September 9, 2019
Drs. Stephen Quake and Christina Fan (“Quake”) appealed a decision of the U.S. Patent and Trademark Office Patent Trial and Appeal Board (“the Board”) finding the four claims of Quake’s U.S. Patent 8,008,018 and Claim 25 of their U.S. Application No. 12/393,833 unpatentable for lack of written description.
The claims at issue were directed to a method of determining the presence of a chromosomal abnormality (aneuploidy) in fetuses by using massively parallel sequencing (MPS) technology to sequence DNA fragments from a sample of the mother’s blood that contains both maternal and fetal DNA. The claims recited a random MPS method for the detection step, meaning that all of the DNA in the sample is sequenced, as opposed to sequencing specific, targeted sequences. Quake’s specification, however, only expressly described detection of target sequences and consistently focused on detection of targeted sequences, using the term “target” more than sixty times throughout the patent.
Quake claimed a method of determining fetal aneuploidy by detecting target sequences in an application filed on February 2, 2007, and also filed a continuation application No. 12/393,803 in February 2009. The original claims of Quake’s ’803 application explicitly recited methods that required the detection of “target sequences.” In 2011, Quake split the ’803 application into multiple applications. In the application which later issued as the ’018 patent, Quake canceled all pending claims and added new claims covering the use of random MPS to determine fetal aneuploidy.
Representative issued claim 1 reads:
1. A method for determining presence or absence of fetal aneuploidy in a maternal tissue sample comprising fetal and maternal genomic DNA, wherein the method comprises:
a. obtaining a mixture of fetal and maternal genomic DNA from said maternal tis-sue sample:
b. conducting massively parallel DNA sequencing of DNA fragments randomly selected from the mixture of fetal and maternal genomic DNA of step a) to determine the sequence of said DNA fragments;
c. identifying chromosomes to which the sequences obtained in step b) belong;
d. using the data of step c) to compare an amount of at least one first chromosome in said mixture of maternal and fetal genomic DNA to an amount of at least one second chromosome in said mixture of maternal and fetal genomic DNA, wherein said at least one first chromosome is presumed to be euploid in the fetus, wherein said at least one second chromosome is suspected to be aneuploid in the fetus, thereby deter-mining the presence or absence of said fetal aneuploidy.
Claim 25 of Application No. 12/393,833, continued from the ’803 application, also recited using random MPS to determine fetal aneuploidy.
In 2007, Yuk-Ming Dennis Lo, Rossa Wai Kwun Chu, and Kwan Chee Chan (“Lo”), filed a patent application that undisputedly described and claimed a method of using “random” MPS to determine fetal aneuploidy. Lo’s application was directed to, and described in considerable detail, randomly sequencing the entire sample by MPS after fragmentation and division. Lo’s application explained that a skilled artisan would need to adjust for chromosome size, i.e., normalize the data by the length of each chromosome, before being able to accurately determine the presence of fetal aneuploidy.
Both Quake and Lo requested interferences to determine who first invented the random MPS method and when the method was invented. Lo attacked the claims of Quake’s ’018 patent and ’833 application as unpatentable for lack of written description. Although the ’018 patent specification is over thirty columns, MPS was discussed in only two paragraphs. In Quake’s view, these two paragraphs not only taught MPS as a sequencing tool, but also described a second detection methodology (random sequencing) different from targeted sequencing.
In its first decision in 2015, the Board disagreed with Quake, found the random MPS claims invalid for lack of written description, and granted Lo’s motions in all three interferences. Quake appealed. On appeal, in 2017, the Court of Appeals for the Federal Circuit (“the Court”) vacated the Board’s 2015 decisions and remanded with instructions for the Board: (1) to consider whether the patent’s written description at columns 19 to 20 discloses random MPS; (2) to explain the meaning of various phrases in that portion of the specification; and (3) to examine whether a skilled artisan would have known, as of the priority date, that the specification’s reference to Illumina products meant random MPS sequencing based on record evidence describing Illumina products or any other random MPS products existing as of the filing date.
On remand, the Board found that a citation to a reference and a single sentence in Quake’s specification support random sequencing, but that the two, on their own, were insufficient to describe the claimed method of determining fetal aneuploidy through random MPS. The Board also found that the specification did not describe the final claimed comparison step in terms that would be applicable to random MPS, namely adjusting/normalizing for chromosome size before assessing the over- or under-representation of a chromosome.
