(admitted pro hac vice) (admitted pro hac vice) Jonathan E. Bachand

Transcription

1 Filed: April 1, 2015 On behalf of Patent Owner Illumina, Inc. by: Kerry S. Taylor Adrian C. Percer William R. Zimmerman (admitted pro hac vice) Edward R. Reines Michael L. Fuller (admitted pro hac vice) Jonathan E. Bachand KNOBBE, MARTENS, OLSON & Derek C. Walter BEAR, LLP (admitted pro hac vice) 2040 Main Street, 14 th Floor Irvine, CA WEIL, GOTSHAL & MANGES, LLP Tel.: (949) Redwood Shores Parkway Fax: (949) Redwood Shores, CA Tel.: (650) Fax: (650) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD ARIOSA DIAGNOSTICS, INC. Petitioner, v. ILLUMINA, INC. Patent Owner. IPR U.S. Patent 7,955,794 B2 ILLUMINA S PATENT OWNER RESPONSE

2 TABLE OF CONTENTS Page No. I. Introduction... 1 II. History of the 794 Patent and cited art... 3 III. Ariosa fails to establish that the Fan Pub is prior art... 5 A. The Fan Pub is not prior art to the 794 patent under 35 U.S.C. 102 (a) or (b)... 6 B. The disclosures of the Fan Pub relied upon by Ariosa are not prior art under 35 U.S.C. 102(e) The Fan Pub is not prior art because its filing date is after the effective filing date of the 794 patent Ariosa s relied-upon teachings from the Fan Pub are not entitled to an earlier effective prior art date a) Ariosa fails to address the 731 patent b) Ariosa improperly relies upon the 810 application as prior art c) Ariosa fails to show where the 810 application supports the cited disclosures from the Fan Pub (1) The cited portions of the Fan Pub for the preamble of Claim 1 are unsupported by the 810 application (2) The cited portions of the Fan Pub for Step (a) of Claim 1 are unsupported or irrelevant (3) The cited portions of the Fan Pub for Steps (b), (c), (d), (f) and (g) of Claim 1 are unsupported i

3 TABLE OF CONTENTS (cont d) Page No. d) Conclusion Ariosa failed to meet its burden Ariosa does not rely upon the earlier filing date of the 810 application for its challenge to Claims 10, 12, 19 and Ariosa failed to prove that the relevant subject matter in the Fan Pub is by another IV. Ariosa did not meet its burden of demonstrating that every element of Claims 1-22 is found in the Fan Pub V. The Fan Pub does not disclose each and every element of independent Claim 1 of the 794 patent A. Dr. Fu confirmed that the Fan Pub does not disclose every element of the claims of the 794 patent B. The Fan Pub does not disclose step (a) of Claim C. The Fan Pub does not disclose step (b) of Claim The Fan Pub s more 10 than [sic] probes does not anticipate more than 100 different single-stranded probes The Fan Pub does not disclose each of said more than 100 different probes has identical universal priming sites D. The Fan Pub does not disclose all elements of Claim 1 as arranged in the claim Paragraphs 15 and 16 are separate and distinct protocols that do not disclose the claimed method of the 794 patent ii

4 TABLE OF CONTENTS (cont d) Page No. 2. The Petition relies on various paragraphs from the Detailed Description section of the Fan Pub Figures 1-6 disclose different and distinct protocols E. Paragraphs 15 and 16 are distinct protocols that do not support anticipation of the claimed method of the 794 patent VI. The 810 Application does not provide an anticipatory disclosure A. Numerous elements of Claim 1 are missing from the 810 application The 810 application does not disclose single-stranded target sequences attached to a first solid support from step (a) The 810 application does not disclose the more than 100 different single-stranded probes from step (b) of Claim The 810 application does not disclose that the 50 to 100 genes are assayed in a single multiplex reaction The 810 application does not disclose 100 different single-stranded probes having identical universal priming sites B. The 810 application does not provide an enabling disclosure for the subject matter relied upon in the Fan Pub C. The 810 application does not disclose all of the limitations arranged or combined in the same way as in Claim The 810 application consists of separate sections and each section contains several distinct protocols iii

5 TABLE OF CONTENTS (cont d) Page No. a) The invention disclosure section of the 810 application has distinct, non-anticipatory protocols b) The grant application section of the 810 application discloses several protocols, none of which anticipates Ariosa improperly relies on several different protocols from the 810 application to allege anticipation The invention disclosure of the 810 application does not disclose a wash step for the two-oligo and threeoligo protocols, and thus do not include step (c) of Claim D. The 810 application does not provide sufficient written description support for the subject matter relied upon to anticipate Claim VII. Ariosa does not identify a relevant disclosure in the 810 Application for the subject matter of Claims 2, 5-8 and VIII. Petitioner is barred under the doctrine of assignor estoppel IX. Conclusion iv

