Boxlnterference@uspto.gov
`571.272.4683
`
`Filed: April 7, 2014
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`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`HEI-MUN CHRISTINA FAN and STEPHEN QUAKE
`Junior Party
`(Patent 8,195,415),
`
`v.
`
`YUK-MING DENNIS LO, ROSSA WAI KWUN CHIU, and KWAN CREE
`CHAN
`Senior Party
`(Application 13/070,266),
`
`Patent Interference No. 105,922 (DK)
`(Technology Center 1600)
`
`Decision on Motions
`
`Bd. R. 125(a)
`
`Before, FRED E. McKELVEY, RICHARD E. SCHAFER, and DEBORAH KATZ,
`Administrative Patent Judges.
`
`KATZ, Administrative Patent Judge.
`
`STANFORD EXHIBIT 2116
`SEQUENOM v. STANFORD
`CASE IPR2013-00390
`
`
`571.272.4683
`
`Filed: April 7, 2014
`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`BEFORE THE PATENT TRIAL AND APPEAL BOARD
`
`HEI-MUN CHRISTINA FAN and STEPHEN QUAKE
`Junior Party
`(Patent 8,195,415),
`
`v.
`
`YUK-MING DENNIS LO, ROSSA WAI KWUN CHIU, and KWAN CREE
`CHAN
`Senior Party
`(Application 13/070,266),
`
`Patent Interference No. 105,922 (DK)
`(Technology Center 1600)
`
`Decision on Motions
`
`Bd. R. 125(a)
`
`Before, FRED E. McKELVEY, RICHARD E. SCHAFER, and DEBORAH KATZ,
`Administrative Patent Judges.
`
`KATZ, Administrative Patent Judge.
`
`STANFORD EXHIBIT 2116
`SEQUENOM v. STANFORD
`CASE IPR2013-00390
`
`
`
`Interference 105,922
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`
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`I. Statement of the Case
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`The interference is before a panel for consideration of the pending non-
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`priority motions. An oral argument was held on 25 February 2014. (Transcript,
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`Paper 99.)
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`Hei-Mun Christina Fan and Stephen Quake (“Fan”) present Motion 1
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`(Paper 26) to argue that it should be accorded an earlier constructive reduction to
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`practice (i.e., benefit for the purpose of priority) of application 61/098,758, which
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`was filed 20 September 2008. Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, and
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`Kwan Chee Chan (“Lo”) do not oppose Fan Motion 1. We grant Fan Motion 1.
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` Fan also presents Motion 2 (Paper 27) and Motion 3 (Paper 28), arguing,
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`respectively, that the specification of the involved Lo application lacks written
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`description and enabling support for the involved Lo claims and that Lo should not
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`have been accorded benefit (i.e., an earlier constructive reduction to practice) of its
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`earlier applications. We deny Fan Motions 2 and 3.
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`Finally, Fan presents Motion 4 (Paper 31), arguing that Fan claim 14 should
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`not have been designated at corresponding to the Count. We deny Fan Motion 4.
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`Lo does not present any motions in this phase of the interference.
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`II. The Parties
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`a. Fan
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`Fan is involved based on the patent 8,195,415 (“the Fan ’415 patent”), which
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`issued 5 June 2012, from application 12/696,509, filed 29 January 2010. Upon
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`declaration, Fan was accorded the benefit of application 12/696,509, filed
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`Interference 105,922
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`29 January 2010, and application 12/560,708, filed 16 September 2009.
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`(Declaration, Paper 1.)
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`Fan represents that its involved application is assigned to The Board of
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`Trustees of the Leland Stanford Junior University. Fluidigm Corporation and
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`Verinata Health, Inc, a wholly owned subsidiary of Illumina, Inc., are identified as
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`licensees. (Paper 9.) Fan also represents that the United States government has
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`certain rights in the patent. (Id.)