The Board looked in the two MPS paragraphs (A and B) of the ’018 patent specification for evidence of written description. The Board found that the citation to Balasubramanian (US 2003/0022207) in Passage A “provides some disclosure of massively parallel sequencing of DNA fragments selected randomly” based on the testimony of Lo’s expert. The Board then found that Passage B “expressly describe[s] random sequencing” because it used the phrase “random sequence information” in the sentence “about 30 bp of random sequence information are needed to identify a sequence as belonging to a specific human chromosome.” But the Board subsequently found that Balasubramanian and the “30 bp of random sequence information are needed to identify a sequence” sentence were not sufficient to meet the requirements of § 112. Passages A and B provided “some express description of individual elements recited in Quake’s claims,” but these disclosures were insufficient to demonstrate that the inventors were in possession of a method of determining fetal aneuploidy with random massively parallel sequencing as claimed by Quake, because the ’018 patent (1) “does not tie these elements together into a complete method” and (2) “does not explain how to use the data from random massively parallel sequencing of a mixture of genomic DNA to determine fetal aneuploidy.”
Quake appealed the Board’s written description finding. The primary issue on appeal was whether the patent specification shared by the ’018 patent and the ’833 application sufficiently described using random MPS to determine fetal aneuploidy, such that it meets the requirements of § 112. The Court found that substantial evidence supported the Board’s findings on lack of adequate written description and affirmed the Board’s findings.
The Court addressed the Board’s findings as to the Balasubramanian citation in Passage A and the single sentence in Passage B, and then its treatment of the chromosome size adjustment necessary for claimed step D. The Court agreed with the Board that the citation to Balasubramanian provided some disclosure of massively parallel sequencing of DNA fragments selected randomly, but noted that skilled artisans would have understood the specification to support targeted MPS.
As for Passage B, first, the Board found that simply using the word “random” was not enough to indicate random MPS (“finding that the phrase “randomly fragmented genomic DNA” from Passage A is “not necessarily the same” as the phrase referring to random MPS in the claims”). Second, the 30 bp language covers identifying the chromosomes of origin for DNA fragments generated through targeted MPS. The Court agreed with the Board that the 30 bp sentence was more generally “about the number of base pairs needed to identify the chromosomal origin of a sequence.” There was no indication in the record that the length of a sequence needed to identify the chromosome of origin was any different for DNA fragments sequenced via random and targeted MPS. However, given the specification’s repeated discussion of targeted sequencing, a bare citation to Balasubramanian and use of the phrase “about 30 bp of random sequence information are needed to identify a sequence” in the context of the patent “would be a highly elliptical, cryptic way to communicate possession of a second method of sequencing to determine fetal aneuploidy. An alternative explanation consistent with the entire patent specification is that Quake invented using targeted MPS for determining fetal aneuploidy and wrote the ’018 patent specification to describe targeted MPS, among other ways of performing targeted detection such as digital PCR.”
The Court noted that in light of the limited disclosure value of the single Balasubramanian citation and the “about 30 bp of random sequence information are needed to identify a sequence” sentence, substantial evidence supported the Board’s finding that those two items together were not adequate to convey using random MPS to determine fetal aneuploidy as claimed. “In terms of Ruschig’s analogy of the written description requirement being akin to creating a trail through the woods, the two are (at most) faint “blaze marks” for determining fetal aneuploidy by random MPS, while the rest of the specification marks a clear trail to targeted MPS. In re Ruschig, 379 F.2d 990, 994–95 (CCPA 1967).”
The Court agreed with the Board that if the ’018 patent had contained some description of adjusting for chromosome size when comparing the data resulting from the MPS step, then a skilled artisan might have had an indirect, but clear indication that the inventor contemplated a method of using random MPS to determine fetal aneuploidy. There was no discussion of adjusting for chromosome size before performing those statistical analyses. The Board was correct that “[i]n the absence of a description of such analysis, [the] teachings in the specification about [the Balasubramanian] equipment useful for random massively parallel sequencing and techniques for determining sequences are not sufficient to demonstrate possession of the claimed method.”
The Court agreed that the claims in Quake’s patent, directed to random MPS, were unpatentable and found that the patent's specification focused primarily on targeted MPS. While a limited number of references to non-targeted DNA sequences were made in the disclosure, there was no embodiment describing the specific statistical analysis needed to determine the presence of a chromosomal abnormality from data generated by random MPS. The Court concluded that substantial evidence supported the Board’s finding that those two items together were not adequate to convey using random MPS to determine fetal aneuploidy as claimed.
To satisfy the written description requirement, a patent application has to provide sufficient disclosure of what is claimed, i.e., provide trails by making blaze marks on trees to find one’s way through the woods of a specification such that a skilled artisan would be able to follow that trail and understand what the inventors had invented. For example for method claims, to satisfy the written description requirement, the claimed method as a whole must be described by the specification. It is important to understand potential embodiments and desired scope of the claims when drafting an application and to describe the embodiments broadly and specifically so that if claims need to be amended during prosecution, e.g., to remove cited references, the description would support such amendments. A prior art search is recommended, while drafting, to help assess the extent of necessary disclosures. A more explicit disclosure, rather than obscure “blaze marks,” may be necessary to support a desired scope of the claims.
Quake v. Lo, Case Nos. 18-1779, -1780, -1782 (Fed. Cir. July 10, 2019)