6 TABLE OF AUTHORITIES Page No(s). Amgen Inc. v. Hoechst Marion Roussel, Inc., 314 F.3d 1313 (Fed. Cir. 2003) Application of Land, 368 F.2d 866, 879 (C.C.P.A. 1966) Applied Materials Inc. v. Gemini Research Corp., 835 F.2d 279 (Fed. Cir. 1988) In re Arkey, 455 F.2d 568 (C.C.P.A. 1972) Atofina v. Great Lakes Chem. Corp., 441 F.3d 991 (Fed. Cir. 2006)... 25, 28 Cisco Systems Inc. v. RPX Clearinghouse LLC, IPR , Decision Instituting Inter Partes Review (Paper 11) (PTAB, Feb. 9, 2015) In re Deckler, 977 F.2d 1449 (Fed. Cir. 1992) DeSilva v. DiLeonardi, 181 F.3d 865 (7 th Cir. 1999) Diamond Scientific Co. v. Ambico, Inc., 848 F.2d 1220 (Fed. Cir. 1988)... 52, 54 Dominion Dealer Solutions, LLC v. AutoAlert, Inc., IPR , Paper 14 (PTAB, Oct. 10, 2013) Dynamic Drinkware LLC, v. Nat l Graphics, Inc., IPR , Paper 42 (PTAB 2014)... 10, 12, 17 Dynamic Drinkware LLC, v. Nat l Graphics, Inc., IPR , Paper 7 (PTAB, Jan. 29, 2015)... 25, 27 v

7 TABLE OF AUTHORITIES (cont d) Page No(s). ebay Inc. v. MercExchange, LLC, 574 U.S. 388 (2006) FedEx Corp. v. IpVenture, Inc., IPR , Paper 24 at 5 (PTAB, Feb. 20, 2014)... 7 Fina Tech., Inc. v. Ewen, 857 F. Supp (N.D. Tex. 1994) In re Giacomini, 612 F.3d 1380 (Fed. Cir. 2010)...passim Innova/Pure Water, Inc. v. Safari Water Filtration Sys., 381 F.3d 1111 (Fed. Cir. 2004) In re Katz, 687 F.2d 450 (C.C.P.A. 1982) In re Klesper, 397 F.2d 882 (C.C.P.A. 1968) Marvell Semiconductor, Inc. v. Intellectual Ventures I LLC, IPR , Decision Denying Institution of Inter Partes Review (Paper 17) (PTAB, Dec. 3, 2014)... 7 Mentor Graphics Corp. v. Quickturn Design Sys., Inc., 150 F.3d 1374 (Fed. Cir. 1998) Metro Traffic Control, Inc. v. Shadow Network Inc., 104 F.3d 336 (Fed. Cir. 1997) Modine Mfg. Co. v. U.S. Int l. Trade Comm n, 75 F.3d 1545 (Fed. Cir. 1996) Net MoneyIN, Inc. v. Verisign, Inc., 545 F.3d 1359 (Fed. Cir. 2008)...passim vi

8 TABLE OF AUTHORITIES (cont d) Page No(s). NEC Corp. of Am. v. Cellular Commc ns Equip. LLC, IPR , Paper 10 (PTAB, Jan. 28, 2015) Osram Sylvania, Inc. v. Am. Induction Techs., Inc., 701 F.3d 698 (Fed. Cir. 2012) Pandrol USA, LP v. Airboss Ry. Prod., Inc., 424 F.3d 1161 (Fed. Cir. 2005) Redline Detection, LLC v.star EnviroTech, Inc., IPR , Decision on Motion for Additional Discovery (Paper 31) (PTAB, Aug. 27, 2013) Richardson v. Suzuki Motor Co., 868 F.2d 1226 (Fed. Cir. 1989)... 37, 38,39 In re Robertson, 169 F.3d 743 (Fed. Cir. 1999)... 37, 39 Sequenom, Inc. v. Bd. of Trustees of Leland Stanford Junior Univ., IPR , Paper 14 (PTAB, Sept. 23, 2014) Singer v. Rehfuss, 59 U.S.P.Q.2d 1190 (B.P.A.I. Jan 21, 1998) Tech. Licensing Corp. v. Videotek, Inc., 545 F.3d 1316 (Fed. Cir. 2008)... 7 Verdegaal Bros., Inc. v. Union Oil Co., 814 F.2d 628 (Fed. Cir. 1987) Westinghouse Elec. & Mfg. Co. v. Formica Insulation Co., 266 U.S. 342 (1924) Woods v. Tsuchiya, 754 F.2d 1571 (Fed. Cir. 1985) vii

9 TABLE OF AUTHORITIES (cont d) Page No(s). Ex Parte Yamaguchi, 88 U.S.P.Q.2d 1606 (B.P.A.I. 2008)... 10, 11, 12 OTHER AUTHORITIES 35 U.S.C passim 35 U.S.C U.S.C U.S.C , U.S.C , U.S.C , 5 35 U.S.C C.F.R C.F.R C.F.R C.F.R C.F.R , 7, C.F.R viii

10 TABLE OF AUTHORITIES (cont d) Page No(s). 157 Cong. Rec. S952 (daily ed. Feb. 28, 2011) Fed. Reg , 48638, (Aug. 14, 2012) ix