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`Fan relies on the testimony of J. Chris Detter, Ph.D. (See Declaration of
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`John Chris Detter, Ph.D. (“Detter Decl.”), Exh. 2050.) Dr. Detter testifies that he
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`has a Ph.D. in molecular genetics and microbiology and that he has held several
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`positions leading genomic sequencing and computational biology groups. (Detter
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`Decl., Exh. 2050, at ¶¶ 3-5.) Dr. Detter testifies that he is currently the Genome
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`Sciences Center Director and Group Leader (B-6) and the Acting Bioscience
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`Deputy Divisional Leader, responsible for programmatic, strategic, and tactical
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`mission areas for bioscience at Los Alamos National Laboratory. (Id. at ¶ 6.)
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`Dr. Detter’s curriculum vitae shows that he has authored numerous research papers
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`regarding genome sequencing of various organisms. (Curriculum Vitae, Exh.
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`2051; see Detter Decl., Exh. 2050, ¶ 8.) In light of his testimony, Dr. Detter is
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`qualified to testify as an expert about the subject matter of this interference.
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`b. Lo
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`Lo is involved based on application 13/070,266 (“the Lo ’266 application”),
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`which was filed 23 March 2011. Lo was accorded the benefit of 12/614,350,
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`Interference 105,922
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`which was filed 6 November 2009, and application 12/178,181, which was filed
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`23 July 2008.
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`Lo represents that at least application 13/070,266 is assigned to The Chinese
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`University of Hong Kong and that Sequenom, Inc. is a licensee. (Paper 4.)
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`Lo relies on the testimony of Stacey Bolk Gabriel, Ph.D. (See Declaration of
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`Stacey Bolk Gabriel, Ph.D. (“Gabriel Decl.”), Exh. 1076.) Dr. Gabriel testifies that
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`she received a Ph.D. degree in genetics in 1998. (Id., ¶ 10.) She testifies further
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`that she has held several positions related to mapping and sequencing the human
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`genomes. (Id., ¶¶ 12-18.) Dr. Gabriel testifies that she is currently the Director of
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`the Genomics Platform of the Broad Institute, which according to Dr. Gabriel, is
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`the largest genome center in the United States. (Id. at ¶ 19.) Dr. Gabriel testifies
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`that she has served on several editorial and advisory boards related to genomic
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`research and that she has authored over 100 peer-reviewed publications involving
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`the application of sequencing technology to the study of human disease. (Id. at
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`¶¶ 20-22.) In light of her testimony, Dr. Gabriel is qualified to testify as an expert
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`about the subject matter of this interference.
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`c. Related Proceedings
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`The involved Lo ’266 application and involved Fan ’415 patent are related
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`to applications and patents involved in concurrent Interferences 105,920, 105,923,
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`and 105,924.1 The Fan (referred to as “Quake”) patents and applications in those
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`1 Interference 105,920 involves Lo application13/070,275 and Quake patent
`8,008,018. Similarly, Interference 105,923 involves Quake application 12/393,833
`and Lo applications 12/178,181; 13/070,240; 12/614,350; and 13/070,251.
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`Interference 105,922
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`interferences are not in the same direct lineage as the involved Fan ’415 patent, but
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`have the same real party-in-interest. As in the current interference, the counts of
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`these concurrent interferences are drawn to methods of detecting chromosomal
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`abnormalities.
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`Inter Partes Review (“IPR”) 2013-00390 is also related to this interference.
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`Review was instituted following a petition filed by Sequenom, Inc. (the real party-
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`in-interest of Lo) against the patentability of the claims of currently involved Fan
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`’415 patent. Sequenom, Inc. argues that the Fan ’415 patent claims are
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`unpatentable over Lo application 12/178,181 (published as U.S. Patent Application
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`Publication 2009/0029377), which is a parent of the Lo ’266 application involved
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`in this interference. A final decision has not been entered in the IPR.
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`III. The Subject Matter
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`The parties claim methods of testing for an abnormal distribution of
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`chromosomes in a person’s cells, a condition called “aneuploidy.” The claimed
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`methods can be used to test for conditions including Down Syndrome, in which
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`chromosome 21 is aneuploid, with three copies instead of the normal two copies.
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`In the past, these chromosomal abnormalities were diagnosed with invasive
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`procedures such as amniocentesis or chorionic villus sampling. The parties’ claims
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`are drawn to methods that allow for the diagnosis of aneuploidies with a simple
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`blood test.
