An Early Test for the USPTO'S Eligibility Analysis

22 December 2014 Personalized Medicine Bulletin Blog

Just last week, the USPTO released its revised subject matter eligibility guidance (2014 Interim Guidance on Patent Subject Matter EligibilityInterim Guidance” reviewed in my prior post of December 16th, 2014). The Interim Guidance replaced the March 2014 Guidance that was much-criticized for its expansive application of U.S. Supreme Court jurisprudence relating to the judicial exceptions to patent-eligibility: abstract ideas, laws of nature and natural phenomenon. Unlike the March 2014 Guidance (that was not circulated to the public for comment prior to its issuance), the Interim Guidance notes that the USPTO’s analysis of patent-eligibility will be an iterative process continuing with “periodic supplements based on developments in patent subject matter eligibility jurisprudence and public feedback.” Interim Guidance at page 4. Embedded within footnote 5 of the Interim Guidance, the USPTO references an appeal pending before the Federal Circuit – University of Utah Research Foundation v. Ambry Genetics Corp. (In re BRCA1- & BRCA2- Based Hereditary Cancer Test Patent Litigation), No. 14-1361 (Fed. Cir. Filed Mar. 18, 2014 (“Myriad II”) that may impact the USPTO’s Interim Guidance. Interestingly, the next day on December 17th, 2014 the Federal Circuit issued its Myriad II decision (attached here) holding that Myriad’s asserted claims were not patent-eligible. The decision is interesting not only because it evaluates yet more claims from Myriad’s impressive patent portfolio but also because it provides an early test of the USPTO’s Interim Guidance.

Myriad’s Asserted Patent Claims

The history of the dispute and the oral argument are covered in my prior posts of September 29th and October 20th, 2014, respectively. The claims at issue relate to the tools and methods that support Myriad’s successful BRCA1/2 genetic tests.

Several plaintiffs that include Myriad Genetics, Inc. (collectively “Myriad”) sought to enjoin the alleged infringement by defendant Ambry Genetics Corp. of six claims of three patents: claims 7 and 8 of U.S. Patent No. 5, 753,441 (the ‘441 patent); claims 16 and 17 of U.S. Patent No 5,747,282 (the ’282 patent); and claims 29 and 30 of U.S. Patent No. 5,873,492 (the ’492 patent). The District Court for the District of Utah denied Myriad’s motion for preliminary injunction. Myriad appealed.

The Composition Claims – Primer Pairs

Four composition of matter claims directed to primer pairs were considered on appeal. Claim 16 of the ’282 patent was considered representative:

“A pair of single-stranded DNA primers for determination of a nucleotide sequence of a BRCA1 gene by a polymerase chain reaction, the sequence of said primers being derived from human chromosome 17q, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA having all or part of the sequence of the BRCA1 gene.”

Claim 17 of the ’282 patent and claims 29 and 30 of the ’492 patent were considered similar to claim 16 of the ’282 patent.

The Federal Circuit began its analysis by referring to the holding of the 2013 Myriad decision (Molecular Pathology v. Myriad, 133 S. Ct. 2107 (2013) (“Myriad I”), wherein the U.S. Supreme Court determined that isolated genomic DNA and DNA fragments were not patent-eligible. cDNA, being a synthetic molecule made by man, was patent-eligible. In evaluating the claims directed to primer pairs, the Federal Circuit determined that primer pairs were more similar to patent-ineligible isolated DNA fragments than patent-eligible cDNA. The court stated that:

“The primers before us are not distinguishable from the isolated DNA found patent-ineligible in [Myriad I] and are not similar to the cDNA found to be patent-eligible. Primers necessarily contain the identical sequence of the BRCA sequence directly opposite to the strand to which they are designed to bind. They are structurally identical to the ends of DNA strands found in nature.”

Slip Op. at page 7.

The Federal Circuit disregard Myriad’s arguments that the primers were distinguished from the patent-ineligible DNA fragments adjudicated by the Supreme Court. The Federal Circuit found that even though the primers were single stranded, the process of isolating the single-stranded DNA from the human body did not make it patent-eligible. The court also determined that the function of the primers – to initiate an amplification reaction – was not markedly different from DNA fragments as they appear in nature. The court stated that:

“In fact, the naturally occurring genetic sequences at issue here do not perform a significantly new function. Rather, the naturally occurring material is used to form the first step in a chain reaction—a function that is performed because the primer maintains the exact same nucleotide sequence as the relevant portion of the naturally occurring sequence. One of the primary functions of DNA’s structure in nature is that complementary nucleotide sequences bind to each other. It is this same function that is exploited here—the primer binds to its complementary nucleotide sequence. Thus, just as in nature, primers utilize the innate ability of DNA to bind to itself.”

Slip Op. at page 9.