11 Illumina, Inc. ( Illumina ) responds to the Petition filed by Ariosa Diagnostics, Inc. ( Ariosa ) regarding U.S. Patent No. 7,955,794 ( the 794 patent ). I. Introduction The technology claimed in the 794 patent was invented by Illumina scientists, including Dr. Jian-Bing Fan, Dr. John Stuelpnagel, and Dr. Arnold Oliphant. Ex at 1; Ex Dr. Stuelpnagel managed patent prosecution at Illumina and under his supervision all inventors swore that they were the original inventors of the 794 patent and assigned their rights in the patent to Illumina. Ex at 53:23-54:13; Ex. 2004; Ex at 251:22-252:2. Drs. Stuelpnagel and Oliphant left Illumina and founded Ariosa, commercializing a product based on the 794 patent for their new company. Ex at 1-2. Now Drs. Stuelpnagel and Oliphant are using this proceeding to attack their own patent hoping that the Board will not apply the doctrine of assignor estoppel. Ex at 33:17-34:2. Even if assignor estoppel is set aside in this proceeding, the evidence shows that Ariosa failed to carry its burden of proof on the merits. The sole issue in this proceeding is whether Ariosa proved that Claims 1-22 of the 794 patent are anticipated by U.S. Pub. No. 2002/ ( Fan Pub, Ex. 1004). Paper 14 at 12; 35 U.S.C. 316(e). Ariosa s Petition alleges anticipation based on a reference that the Patent Office considered during prosecution of the 794 patent and over which the Examiner properly determined that Claims

12 were novel. Ex at 7 (considering U.S. 6,812,005 1 ). As documented below, Ariosa s Petition provides no reason to reverse the Examiner s patentability determination. In particular, Ariosa failed to meet its burden to prove anticipation for at least the following reasons: the Petition fails to establish that the Fan Pub is prior art to the 794 patent; the Petition fails to provide necessary analysis how the cited portions of the Fan Pub disclose the elements of the 794 patent claims; the Petition fails to establish that the Fan Pub discloses single stranded target sequences attached to a first solid support, as required by Claim 1, step (a); the Petition fails to establish that the Fan Pub discloses more than 100 different single-stranded probes having identical universal priming sites, as required by Claim 1, step (b); and the Petition inappropriately selects and combines various different protocols within the Fan Pub and its priority application (U.S. Prov. Appl. No. 60/180,810 ( the 810 application, Ex. 1012)) to assert anticipation of the claims of the 794 patent. Each of the above deficiencies is an independent basis to confirm the novelty of 1 The patent application that issued as U.S. Patent No. 6,812,005 was published as the Fan Pub (Ex. 1004). See Paper 1 at 8-9; Ex at 1. 2

13 Claims 1-22 of the 794 patent. Indeed, Ariosa s own expert Dr. Fu, a listed inventor on the Fan Pub, directly admitted that the Fan Pub does not anticipate Illumina s claims: Q: And you ll agree that the 946 application does not teach every element of any of the 794 claims properly because of the problem that you identified, correct? THE WITNESS: Yes. BY MR. REINES: Q: You ll agree with that, won t you? A: Right. Ex at 172:24-173:7. 2 Dr. Fu s testimony as a listed inventor of the Fan Pub and paid Ariosa expert provides powerful evidence of the novelty of the 794 patent. After considering all the relevant evidence, it is evident that Ariosa did not carry its burden of proving anticipation of Claims II. History of the 794 Patent and cited art Dr. Fan from Illumina and Dr. Fu from the University of California at San Diego (UCSD) were close personal friends who lived in the same neighborhood. Ex at 30:15-17, 212:1-4. The two scientists worked together to create a grant application to fund new research. Id. at 54:1-24. As Dr. Fu was aware, Illumina filed part of this grant application in the 810 application (Ex at 15-2 Speaking objections from deposition transcripts are omitted from this Response. 3

14 45), along with Dr. Fan s invention disclosure form. Id. at The invention disclosure form contained ideas unique to Dr. Fan. Ex at 90:24-92:6. The grant application (and the 810 application) lack many details needed to make the contemplated protocols work. Ex at 77:2-78:15. For example, the grant application stated that it was difficult to accurately predict the outcome of some proposed protocols. Ex at 39. This proved to be true. For example, while the grant application hoped to test 50 to 100 genes at a time in the second (R33) phase of the research (id. at 35), the outcome of the proposed research successfully tested only 23 genes. Ex at 192:23-193:18; Ex at 355. In the time following this initial collaboration, scientists at Illumina worked intently to solve problems that arose, making many improvements to the proposed protocols. Illumina s improvements were the subject of several patent filings, including the Fan Pub (Ex. 1004) and U.S. Pat. Appl. No. 09/779,376 ( the 376 application, Ex. 2018). As Dr. Fu testified, he was not involved in creating the Fan Pub (Ex at 237:11-19), and the relevant new ideas in that publication came from the Illumina inventors (id. at 90:24-92:4, 144:12-20, 192:1-17, 206:5-207:23). See also Ex at 144: Notably, the Fan Pub and 376 application were filed on the same day by the same attorney for Illumina. Ex at 1:8-9; Ex at 1. While containing much of the disclosure of the Fan Pub, the 376 application also uniquely reflected new ideas developed by Illumina. 4