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`In general, the methods include the determination of a ratio between the
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`number of different chromosomes in the blood sample without distinguishing
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`Interference 105,924 involves Lo application 13/417,119 and Quake application
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`Interference 105,922
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`between the chromosomes of the mother and fetus. The ratio of chromosomes
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`suspected of being aneuploid to the number of chromosomes not likely to be
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`aneuploid indicates whether there is an extra or missing chromosome. To count
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`chromosomes, small portions of the DNA present in the blood sample are
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`sequenced and aligned to reference chromosomes to identify with a specific
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`chromosome. This method requires sequencing of many, many such “sequence
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`tags” to make a statistically significant determination of aneuploidy. (Fan ’415
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`patent, 3:35-64; Detter Decl., Exh. 2050, at ¶ 34.)
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`IV. Fan Motion 2
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`Fan requests that we find that the specification of the involved Lo ’266
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`application fails to provide sufficient written description supporting Lo claims
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`designated as corresponding to the Count. (Fan Motion 2, Paper 27, at 1:3-11.)
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`Under 35 U.S.C. § 1122 the
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`specification shall contain a written description of the invention, and
`of the manner and process of making and using it, in such full, clear,
`concise, and exact terms as to enable any person skilled in the art to
`which it pertains, or with which it is most nearly connected, to make
`and use the same . . . .
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`To determine if a claim complies with this statute, we ask, “whether the
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`disclosure of the application relied upon reasonably conveys to those skilled in the
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`art that the inventor had possession of the claimed subject matter as of the filing
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`12/393,833.
`2 Patent interferences continue under the relevant statutes in effect on 15 March
`2013. Pub. L. 112-29, § 3(n), 125 Stat. 284, 293 (2011).
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`Interference 105,922
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`date.” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F3d 1336, 1351 (Fed. Cir. 2010).
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`We need not find literal support for claim terms in a specification to find that the
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`claims are sufficiently supported, as long as the specification reasonably conveys
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`to the artisan that the inventor had possession at the time of the later claimed
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`subject matter. See In re Kaslow, 707 F.2d 1366, 1375 (Fed. Cir. 1983).
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`Compliance with the written description requirement is a question of fact, Yorkey
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`v. Diab, 601 F.3d 1279, 1283 (Fed. Cir. 2010), which is often case-specific, see In
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`re Wertheim, 541 F.2d 257, 262, 191 USPQ 90, 96 (CCPA 1976) (“The primary
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`consideration is factual and depends on the nature of the invention and the amount
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`of knowledge imparted to those skilled in the art by the disclosure.”).
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`Fan argues that the Lo specification fails to support one of the steps of the
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`method recited in Lo’s claims, focusing specifically on the term “windows.” (Fan
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`Motion 2, Paper 27, at 1:3-11.) According to Fan, the term should be narrowly
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`construed in include limitations not literally described in Lo’s specification. Fan
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`carries the burden of persuading us that Lo’s claims must be construed under this
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`limited construction and that the Lo specification does not support a method with
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`such a limitation. See 37 C.F.R. § 41.121(b) (“The party filing the motion has the
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`burden of proof to establish it is entitled to the requested relief.”).
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`Fan and Lo agree that because Lo copied its claims from Fan’s involved
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`’415 patent, Lo’s claims must be construed according to the specification of the
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`Fan ’415 patent. (See Fan Motion 2, Paper 27, at 3:9-11, and Material Fact (“MF”)
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`6; see Lo Opp. 2, Paper 49, at 3:2-5, and response to Fan MF6.) See Agilent Tech.,
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`Inc. v. Affymetrix, Inc., 567 F.3d 1366, 1375 (Fed. Cir. 2009) (“when a party
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`Interference 105,922
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`challenges written description support for an interference count or the copied claim
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`in an interference, the originating disclosure provides the meaning of the pertinent
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`claim language.”).
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`The following findings of fact, as well as others presented elsewhere in this
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`opinion, are supported by a preponderance of the evidence.
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`Findings of Fact
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`1.