The Method Claims – Detecting Sequences

Claims 7 and 8 of the ’441 patent related to methods for detecting certain DNA sequences. Claim 7 (revised to include the language of claim 1 from which it depends) was considered representative:

“A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject[,]

wherein a germline nucleic acid sequence is compared by hybridizing a BRCA1 gene probe which specifically hybridizes to a BRCA1 allele to genomic DNA isolated from said sample and detecting the presence of a hybridization product wherein a presence of said product indicates the presence of said allele in the subject.”

Claim 8 (revised to include the language of claim 1, from which it depends) recites:

“A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject[,]

wherein a germline nucleic acid sequence is compared by amplifying all or part of a BRCA1 gene from said sample using a set of primers to produce amplified nucleic acids and sequencing the amplified nucleic acids.”

In analyzing the method claims, the court looked to the Supreme Court’s analysis in Association for Molecular Pathology v. United States Patent and Trademark Office, 132 S. Ct. 1794 (2012) and Alice Corp. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014)(“Alice”). The court stated that:

“Recently in Alice the Supreme Court reiterated its two-step test to determine patent eligibility for any claims that allegedly encompass abstract ideas. First, “we determine whether the claims at issue are directed to [a] patent-ineligible concept[]. If so, we then ask, ‘what else is there in the claims before us?” … Here, we treat separately the first paragraphs of claims 7 and 8, which describe the comparison of wild-type genetic sequences with the subject’s genetic sequence and correspond to the first step of Alice, and the second paragraphs, which describe the techniques to be used in making the comparisons and correspond  to the second step of Alice.”

Slip Op. at page 14.

The Federal Circuit stated that the first step of the methods are not patent-eligible because the steps comprise nothing more than comparing sequences. The court also focused on the breadth of the claims, noting that the covered comparisons were not restricted by the purpose of the comparison or the alteration being detected, and therefore may pre-empt future use outside the field of cancer detection.

Having determined that the first step of the claims were abstract ideas under an Alice analysis, the court then looked at the second step to determine if this step alone or in combination with the first step, transform the patent-ineligible method to a patent-eligible one. The court noted that “[t]here must be a further inventive concept to take the claim into the realm of patent-eligibility.” Slip Op. at page 16.

The Federal Circuit also determined that the use of conventional methods in the second steps, such as sequencing or hybridization, did not add a further inventive concept to the abstract idea embodied by the first steps of the claims.

Patent-Eligible Applications

The court also dismissed Myriad’s argument that the method claims were similar to claim 21 of  the ‘441 patent which Judge Bryson suggested was patent-eligible in the Federal Circuit’s earlier 2012 Myriad I decision. Myriad asserted that Judge Bryson indicated that as a first party with knowledge of sequences, they were in an excellent situation to claim applications of that knowledge. The court noted that even if claim 21 was patent-eligible, which the court expressly declined to opine on, the claim was qualitatively different from the method claims at issue in this dispute. The court noted that claim 21 is limited to particular mutations that the inventors had discovered whereas the claims in Myriad II were significantly broader and more abstract, as they claim all comparisons between the patient’s BRCA genes and wild-type BRCA genes.

A Review of the USPTO Interim Guidance

The USPTO’s Interim Guidance and the Federal Circuit’s recent Myriad II decision appear fairly aligned in their respective application of the Supreme Court patent-eligibility precedent. For claims that relate to a product of nature, the court’s and the USPTO’s analyses consider not only the structural differences between the claimed subject matter and its natural counterpart, but also whether the claimed product exhibits markedly different characteristics from its naturally occurring counterpart in its natural state. Interim Guidance at page 15. However, the USPTO Interim Guidance also notes that if the claimed product does not appear to monopolize or tie-up a judicial exception, it is not necessary to conduct a markedly different analysis. Interim Guidance at page 16. The Federal Circuit’s opinion, in contrast, only evaluated the product claims in terms of structural and functional differences between the claimed material and its natural counterpart.

For claims that may related to natural phenomenon or an abstract idea, the current opinion and the Interim Guidance similarly note that the claim elements must be evaluated to determine whether the elements of the claim, considered in both individually and as an ordered combination, are sufficient to ensure that the claim as a whole amounts to significantly more than the exception itself. Interim Guidance at page 20. The Interim Guidance and the Federal Circuit each look to whether a claim contains elements in addition to the judicial exception that amount to significantly more that the judicial exception itself, and that the claim does not monopolize the exception. Interim Guidance on page 21.

Looking Ahead

The USPTO Interim Guidance is less restrictive in its approach to patent-eligibility. Application of the Interim Guidance is anticipated to allow patenting of more nature-based inventions as compared to the 2014 Guidance. However, even with the Interim Guidance, it is clear that the Federal Circuit will not find broad, expansive claims that relate in whole or in part to a judicial exception to subject matter eligibility to be valid and patent-eligible. Thus, challenges remain and patentees should continue to pay careful consideration to the USPTO’s Interim Guidance and the evolving jurisprudence involving subject matter eligibility.

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