15 While the 376 application was still pending, Illumina filed the application that issued as the 794 patent with priority to the 376 application. Ex at 1:8-9. The claims of that application (and the resulting 794 patent) cover the improvements made by Illumina scientists that are exclusively disclosed in the 794 patent and the 376 application. Illumina s improvements, as claimed in the 794 patent, allowed for a large expansion in the number of targets that can be tested. For example, the 376 application explains that rather than isolating target sequences by hybridizing a poly(a) tail to a poly(t) bead as disclosed in the Fan Pub, the target sequences can instead be attached to solid supports using biotin. Ex at 22: Thus, while the grant research tested 23 genes with its poly(t) capture protocol (Ex at 35; Ex at 355), Illumina s 376 application target attachment method, as claimed in the 794 patent, successfully tested 400 different genes. Ex at 881; Ex at 5:60-6:3. III. Ariosa fails to establish that the Fan Pub is prior art Ariosa bears the burden to prove anticipation. 35 U.S.C. 316(e). To do so, Ariosa must establish that the Fan Pub qualifies as prior art to the 794 patent. The Petition asserts, without explanation, that the Fan Pub is prior art to the 794 patent under 35 U.S.C. 102 (a), (b), and/or (e). Paper 1 at 4. Ariosa makes no attempt to explain how the Fan Pub might be prior art under any of these 5

16 statutory sections. 37 C.F.R (b)(5); 35 U.S.C. 312(a)(3). Instead, Ariosa leaves the Board and Illumina guessing. If Ariosa plans to finally reveal its 102 position in its Reply, it will violate this Tribunal s rules, harm Illumina s right to due process, and deprive the Board of Illumina s response. As documented below, Ariosa did not meet its burden to show that the Fan Pub is prior art. A. The Fan Pub is not prior art to the 794 patent under 35 U.S.C. 102 (a) or (b) The 794 patent has a filing date of June 20, Ex at 1. The Fan Pub published 5 months later on November 21, Ex at 1. Nothing in the Petition explains how the Fan Pub could qualify as prior art under 35 U.S.C. 102(a) or (b) given this sequence of events. Thus, Ariosa failed to meet its burden with respect to these subsections. B. The disclosures of the Fan Pub relied upon by Ariosa are not prior art under 35 U.S.C. 102(e) As with 102(a) or (b), Ariosa made no attempt to explain how the Fan Pub was prior art under 102(e). The application for the Fan Pub was filed on the same day or after the effective priority date of the 794 patent (indeed, the Petition does not contest the 794 patent s claimed priority). Further, the relied upon portions of the Fan Pub do not trace their origin to the 810 application, and thus do not get the 810 application s filing date and for at least Claims 10, 12, 19, and 20 the Petition appears to concede this point. Finally, Dr. Fu admitted that 6

17 certain features of the Fan Pub cited in the Petition were improvements derived from the Illumina inventors, and thus were not by another. A showing of prior art under 102(e) requires a petitioner to establish the invention was described in (1) an application for patent, published under section 122(b), by another filed in the United States before the invention by the applicant for patent U.S.C. 102(e). A petitioner must establish that a reference qualifies as prior art under 102(e) in its petition. See Marvell Semiconductor, Inc. v. Intellectual Ventures I LLC, IPR , Paper 17 at 10 (PTAB, Dec. 3, 2014); 37 C.F.R (b)(5). Only if a petitioner successfully meets its burden does the burden of production shift to the patent owner. FedEx Corp. v. IpVenture, Inc., IPR , Paper 24 at 5 (PTAB, Feb. 20, 2014) (citing Tech. Licensing Corp. v. Videotek, Inc., 545 F.3d 1316, 1327 (Fed. Cir. 2008)). Ariosa bore the burden of establishing that the portions of the Fan Pub asserted in the Petition were disclosed in a patent application filed before the invention date of Claims 1-22 of the 794 patent. This burden was not met. The Petition does not go through any of the steps necessary to establish that the cited portions of the Fan Pub are prior art under 102(e). See Paper 1 at The Fan Pub is not prior art because its filing date is after the effective filing date of the 794 patent The Fan Pub came from an application filed on Feb. 7, Ex at 1. In contrast, the 794 patent claims priority to three priority applications that were 7

18 filed Feb. 7, 2001 or earlier: U.S. Pat. Appl. No. 09/779,376 was filed on Feb. 7, 2001; U.S. Prov. Appl. No. 60/234,732 was filed on Sep. 22, 2000; and U.S. Prov. Appl. No. 60/234,143 was filed on Sep. 21, See Ex at 1; id. at col. 1:3-14; id. at 54 (Certificate of Correction). Thus, on its face, the Fan Pub s filing date of Feb. 7, 2001 does not establish a 102(e) priority date before the filing of the 794 patent priority applications. The Petition makes no attempt to establish that the Fan Pub s Feb. 7, 2001 filing date is before the invention by the applicant for patent of any of Claims 1-22 of the 794 patent, as required under 35 U.S.C. 102(e). Ariosa s Petition acknowledges that the 794 patent claims a priority date as early as September of Paper 1 at 47. Yet the Petition makes no attempt to assert, let alone prove, that any of Claims 1-22 are not entitled to this acknowledged priority date. Ariosa failed to submit a single priority application for the 794 patent into the record. In fact, many of the teachings from the Fan Pub cited in the Petition are present verbatim in the priority documents of the 794 patent. For example, Ariosa cites 178 of the Fan Pub as teaching at least 100 different target sequences recited in the preamble of Claim 1, and Ariosa cites 43 of the Fan Pub as teaching more than 100 different single-stranded probes as recited in step (b) of Claim 1. Paper 1 at 15-16; Ex at 90:20-91:11. However, the 794 patent claims priority to the 376 application, which was filed on the same date as the Fan 8