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`Lo independent claim 24 recites:
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`A method of testing for an abnormal distribution of a specified
`chromosome portion in a mixed sample of normally and abnormally
`distributed chromosome portions obtained from a subject, the method
`comprising:
`(a) sequencing DNA from the mixed sample to obtain
`sequences from multiple chromosome portions, wherein said
`sequences comprise a number of sequence tags of sufficient length of
`determined sequence to be assigned to a chromosome location within
`a genome;
`(b) assigning the sequence tags to corresponding chromosome
`portions including at least the specified chromosome by comparing
`the determined sequence of the sequence tags to a reference genomic
`sequence;
`(c) determining values for numbers of sequence tags mapping
`to chromosome portions by using a number of windows of defined
`length within normally and abnormally distributed chromosome
`portions to obtain a first value and a second value therefrom; and
`(d) using the values from step (c) to determine a differential,
`between the first value and the second value, which is determinative
`of whether or not the abnormal distribution exists.
`
`
`
`(Lo Clean copy of Claims, Paper 7 (emphasis added).)
`
`2.
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`The Fan ’415 patent provides that
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`Interference 105,922
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`a number of windows of defined length are created along a
`chromosome, the windows being on the order of kilobases in length,
`whereby a number of sequence tags will fall into many of the
`windows and windows covering each entire chromosome in question,
`with exceptions for non-informative regions, e.g., centromere regions
`and repetitive regions.
`
`(Fan ’415 patent, Exh. 2011, at 4:53-59.)
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`3.
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`The Fan ’415 patent provides that “[b]y counting sequence tags within
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`a series of predefined windows of equal lengths along different chromosomes,
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`more robust and statistically significant results may be obtained.” (Fan ’415
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`patent, Exh. 2011, at 4:61-64.)
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`4.
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`Fan’s witness, Dr. Detter testifies that using “windows” in the method
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`described in the Fan ’415 specification enables an improved statistically significant
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`comparison because the windows eliminate the over- and under-representation of a
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`particular chromosome, or chromosome portion that could be due to bias, such as
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`sequencing bias, but not to aneuploidy. (Detter Decl., Exh. 2050, at ¶ 44.)
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`5.
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`Dr. Detter testifies that an additional advantage of using “windows of
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`defined length” is to mitigate the computational demand of whole genome
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`sequencing because when isolated, predefined windows of equal length are
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`considered, the mapping of the millions of sequencing tags generated can become
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`more manageable. (Detter Decl., Exh. 2050, at ¶ 45.)
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`6.
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`Dr. Detter testifies that another advantage of using “windows of
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`defined length” is that the results are more informative because the examination of
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`smaller amounts of information at a time makes it easier to identify the presence of
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`Interference 105,922
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`an abnormal amount of chromosomes or chromosome portions. (Detter Decl.,
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`Exh. 2050, at ¶ 45.)
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`7.
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`Dr. Detter explains that Figure 9 of the Fan ’415 patent is a schematic
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`showing a method in which one segments a chromosome into windows and then
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`counts the sequence tags that map to particular windows to determine a
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`representative number of sequence tags for the chromosome, allowing one to
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`calculate a normalization constant for that chromosome. (Detter Decl., Exh. 2050,
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`at ¶¶ 47 and 48.)
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`8.
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`Dr. Detter testifies that the normalization constant determined for each
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`chromosome using “windows” of equal length, as depicted in Figure 9, can detect
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`over or under-representation of a chromosome without using an external reference.
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` (Detter Decl., Exh. 2050, at ¶¶ 47 and 48.)
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`9.
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`Dr. Detter testifies that “windows,” as provided in the Fan ’415
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`specification, may be used to compensate for sequence bias that may arise as a
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`result of nucleotide content, such as for the guanosine and cytosine base content
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`(“G/C content”). (Detter Decl., Exh. 2050, at ¶ 49-54.)
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`10. Dr. Detter testifies that after reviewing the Lo ’266 application and its
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`file history, he cannot identify any written description support for the claim term
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`“using a number of windows of defined length within normally and abnormally
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`distributed chromosome portions.” (Detter Decl., Exh. 2050, at ¶¶ 58 and 91.)
