercut the very reasoning that the Federal Circuit used weeks later to invalidate a patent drawn to a machine readable medium in Cybersource Corp. v. Retail Decisions, Inc., App. No. 2009-1358 (Fed. Cir. Aug 16, 2011).  In Cybersource, the court addressed both method and machine-readable medium claims.  The court first held that the method claims were invalid under 35 U.S.C. 101 as drawn to an abstract idea.  Continuing with the machine-readable medium claim, the court held that “[r]egardless of what statutory category . . . a claim’s language is crafted to literally invoke, we look to the underlying invention for patent-eligibility purposes.  Here, it is clear that the invention underlying both claims 2 and 3 is a method . . . “ Id. at 17.  So in essence, the court ignored the structural limitations that are inherent when discussing a machine readable medium (e.g. the physical re-arrangement of electrons on a medium) to look at what the machine-readable medium does as opposed to what it is.

The Myriad panel had three separate opinions.  The opinion from Judge Lourie took an approach that is inconsistent with the Cybersource court to save the gene fragment claims.  Namely, Judge Lourie ignored the functional similarities between the function of an isolated gene fragment and the function of that same gene fragment as a part of the full gene in the human body and focused instead on the structural differences between the gene in the human body and the patented fragment.  Judge Lourie found that in nature, isolated DNA fragments are covalently bonded to other such molecules.  When cleaved to form the claimed fragment, those bonds are broken forming an isolated DNA molecule that is a “distinct” entity. Myriad, 43-4.  Dismissing arguments from the Plaintiffs’ that despite any change in the chemical makeup of this molecule, the serve the same purpose – they both store the same set of information (e.g. to encode for protein production), the court stated: “[w]e disagree, as it is the distinctive nature of DNA molecules as isolated compositions of matter that determines their patent eligibility rather than their physiological use or benefit.”

Judge Lourie here is clearly going to great lengths to uphold the patentability of the gene fragment, going into extreme detail regarding slight changes in chemical composition (one wonders why these small changes aren’t an obvious variation of the gene found in nature – but I digress) and ignoring altogether the function and purpose of the gene fragments.  This is contrary to the court’s reasoning in the Cybersource case where they only looked at the function of the product as opposed to its structure.

Judge Moore’s opinion further highlights the structural differences between natural DNA and the patented fragments, but qualifies it saying that the structural differences are not enough without some new utility.  And what was Judge Moore’s unique utility for the gene fragments? Nothing more than the fragment’s diagnostic abilities, something Judge Moore points out, cannot be inherently done by the body.  However, as with the chemical structure, this seems to be a thin distinction, and certainly the machine readable medium in Cybersource achieves some “new” utility – namely it causes a computer to perform the method steps.

In some ways the structure of the machine readable medium claim may be to blame for the Cybersource decision as it is a hybrid claim type in that it recites both structure and method limitations.  However, this is by necessity, as the actual structure of the machine readable medium is a series of electrons arranged in a certain fashion and such an arrangement is indescribable. Rather than claim a machine-readable medium comprising: one, zero, one, one, zero, one (etc…), the claim is written in terms of its result – i.e. what the machine-readable medium does, rather than what it is.  This may give the false impression that a machine-readable medium claim is a method claim wrapped in a product shell.  Perhaps if practitioners’ began describing how the machine readable medium is created (e.g. including the instructions AND including compiling steps, etc…) rather than simply what it does, these claims would find a more favorable reception.

Regardless, it is clear that the court is viewing these two technologies differently and appears to be applying a more lenient standard to biotechnology cases than computer science cases.  It will be interesting to see how this plays out as Cybersource is likely headed to further review.

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