19 Pub and also includes these same disclosures. See, e.g., Ex at 13:9-12, 57: Similarly, Ariosa cites 57 of the Fan Pub for step (d) of Claim 1 (Paper 1 at 17-18; see also Ex ; Ex ), and this disclosure is included in the 376 application. See, e.g., Ex at 19:4-7. Further, Ariosa cites 69 of the Fan Pub for step (e) of Claim 1. Paper 1 at 18; see also Ex This disclosure is likewise in the 376 application. See, e.g., Ex at 23:25-24:6. Ariosa cites 56 of the Fan Pub as teaching Claim 9. Paper 1 at 22; see also Ex ; Ex This disclosure is also found in the 376 application. See, e.g., Ex at 19:1-3. Numerous other disclosures of the Fan Pub cited by Ariosa and its experts are in common with the 376 application. Compare Ex , 44, 60, 85, 97, 99, 102, 106, 107, 119, 120, 153, and Figures 1-6 with Ex at 11:13-17, 13:13-22, 19:23-20:2, 27:17-24, 38:8-16, 38:30-39:15, 40:1-7, 41:1-12, 41:13-18, 44:4-16, 44:17-20, 52:4-6, and Figures 1-6, respectively. In fact, the 376 application includes further relevant disclosures that were not copied into the Fan Pub. See, e.g., Ex at 4:1-9, 4:20-5:2, 6:7-22, 6:23-7:4, 7:7-13, 7:20-8:3, 14:3-7, 18:1-4, 10:19-30, 20:27-21:8, 21:9-17. Ariosa did not contest that the 376 application supports Claims 1-22 of the 794 patent, or assert that the Fan Pub s Feb. 7, 2001 filing date is before the invention by the applicant for patent of Claims As a result, Ariosa failed to establish that the Fan Pub s disclosure is prior art to any of Claims

20 2. Ariosa s relied-upon teachings from the Fan Pub are not entitled to an earlier effective prior art date Ariosa did not attempt to show that the disclosures it cited from the Fan Pub are entitled to priority in its cited provisional applications. Even if Ariosa had tried, it would have failed. Under 102(e), a publication may be entitled to the benefit of a provisional application filing date under 35 U.S.C. 119(e) if the provisional properly supports, in compliance with 35 U.S.C. 112, first paragraph, the cited subject matter. In re Giacomini, 612 F.3d 1380, (Fed. Cir. 2010); Ex Parte Yamaguchi, 88 U.S.P.Q.2d 1606, 1609 (B.P.A.I. 2008) (precedential). Petitioner bears the burden of making the initial showing of adequate support by the priority application. Dynamic Drinkware LLC, v. Nat l Graphics, Inc., IPR , Paper 42 at 5-6 (PTAB 2014). a) Ariosa fails to address the 731 patent The Fan Pub cites U.S. Prov. Appl. No. 60/234,731 ( the 731 application ). Ariosa and its two experts never mention the 731 application and make no assertions regarding its teachings. Thus, Ariosa failed to show that the Fan Pub is entitled to an effective date corresponding to the filing date of the 731 application. b) Ariosa improperly relies upon the 810 application as prior art Regarding the 810 application, Ariosa states [o]ne of the more relevant prior art references is U.S. Provisional Patent Application 60/180,810, filed Feb. 7, Paper 1 at 7. Thus, instead of asserting that the 810 application supports 10

21 the cited disclosures of the Fan Pub, Ariosa asserts that the 810 application is itself prior art. However, a provisional application itself cannot serve as a prior art document as of its filing date. Sequenom, Inc. v. Bd. of Trustees of Leland Stanford Junior Univ., IPR , Paper 14 at 3-4 (PTAB, Sept. 23, 2014) (citing Yamaguchi, 88 U.S.P.Q.2d at 1613; Giacomini, 612 F.3d at ). Accordingly, Ariosa s statement that the 810 application is prior art is unsupported and improper. Ariosa cannot rely on incorporation by reference of the 810 application into the Fan Pub to save its Petition. Paper 1 at 14. [I]ncorporation by reference does not convert the invention of the incorporated patent into the invention of the host patent. Modine Mfg. Co. v. U.S. Int l Trade Comm n, 75 F.3d 1545, 1553 (Fed. Cir. 1996). As documented herein, the portions of the Fan Pub cited by Ariosa are not entitled to the earlier effective date of the 810 application because the 810 application does not support the cited subject matter. Ex Parte Yamaguchi, 88 U.S.P.Q.2d at c) Ariosa fails to show where the 810 application supports the cited disclosures from the Fan Pub While the Petition makes a passing reference to the 810 application as the earliest priority document for the Fan Pub (Paper 1 at 8), Ariosa failed to prove that the subject matter cited from the Fan Pub is supported by the 810 application. In fact, Ariosa s own experts effectively admit that it was unsupported. Ex