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`11. Lo’s witness, Dr. Gabriel testifies that one of skill in the art would
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`interpret the word “windows” in the Fan ’415 patent specification as predefined
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`subsections of a chromosome. (Gabriel Decl., Exh. 1076, ¶¶ 33, 43, 49, and 55.)
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`Interference 105,922
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`12. Dr. Gabriel testifies that “windows” as provided in the Fan ’415
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`patent specification are not required to have the same length. (Gabriel Decl., Exh.
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`1076, ¶¶ 43, 48, 50, and 53.)
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`13. Dr. Gabriel testifies that Dr. Detter’s understanding of “windows” is
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`based only on preferred embodiments provided in the Fan ’415 patent
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`specification, but that the patent provides a broader disclosure overall. (Gabriel
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`Decl., Exh. 1076, ¶ 47.)
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`14. Dr. Gabriel testifies that a person of skill in the art would understand
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`the disclosure of the Fan ’415 patent specification:
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`By analyzing sequence tag density in predefined subsections of
`chromosomes (e.g., 10 to 100 kb windows), a normalization constant
`can be calculated, and chromosomal subsections quantified (e.g.,
`21q22.2).
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`(Fan ’415 patent, Exh. 2011, at 4:9-12), to mean that “windows” are predefined
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`subsections of chromosomes that may vary in length from 10 to 100 kb and are not
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`required to be of equal length. (Gabriel Decl., Exh. 1075, ¶ 50.)
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`15. Dr. Gabriel testifies that a person of skill in the art would understand
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`the disclosure of the Fan ’415 patent specification:
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`Each autosome (chr. 1-22) is computationally segmented into
`contiguous, non-overlapping windows. (A sliding window could also
`be used). Each window is of sufficient length to contain a significant
`number of reads (sequence tags, having about 20-100 by [sic – bp] of
`sequence) and not still have a number of windows per chromosome.
`Typically, a window will be between 10 kb and 100 kb, more
`typically between 40 and 60 kb.
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`Interference 105,922
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`(Fan ’415 patent, Exh. 2011, at col. 5:4-11), to mean that “windows” are
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`predefined subsections of chromosomes that are contiguous, non-overlapping
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`segments and are typically between 10 to 100 kb, more typically between 40 and
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`60 kb, but are not required to be of equal length. (Gabriel Decl., Exh. 1075, ¶ 53.)
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`16. The Lo ’266 application provides the following:
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`Embodiments of this invention provide methods, systems, and apparatus
`for determining whether an increase or decrease (diseased state) of a
`clinically-relevant chromosomal region exists compared to a non-
`diseased state. This determination may be done by using a parameter of
`an amount of a clinically-relevant chromosomal region in relation to
`other non-clinically-relevant chromosomal regions (background regions)
`within a biological sample. Nucleic acid molecules of the biological
`sample arc sequenced, such that a fraction of the genome is sequenced,
`and the amount may be determined from results of the sequencing. One
`or more cutoff values are chosen for determining whether a change
`compared to a reference quantity exists (i.e. an imbalance), for example,
`with regards to the ratio of amounts of two chromosomal regions (or sets
`of regions).
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`The change detected in the reference quantity may be any deviation
`(upwards or downwards) in the relation of the clinically-relevant nucleic
`acid sequence to the other non-clinically-relevant sequences. Thus, the
`reference state may be any ratio or other quantity (e.g. other than a 1-1
`correspondence), and a measured state signifying a change may be any
`ratio or other quantity that differs from the reference quantity as
`determined by the one or more cutoff values.
`
`(Lo ’266 application, Exh. 2016, ¶¶ [0061] and [0062].)
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`17. The Lo ’266 application provides that
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`dosage imbalance of a particular chromosome or chromosomal regions
`can be quantitatively determined. In other words, the dosage imbalance
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`Interference 105,922
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`of the chromosome or chromosomal regions is inferred from the
`percentage representation of the said locus among other mappable
`sequenced tags of the specimen.
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`(Lo ’266 application, Exh. 2016, ¶ [0078].)
