- Ariosa Diagnostics v. The Board Of Trustees Of The Leland Stanford Junior UniversityAll claims unpatentablePTAB · Nov 19, 2014 · IPR2013-00308 · APJ Lora M Green · IPR · Final written decision
Claims 1–13 are unpatentable: claims 1–5, 7–9, 12, and 13 as anticipated by Lo; claims 10–11 and 6 as obvious over Lo with Brenner and Li, respectively.
RulingsFinal written decision- Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed board ownDecided for petitioner
“recites (emphasis added) “sequencing predefined subsequences of the maternal and fetal DNA to obtain a plurality of sequence tags aligning to the predefined subsequences.” Thus, the claim language associates “sequencing predefined sequences” with obtaining “sequence tags.” The Specification of the ’076 patent discusses sequence tags in the context of shotgun sequencing. See, e.g., Ex. 1001, col. 14, ll. 56–66. As Petitioner notes, there is no discussion in the Specification of the term “targeted sequencing.” Reply 1. Instead, the ’076 patent also discloses the use of a large number of windows of defined length created along the chromosome, such that the windows cover each chromosome in question, except for the non-informative regions of the chromosome, such as centromere and repetitive regions, may be omitted. Id. at col. 4, ll. 56–62. Thus, “[v]arious average numbers, i.e., median values, are calculated for different windows and compared. 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.” Id. at col. 4, ll. 62–67 (emphasis added). As taught by the ’076 patent, “[e]ach autosome (chr. 1–22) is computationally segmented into contiguous, non-overlapping windows,” although sliding windows could also be used. Id. at col. 5, ll. 4–9. In addition, as noted above, the ’076 patent also provides examples that describe “direct sequencing of cell-free DNA from plasma of pregnant women with high throughput shotgun sequencing technology,” wherein sequences were mapped to specific chromosomal regions, allowing for the measurement of over- and under-representation of chromosomes from an aneuploid fetus. Id. at col. 20, ll. 30–36. Thus, the Specification does not disclose sequencing only the defined sequences as Patent Owner would have us construe this phrase, but instead, it discloses sequencing the predefined sequences along with other sequences, and then using various techniques to locate the predefined sequences in the material that has been sequenced. Thus, we conclude that the broadest reasonable interpretation of the phrase “sequencing predefined subsequences” is that the subsequences may be predefined through comparison with the predefined windows that are created along the length of the chromosome. The predefined subsequences may walk along the entire length of the chromosome. Thus, although one predefined subsequence would not include the entire chromosomal sequence, two or more subsequences may include the entire length of the chromosomal sequence. That interpretation encompasses the preferred embodiment of the ’076 patent, whereas Patent Owner’s proffered construction limiting the method of claim 1 to “targeted” sequencing, as Patent Owner defines that term, would not” slip op. at 10
- Novelty / Anticipation (§102) › Anticipation standard (single reference, every element)UnpatentableUnpatentable
“may then be sequenced, for example, by using massively parallel sequencing methods. Id. ¶¶ 55–56. As taught by Lo, sequence tags are generated, aligned to each chromosome, and tags identified as originating from a potentially aneuploid chromosome are compared quantitatively to tags originating from a reference chromosome, to allow for the identification of chromosomal gains or losses. Id. ¶ 70. That falls within the scope of the limitation of step (b) of claim 1 of “sequencing predefined subsequences of the maternal and fetal DNA to obtain a plurality of sequence tags aligning to the predefined subsequences, wherein said sequence tags are of sufficient length to be assigned to a specific predefined subsequence.” That is, as construed above, the sequencing step is not limited to sequencing only the predefined subsequences, but encompasses sequencing other portions of the genome. And, as Lo teaches that the sequence tags are aligned to a chromosome to allow for the identification of chromosomal gains or losses (id. ¶ 70), the tags generated must necessarily be of sufficient length to be assigned to a specific predefined subsequence. See, e.g., Ex. 1008 ¶ 60 (noting that although Lo “does not describe specifically that the sequence tags were of sufficient length to be assigned to a specific region of the genome, one skilled in the art would understand this to be the case, because the sequence tags used to identify chromosomal origin must have been of sufficient length to allow assignment to a particular genomic region”).” slip op. at 20
- Obviousness (§103) › Motivation to combine / reasonable expectation of successMotivation not foundNot shown unpatentableNot shown unpatentable
“us, Petitioner has not demonstrated that the ordinary artisan would have combined Quake and Kapur as set forth in the Petition (29–39) to arrive at the method of challenged claim 1. In particular, Petitioner relies on Figures 6 and 7 of Kapur as teaching “a method for sequence determination of randomly generated DNA fragments using arrays having oligonucleotides of known sequence. Sequencing of a randomly generated genomic fragment via binding to a predefined sequence on an array aligns a random sequence to a probe indicative of a specific genomic region.” Pet. 31. The evidence relied upon by Petitioner does not explain, however, why one would have a used a method for detecting SNPs as taught by Kapur to perform the sequencing of Quake. That is, what is lacking in the Petition and accompanying Declarations is an “articulated reason[] with some rational underpinning to support the legal conclusion of obviousness.” Kahn, 441 F.3d at 988. Petitioner responds that the “sequencing by array technology of Balasubramanian (US 2003/0022207 A1, published Jan. 30, 2003, Ex. 1040) is cited in all of Kapur (Ex. 1005 ¶ 163), Quake (Ex. 1006 ¶ 120), and the ‘076 patent (Ex. 1001 at col. 10, lines 50–56).” Paper 34 ¶ 19. Figures 6 and 7 relied upon by Petitioner, however, are drawn to methods of detecting SNPs, and not to the sequencing array technology of Balasubramanian. In fact, Petitioner first relies on paragraph 163 of Kapur, which it contends cites the sequencing array technology of Balasubramanian, in its challenge of claim 3, which is drawn to the use of massively parallel sequencing. Petitioner cannot rely upon Balasubramanian in its Reply to make up for the deficiencies in its Petition. See, e.g., 37 C.F.R. § 42.23(b) (noting that “[a]ll arguments for the relief requested in a motion must be made in the motion,” and that a “reply may only respond to arguments raised in the corresponding opposition or patent owner response”).” slip op. at 32
- ExcludeMotion to exclude, deniedDenied
“Patent Owner’s objections go more to the weight that paragraph 15 of Exhibit 1043 should be afforded, rather than to its admissibility. It is within our discretion to assign the appropriate weight to be accorded to Dr. Morton’s testimonial evidence. The Board, sitting as a non-jury tribunal with administrative expertise, is well-positioned to determine and assign appropriate weight to evidence presented. Gnosis S.P.A. v. S. Alabama Medical Science Foundation, IPR2013-00118, slip op. at 43 (PTAB June 20, 2014) (Paper 64). See also Donnelly Garment Co. v. NLRB, 123 F.2d 215, 224 (8th Cir. 1941) (“One who is capable of ruling accurately upon the admissibility of evidence is equally capable of sifting it accurately after it has been received.”). We thus decline to exclude paragraph 15 of Exhibit 1043.” slip op. at 36
Patent outcomesUS 8,296,076 unpatentableClaim construction§ 102 anticipation§ 103 obviousnesscites KSR · GrahamPatents in suitUS 8,296,076
Holdings, summaries, rulings, issues, outcomes, winners and claim constructions shown for a decision were generated by a large language model reading the opinion. They are a guide to the decision, not the decision. Confirm every one against the court's own text before relying on it. Outcomes read from the patent owner’s side. Party names are extracted from the decision and are missing on about 900 short Director denials and scans, which carry the trial number instead.