22 at 77:2-79:11, 158:10-160:2; Ex at 117:6-14, 125:2-17, 153:5-9, 156:7-11, 122:8-15, 96:7-99:6. Conclusory assertions that the 810 application discloses certain claim elements is not the same as showing that the disclosures made in the Fan Pub are supported by the 810 application. In re Giacomini at 1385; see also In re Klesper, 397 F.2d 882, (C.C.P.A. 1968). The 810 application is a document having content that appears, on its face, significantly different from the content of the Fan Pub. Ex 2016 at 173:11-174:3. Essentially all terminology, syntax, and verbiage found in the Fan Pub is different from the 810 application. And in some important instances, the teachings directly contradict each other. See Section III.B.2.c.3, infra; Ex at 158:10-160:5. For the Fan Pub to obtain the benefit of the earlier filing date of the 810 application, Ariosa must show how the subject matter relied on in the Fan Pub is present in and supported by the 810 application. In re Giacomini at And it is Ariosa s burden to do so by providing an analysis of common subject matter between the Fan Pub and the 810 application. Dynamic Drinkware, IPR , Paper 42 at 6 (citing In re Giacomini and Ex Parte Yamaguchi.). No such showing was made in the Petition. When it is not readily apparent whether or how disclosure in a significantly different provisional application supports the asserted teachings of a 102(e) reference, the burden is on petitioner to make such a 12

23 showing. NEC Corp. of Am. v. Cellular Commc ns Equip. LLC, IPR , Paper 10 at 9-10 (PTAB, Jan. 28, 2015). Despite the stark differences between the two documents, neither Ariosa nor its experts explain how the 810 application establishes an effective prior art date for any disclosure cited from the Fan Pub. Ex at 26: Thus, Ariosa fails to carry its burden. Id. At most, Ariosa provided a claim chart containing both citations to the Fan Pub and the 810 application. However, this falls far short of demonstrating how the teachings in the Fan Pub are properly supported by the 810 application. (1) The cited portions of the Fan Pub for the preamble of Claim 1 are unsupported by the 810 application The Petition cites a portion of the Fan Pub 178 that describes a spatial coding system with subarrays that form 5000 different capture probes. Paper 1 at 15. In contrast, the Petition cites p. 61 of the 810 application, which teaches examining 50 to 100 genes in an undetermined assay. Id. Ariosa provides no explanation how a portion of the 810 application describing genes supports a disclosure about capture probes on subarrays, let alone how 50 to 100 genes supports a nearly 100-fold greater number of capture probes. Moreover, it was not. Dr. Fu admitted that this spatial coding disclosure from the Fan Pub was obtained from subsequent Illumina work, not the 810 application. Ex at 192:

24 (2) The cited portions of the Fan Pub for Step (a) of Claim 1 are unsupported or irrelevant The Petition cites two paragraphs of the Fan Pub for step (a) of Claim 1. The first is 32, which describes a method where two poly(t) steps are used. As support, the Petition only cites p. 50 of the 810 application, which teaches only a single step that uses poly(t). There is no explanation how a one poly(t)-stepcontaining method supports a two poly(t)-step-containing method. Ex 2016 at 224:1-225:6. The second paragraph cited by the Petition is 66, which describes a protocol that does not discuss ligation or other modification of probes prior to PCR amplification. As Dr. Fu admitted, protocols without modification have nothing to do with the claims of the 794 patent and should not be considered by the Board. Ex at 142:22-143:23. (3) The cited portions of the Fan Pub for Steps (b), (c), (d), (f) and (g) of Claim 1 are unsupported In asserting that Claim 1 is anticipated, the Petition cites to 16 of the Fan Pub more than any other disclosure from the Fan Pub. Specifically, the Petition relies on the Fan Pub s 16 to try to meet steps (b), (c), (d), (f) and (g) of Claim 1. Paper 1 at In contrast, Ariosa cites to four different teachings in the 810 application as teaching steps (b), (c), (d), (f) and (g) of Claim 1. Paper 1 at As discussed below, Dr. Fu admitted that 16 describes an entirely different 14

25 protocol than the protocols described in the 810 application. Ariosa provides no explanation for these inconsistent citations. Specifically, 16 of the Fan Pub describes a step of removing unhybridized probes after ligation of the two probes. Ex at 158:10-159:19. On the other hand, the cited pages of the 810 application teach the unhybridized probes are removed before the ligation of the probes. Ex 2016 at 95:22-96:19, 173: Dr. Fu emphasized that 16 is incompatible with and distinct from any teaching in the 810 application. Ex at 158:21-160:2, 165:1-21, 167:8-169:5, 173: Moreover, Dr. Fu admitted that he did not carefully compare 16 of the Fan Pub and the 810 application when he was preparing his declaration. Ex at 164:4-25, 169:20-170:9, 171:3-15, 173:21-174:13. But when provided an opportunity to more thoroughly review 16, Dr. Fu confirmed that his declaration should not have relied on 16, and that 16 is distinct from anything in the 810 application. Ex at 171:24-172:1 ( [The] 946 application get the sequence wrong. My 810 application has contained all corrected information. ), 158:10-160:2; see also Ex at 125:2-17. Thus, the record is clear that at least 16 of the Fan Pub is unsupported by the 810 application. Since 16 is the key paragraph of the Fan Pub relied upon by Ariosa, it is clear that Ariosa s relied upon teaching from the Fan Pub is not supported by the 810 application and, thus, cannot claim priority to it. 15