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`18. Dr. Gabriel testifies that one of ordinary skill in the art would have
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`understood “chromosomal regions” as discussed in the ’266 application to be used
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`to compare the number of sequence tags originating from a clinically relevant
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`chromosomal region, or test window, relative to the number of sequence tags
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`originating from a non-clinically relevant chromosomal region, or background
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`reference, window to determine whether a chromosomal dosage imbalance exists.
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`(Gabriel Decl., Exh. 1076, ¶ 63.)
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`19. Dr. Gabriel testifies that the “chromosomal regions” discussed in the
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`Lo ’266 application are used in the same way as the “windows” discussed in the
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`’415 patent. (Gabriel Decl., Exh. 1076, ¶ 63.)
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`Analysis
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`To analyze whether the Lo ’266 application supports the term “using a
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`number of windows of defined length within normally and abnormally distributed
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`chromosome portions” in Lo’s claims, we must construe the term “windows.”
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`First, we look to the plain language of the claims. Although claim terms are
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`construed in light of the context of the entire patent, the claims themselves provide
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`“substantial guidance” for the meaning of particular terms. Phillips v. AWH Corp.,
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`415 F.3d 1303, 1314 (Fed. Cir. 2005) (en banc); see also See Aria Diagnostics,
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`Inc. v. Sequenom, Inc., 726 F.3d 1296, 1300-01 (Fed. Cir. 2013) (refusing to
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`narrowly construe the term “paternally inherited nucleic acid” where the claim
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`Interference 105,922
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`language did not incorporate any inherent meaning about the timing or method
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`detecting the paternal characteristic and neither the specification nor the
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`prosecution history showed a clear statement of intent to limit the term).
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`The only purpose of the “windows” stated in Lo’s copied claims is to
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`determine “values” for numbers of sequence tags mapped to the chromosome
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`portions, specifically “a first value and a second value,” which are then used in step
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`(d) to determine whether or not an abnormal distribution exists. The claims do not
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`expressly indicate that the “windows” are to be used for normalization against any
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`biases and do not expressly indicate that the “windows” must be of equal length.
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`Fan has not directed us to evidence that “windows” is a term of art that skilled
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`artisans would have known inherently indicates equal length or a specific
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`normalization protocol. Thus, if we are to limit step (c) beyond its express
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`language, we must find a reason to do so from other sources. See Telemac Cellular
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`Corp. v. Topp Telecom, Inc., 247 F.3d 1316, 1324 (Fed. Cir. 2001) (“Unless
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`something in the written description suggests that the patentee intended the
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`unambiguous language to be construed in a manner inconsistent with its ordinary
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`meaning, we are bound by that language.”).
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`Fan directs us to the specification of the Fan ’415 patent, arguing that it
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`limits the purpose of the claimed “windows” to be for calculating a normalization
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`constant. (Fan Reply 2, Paper 55, at 2:6-8.) Fan argues further that the
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`specification of the Fan ’415 patent makes clear that these “windows” must be of
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`equal length. (Id. at 2:8-14.) Fan does not point to an express definition of the
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`term “windows” in the specification that includes an “equal length” limitation.
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`Interference 105,922
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`Pointing generally to columns 3-5 and 22 of the specification, Fan asserts
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`“windows” are a unit of defined length created along a chromosome, possibly
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`along the whole length of the chromosome, except at the centromere and repetitive
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`regions. (Fan Motion 2, Paper 27, at 4:19-24; see Finding of Fact (“FF”) 2, Fan
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`’415 patent, Exh. 2011, at 4:53-59.) Though there are portions of the specification
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`discussing “windows” of equal length (see, e.g., Fan ’415 patent, Exh. 2011, at
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`4:61-64), Fan does not point to language in the specification requiring all
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`“windows” be of equal length. Furthermore, even though “windows” of equal
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`length were disclosed, the Fan claims that Lo copied do not include this language
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`as an express limitation of the claimed methods.
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`In support of its argument for a narrow construction of the term “windows,”
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`Fan relies on the testimony of Dr. Detter, who explains that using windows allows
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`for an improved statistical significance of the comparison between suspected
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`abnormally and normally distributed chromosomes. (FF 4, Detter Decl., Exh.
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`2050, at ¶ 44; see also FFs 7-9, Detter Decl., Exh. 2050, at ¶¶ 47-54.) But, Dr.
