A diagnostic method that raises, not patent-eligibility, but written description issues.

Nicolas Seckel | July 24, 2017

Stanford Univ. v. The Chinese Univ. of Hong Kong (Precedential)

June 27, 2017

Before O’Malley, Reyna, and Chen.  Opinion by O’Malley.


In interferences involving a patent by Stanford and applications by the Chinese University of Hong Kong, the USPTO found the Stanford patent’s claims unpatentable as lacking written description. The Federal Circuit vacated and remanded. The USPTO was faulted for relying on post-filing date information as evidence of what the person of the art knew at the filing date.


These interferences before the U.S. Patent and Trademark Office’s Patent Trial and Appeal Board (PTAB) pitched Steven Quake for Stanford University against Dennis Lo for the Chinese University of Hong Kong (CUHK). The invention in dispute is a method of diagnosing genetic abnormalities (“aneuploidies”) of a fetus by testing the cell-free fetal DNA (cff-DNA) which is present in maternal blood. The method provides a non-invasive test to detect too many or too few chromosomes, such as trisomy 21 (Down’s syndrome).

The discovery of cff-DNA is attributed to Dennis Lo. In 2015, basic diagnostic claims for detecting this cff-DNA were held unpatentable as directed to the observation of a natural phenomenon (Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015)), but the claims at issue in these interferences raised written description, not patent-eligibility issues.

For Stanford, Steven Quake and others filed a first patent application in February 2007, followed by a continuation application which resulted in the ‘018 patent. For CUHK, Dennis Lo and others filed a provisional application in July 2007, followed by a nonprovisional ‘275 application. The three interferences whose appeals were consolidated involved Lo’s (CUHK’s) ‘275 application and Quake’s (Stanford’s) 018 patent, and related applications.

The testing method whose priority was in dispute is generally as follows:

1) obtain a test sample from the mother (for example, a blood sample),

2) distribute single DNA molecules from the test sample into a large number of reaction samples,

3) detect the target in the DNA of the large number of reaction samples,

4) perform quantitative analysis leading to detection.

The interference dispute centered on the detection step, which is performed using a technique called “massive parallel sequencing” (“MPS”). There are two types of MPS: “targeted” MPS, where the target DNA is amplified and counted using target-specific primers, and “random” MPS, in which all DNA is linked to a “leader” and amplified using a primer for the leader. Lo’s application claimed random MPS, and Quake’s continuation application that resulted in the 018 patent was amended to also claim detection of the DNA fragments using random MPS. The Quake patent description focused generally on a “digital analysis” method in order to differentiate “target sequences”, and on the use of “MPS”. The initial claims in Quake’s application recited detecting “target sequences” and “different target sequences”. For descriptive support of the claimed “random” MPS, Stanford pointed to a mention in the Quake patent description about performing MPS using the “Illumina sequencing platform”.

The PTAB held that the Quake patent claims lacked written description. The PTAB relied heavily on CUHK’s expert, who opined that the person of the art at the relevant filing date would have known that the Illumina sequencing platform could be used, not only for random MPS, but also for targeted MPS, so that the person of the art would not understand the reference to the Illumina sequencer in the Quake patent’s description as a disclosure of random MPS. The PTAB concluded that since the reference to Illumina “does not preclude” targeted MPS, “the facts do not indicate that those of ordinary skill in the art would have understood the inventors had put these pieces together into a complete method of sequencing random DNA fragments”.

The Federal Circuit found that the PTAB’s conclusion lacked substantial evidence, because it relied on unsupported statements by CUHK’s expert about the knowledge of the person of the art at the relevant filing date. CUHK’s expert relied on post-filing date publications about a similar sequencer, the “Roche 454” sequencer. Post-filing date information may be relevant to evidence the state of the art at the critical date, such as the non-existence of a particular class of later-developed amorphous polymers (evidencing sufficient written description in In re Hogan, 559 F.2d 595 (CCPA 1977)), or the desirability but non-feasability of a genetic transformation on monocotyledons (evidencing lack of written description in Plant Genetic Sys., N.V. v. DeKalb Genetics Copr., 315 F.3d 1335 (Fed. Cir. 2003)). But post-filing date publications cannot be used to prove pre-filing date knowledge of facts by the person of the art, which was the relevant question here in interpreting the reference to the Illumina sequencer in the written description.

In addition, the Federal Circuit criticized the PTAB for not explaining how it found the expert’s discussion of the Roche 454 sequencer relevant to the capabilities of the Illumina sequencer, and for failing to explore the meaning of other passages of the Quake patent’s description which appeared more detailed on MPS (“using attachment of randomly fragmented genomic DNA”…)

The case was remanded to the PTAB to re-evaluate the written description issue. The Federal Circuit suggested that the PTAB should focus on evidence of whether the post-filing date publications contain information on pre-filing date facts regarding random MPS sequencing.


In drafting a patent application, it is beneficial, not only to describe multiple embodiments, but also to list features and capabilities of materials and equipment used in making and using these embodiments. When developing evidence in a contested proceeding or in litigation, post-filing information can be used as evidence of pre-filing facts, but not as evidence of the knowledge of such facts by the person of the art.

Procedural note:

Initially, the case had been appealed from the PTAB to the District Court for the Northern District of California, but it was transferred to the Federal Circuit after the Federal Circuit’s 2015 decision holding that for interferences declared after September 15, 2012, the American Invents Act excludes an intermediate appeal to the District Court (Biogen MA, Inc. v. Japanese Found. for CancerResearch, 785 F.3d 648 (Fed. Cir. 2015)). The Federal Circuit did not consider the discovery that had taken place in the N.D. Cal, but it did not take position whether the PTAB on remand should reopen the record for more evidence.


Claim 1 of U.S. Pat. No. 8,008,018 to Quake (Stanford) involved in the interference:

 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 tissue 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 Stanfordof 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 determining the presence or absence of said fetal aneuploidy.

Full Opinion

U.S. Patent 8,008,018 B2

U.S. Pub. No.: 2011/0318734 A1


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