26 Additionally, for steps (b) and (c), the Petition also cites 15 of the Fan Pub. However, 15 relates to a single-probe method in which the probe is not modified. As Dr. Fu acknowledged, the single-probe method is irrelevant to anticipation and should be disregarded by the Board. Ex at 142:22-143:23. For step (b), the Petition further cites to 43 of the Fan Pub which refers to more 10 than [sic] probes. Paper 1 at 16. The Petition cites to a disclosure from the 810 application that recites 50 to 100 genes. Id. Dr. Ward testified that the disclosure of 50 to 100 genes does not support any particular number of probes. Ex at 117:6-14. For step (c), the Petition further cites 65 of the Fan Pub which relates to a single-probe embodiment. Thus it is also irrelevant to anticipation. Ex at 142:22-143:23. For step (d), the Petition further cites 52 and 57 of the Fan Pub which elaborate on variations of the ligation used in 16. As the method of 16 is very different from and not supported in the 810 application, the paragraphs that elaborate on its method are likewise not supported. Further, Dr. Fu admitted that the extension-ligation methods described in 52 and 57 were derived from further work by Illumina inventors, and not present in the 810 application. Ex at 207: Dr. Oliphant concurred. Ex at 192:

27 For both steps (f) and (g), the only other paragraph of the Fan Pub cited by the Petition is 15. However, 15 of the Fan Pub relates to the single probe embodiment, so is irrelevant to anticipation. Ex at 142:22-143:23. The declarations of Dr. Fu and Dr. Ward fail to remedy these deficiencies in the Petition. Like the Petition, the declarations list these same portions of the Fan Pub, and fail to provide any discussion how any cited portion of the Fan Pub has a clear counterpart in the 810 application. Drs. Fu and Ward admitted that this omission occurred because they failed to perform the required analysis. Ex at 170:2-9, 198:16-199:7; Ex at 25:6-20. d) Conclusion Ariosa failed to meet its burden Ariosa bore the burden of making the initial showing of adequate support for the Fan Pub by the 810 application. Dynamic Drinkware LLC, v. National Graphics, Inc., IPR , Paper 42 at 5-6 (PTAB 2014). The Petition is altogether silent on whether any relied upon part of the Fan Pub is supported by the 810 application. Further, Dr. Fu testified that the documents are different and distinct, particularly at the key 16 relied upon by Ariosa. Thus, the record does not just lack a showing of support, but affirmatively demonstrates that the key teachings of the Fan Pub relied upon by Ariosa are not supported by the 810 application. Therefore, Ariosa did not carry its burden. See Cisco Sys. Inc. v. RPX Clearinghouse LLC, IPR , Paper 11 at (PTAB, Feb. 9, 2015). 17

28 Accordingly, the portions of the Fan Pub cited in the Petition are not entitled to the earlier filing date of the 810 application and, thus, are not prior art to the 794 patent under 35 U.S.C. 102(e). 3. Ariosa does not rely upon the earlier filing date of the 810 application for its challenge to Claims 10, 12, 19 and 20 The Petition does not cite to any part of the 810 application for the elements of Claims 10, 12, 19 and 20. Paper 1 at 22-23, 25. Neither do Ariosa s experts. Ex , 46, 53, 54; Ex , 48, 55, 56; Ex at 143:15-18, 150:23-151:1, 153:1-4. This is further evidence that for at least these claims, the Fan Pub is not supported by the 810 application. 4. Ariosa failed to prove that the relevant subject matter in the Fan Pub is by another A disclosure of one s own invention cannot serve as prior art against one s claims under 102(e), absent a statutory bar. In re Katz, 687 F.2d 450, 454 (C.C.P.A. 1982). As stated in Application of Land, 368 F.2d 866, 879 (C.C.P.A. 1966), [w]hen the 102(e) reference patentee got knowledge of the applicant s invention from him, as by being associated with him, or, as here, had knowledge of the joint applicants invention by being one of them, and thereafter describes it, he necessarily files the application after the applicant s invention date and the patent as a reference does not evidence that the invention, when made, was already known to others. The fact that an application has named a different inventive 18