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`Detter also explains that using windows mitigates the computational demand of
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`whole genome sequencing by making an amount of sequence more manageable
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`and makes the results more informative by examining smaller amounts of
`
`information. (FFs 5 and 6, Detter Decl., Exh. 2050, at ¶ 45.) Therefore, though we
`
`agree that the Fan ’415 patent specification provides for using “windows” of equal
`
`length for a particular normalization protocol, Dr. Detter’s testimony indicates that
`
`“windows” can be used for other purposes related to the methods described in the
`
`Fan ’415 patent specification.
`
`-15-
`
`
`
`
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`Interference 105,922
`
`
`
`We note that the passage of the Fan ’415 specification referring to
`
`“windows” of equal length appears to qualify their purpose as being only to obtain
`
`better results. The specification provides: “By counting sequence tags within a
`
`series of predefined windows of equal lengths along different chromosomes, more
`
`robust and statistically significant results may be obtained.” (Fan ’415 patent, Exh.
`
`2011, at 4:61-64.) Because the Lo claims do not restrict the statistical significance
`
`of the results obtained by the claimed method, we are not persuaded that the recited
`
`method must use “windows” of equal length. (See Lo Opp. 2, Paper 49, at
`
`10:10-15.) By referring to “more robust and statistically significant results” when
`
`“windows” of equal length are used (Fan ’415 patent, Exh. 2011, at 4:61-64
`
`(emphasis added)), the passage in the Fan ’415 specification indicates to one
`
`skilled in the art that “windows” of unequal length could be used in the claimed
`
`method, though with less robust results.
`
`When we look to the specification for guidance in construing claim terms,
`
`we avoid limitations that are reflected only in specific embodiments, particularly if
`
`those embodiments are not reflected in the claims. See Aventis Pharma S.A. v.
`
`Hospira, Inc., 675 F.3d 1324, 1330 (Fed. Cir. 2012) (it is “not enough that the only
`
`embodiments, or all of the embodiments, contain a particular limitation to limit a
`
`claim term beyond its ordinary meaning.”); see also Liebel-Flarsheim Co. v.
`
`Medrad, Inc., 358 F.3d 898, 906 (Fed. Cir. 2004) (“Even when the specification
`
`describes only a single embodiment, the claims of the patent will not be read
`
`restrictively unless the patentee has demonstrated a clear intention to limit the
`
`claim scope using ‘words or expressions of manifest exclusion or restriction.’”
`
`-16-
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`
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`Interference 105,922
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`
`
`(quoting Teleflex, Inc. v. Ficosa N. Am. Corp., 299 F.3d 1313, 1327
`
`(Fed.Cir.2002))). Fan has not persuaded us that the specification of the Fan ’415
`
`patent exhibits intent to limit the term “windows” to regions that must be used for a
`
`specific normalization protocol or must be of equal length.
`
`Lo argues that instead of Fan’s narrow construction, the term “window” is
`
`properly construed more broadly as “predefined subsections of a chromosome” or
`
`a “chromosomal region,” as that term is used in the Lo ’266 application. (Lo Opp.
`
`2, Paper 49, at 5:24-26 and 34:2-3, Material Fact (“MF”) 101.) We give claims
`
`their broadest reasonable interpretation. See Harari v. Lee, 656 F.3d 1331, 1334
`
`(Fed. Cir. 2011) (“Because this is an interference and Harari substantially copied
`
`Lee claim 1, we give the claim its broadest reasonable construction in light of the
`
`Lee patent specification.”); In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364
`
`(Fed.Cir.2004) (providing that the Patent and Trademark Office determines the
`
`scope of claims in patent applications by giving them their broadest reasonable
`
`construction in light of the specification as interpreted by one of ordinary skill in
`
`the art.). Thus, we must determine whether Lo’s construction is unreasonably
`
`broad.
`
`Lo relies on the testimony of Dr. Gabriel to argue that the windows of the
`
`Fan ’415 patent and the “chromosomal regions” of the Lo ’266 application are both
`
`used to compare a ratio of the number of sequence tags originating from a
`
`clinically relevant region relative to the number of sequence tags from a non-
`
`clinically relevant region. (Lo Opp. 2, Paper 49, at 6:33-7:3; FF 19, Gabriel Decl.,
`
`Exh. 1076, ¶ 63.) Fan argues that this construction is not reasonable because it
`
`-17-
`
`
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`
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`Interference 105,922
`
`
`
`allows a “window” to be the polynucleotide being tested for a potential aneuploidy,
`
`while the “windows” referred to in the Fan ’415 patent specification are not being
`
`tested for aneuploidy. (Fan Reply 2, Paper 55, at 4:22-6:13.) As discussed above,
`
`though, Fan has not persuaded us that the term “windows” refers only to regions
`
`used for normalization.
`
`Instead, returning to the language of step (c) in Lo claim 24, and substituting
`
`Lo’s asserted meaning of “windows,” Dr. Gabriel’s testimony supports the finding
`
`that one of skill could
`
`determin[e] value[s] for the number of sequence tags mapping to
`chromosome portions by using a number of [“predefined subsections
`of a chromosome” or a “chromosomal regions”] of defined length
`within the normally and abnormally distributed chromosome portions
`to obtain a first value and a second value therefrom
`
`(Lo Clean Copy of Claims, Paper 7), in order to determine whether or not an
`
`abnormal chromosome distribution exists. (FF 18, Gabriel Decl., Exh. 1076, ¶ 63.)
`
`Fan does not direct us to other evidence supporting its argument that Lo’s broader
`
`interpretation is unreasonable. Accordingly, on the record before us, Lo’s
`
`interpretation is reasonable and we construe the term “windows” as a “predefined
`
`subsections of a chromosome” or a “chromosomal regions.” Because the Lo ’266
`
`application supports this claim term (see FFs 16 and 17, Lo ’266 application, Exh.
`
`2016, at ¶¶ [0061], [0062], and [0078]) and Fan does not argue that any other claim
`
`terms are unsupported, we find that the subject matter Lo’s claims are described by
`
`the Lo ’266 application.
`
`Fan has failed to persuade us that the involved Lo claims lack sufficient
`
`-18-
`
`
`
`
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`Interference 105,922
`
`
`
`written description support under 35 U.S.C. § 112, first paragraph. Accordingly,
`
`we deny the relief Fan requests in its Motion 2.
`
`V.
`
`Fan Motion 3
`
`Fan requests that the benefit of priority as to the Count for application
`
`12/614,350 (“the Lo ’350 application”) or 12/178,181 (“the Lo ’181 application”),
`
`which was accorded to Lo upon declaration, be revoked. (Fan Motion 3, Paper
`
`28.) Fan argues that Lo is not entitled to this priority benefit because those
`
`applications do not provide a constructive reduction to practice of “determining
`
`values for numbers of sequence tags mapping to chromosome portions by using a
`
`number of windows of defined length within normally and abnormally distributed
`
`chromosome portions,” as recited in step (c) of the Count. (Id., at 1:3-11.) Fan
`
`puts forth arguments and evidence that are similar to the arguments and evidence it
`
`put forth in its Motion 2 to argue that the Lo ’266 application fails to provide a
`
`sufficient disclosure under 35 U.S.C. § 112, first paragraph, for step (c) of its
`
`involved claims.
`
`As Lo argued in opposition to Fan Motion 2, the Lo ’350 application and the
`
`Lo ’181 applications describe how “chromosomal regions” are used to analyze
`
`sequence tags for a determination of aneuploidy. (Lo Opp. 3, Paper 50, at 5:13-
`
`8:9, citing Lo ’350 application, Exh. 2008, at ¶¶ 0061, 0062, and 0078; and Lo
`
`’181 application, Exh. 2009, at ¶¶ 0050, 0051, and 0067.) For the reasons
`
`provided above in regard to Fan Motion 2, we deny the relief Fan requests in
`
`-19-
`
`Motion 3.
`
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`
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`Interference 105,922
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`
`
`VI. Fan Motion 1
`
`Fan requests that it be accorded the benefit of priority as to the Count for its
`
`provisional application 61/098,758 (“the Fan ’7
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