29 entity than a patent does not necessarily make that patent prior art. Applied Materials Inc. v. Gemini Research Corp., 835 F.2d 279, 281 (Fed. Cir. 1988). Ariosa relies upon the 810 application to try to show that Dr. Fu s published work predated the 794 patent. However, that application is in the name of Dr. Fan, and is thus presumptively the work of Dr. Fan (and Illumina), not Dr. Fu. Ariosa cannot rely upon Dr. Fan s 810 application to prove that Dr. Fu s work has priority to the 794 patent. Dr. Fu admitted that many of the disclosures in the Fan Pub that Ariosa relies on were Dr. Fan s contributions. For example, Dr. Fu admitted that the disclosure at 178 of the Fan Pub that Ariosa relies on for the preamble of Claim 1 was Dr. Fan s contribution. Ex at 192:1-17; Paper 1 at 15. As another example, Dr. Fu admitted that the three-probe embodiment at 56 of the Fan Pub and at page 6 of the 810 application that Ariosa relies on for Claim 9 came from Dr. Fan. Ex at 90:24-92:4; Paper 1 at And the discussion of extension and ligation from 57 of the Fan Pub that Ariosa relies on for Claims 19 and 20 also came from inventors at Illumina. Ex at 214:20-24; Ex at 192:1-11. In fact, Dr. Fu admitted that he was not involved in creating the Fan Pub. Ex at 237: Since these claimed improvements were first possessed by and derived from the named Illumina 794 patent inventors, they are not properly prior art under 102(e). Ariosa wholly failed to carry its burden of showing that the material it relies upon meets the requirements of 102(e). 19

30 IV. Ariosa did not meet its burden of demonstrating that every element of Claims 1-22 is found in the Fan Pub A petition must include a full statement of the reasons for the relief requested, including a detailed explanation of the significance of the evidence C.F.R (a)(2); 35 U.S.C. 312(a)(3). Evidence should be excluded where its relevance has not been explained. 37 C.F.R (b)(5). The Petition contains conclusory assertions that the Fan Pub anticipates Claims The only specific portions of the Fan Pub and 810 application relied on for anticipation by Ariosa are found within the claim chart on pages of the Petition. This claim chart contains unexplained quotations and citations to the Fan Pub and the 810 application. There is no of analysis or explanation how the claim elements from the 794 patent might relate to the Fan Pub. Therefore, Ariosa s anticipation position is defective; Ariosa did not carry its burden. Dominion Dealer Solutions, LLC v. AutoAlert, Inc., IPR , Paper 14 at 4 (PTAB, Oct. 10, 2013) (citing DeSilva v. DiLeonardi, 181 F.3d 865, (7 th Cir. 1999). V. The Fan Pub does not disclose each and every element of independent Claim 1 of the 794 patent As discussed in Section III, above, the Fan Pub does not qualify as prior art. Even if it did, the Fan Pub does not anticipate Claim 1 because no disclosure in the Fan Pub provides each element as recited in Claim 1. 20

31 A. Dr. Fu confirmed that the Fan Pub does not disclose every element of the claims of the 794 patent On cross-examination, Dr. Fu acknowledged that his initial anticipation analysis was not careful, and that he had instead relied upon Ariosa s counsel in formulating his opinions. Ex at 174:4-13, 170:2-9, 198:16-199:7. Dr. Fu realized the specific teachings of the Fan Pub for the first time during his deposition. Id. at 137:12-138:16, 164:15-21, 219:7-11. Upon this realization, Dr. Fu confirmed that his analysis suffered from major problems (id. at 203:17-204:12), and he admitted that all claims of the 794 patent are not anticipated by the Fan Pub. Id. at 172:24-173:7, 229:10-230:3 (acknowledging that the experimental procedures in the Fan Pub are different from the methods claimed in the 794 patent); MoneyIN, Inc. v. Verisign, Inc., 545 F.3d 1359, 1371 (Fed. Cir. 2008) ( differences between the prior art reference and a claimed invention, however slight, invoke the question of obviousness, not anticipation ). B. The Fan Pub does not disclose step (a) of Claim 1 Before founding Ariosa and becoming the chairman of its board of directors, Dr. Stuelpnagel was deposed in 2006 by Affymetrix in a matter unrelated to the patents at issue here. In that deposition, Dr. Stuelpnagel affirmed that the idea of first putting the DNA on a solid support... was a very crucial contribution (Ex at 168:19-169:19) by Dr. Mark Chee, notwithstanding Dr. Stuelpnagel s awareness of some earlier discoveries by Dr. Fan and Dr. Fu about... how you 21

32 could capture the poly A on a solid support. Id. at 173:13-174:10. As explained in Section II, supra, Dr. Stuelpnagel was correct. Having left Illumina and coopted Illumina s patented method for his new company (Ariosa), Dr. Stuelpnagel and Ariosa recruited Dr. Fu to effectively ask the Board to render this crucial contribution meaningless. Ariosa s attempt back-fired. Dr. Fu testified that the Fan Pub (and its priority document the 810 application) does not teach the single-stranded target sequences attached to a first solid support recited in step (a) of Claim 1: Q: But you ll agree that there s no single-stranded target sequence attached to the solid support in your patent application? THE WITNESS: That s correct. THE REPORTER: Okay. Hold on. Finish your question. You ll agree there's no single-stranded target sequence attached to the solid support? BY MR. REINES: Q: The answer is yes? A: Yes. Ex at 186:9-20; see also id. at 186:21-188:10 (confirming that the bases for his opinion that this element of Claim 1 was not disclosed in the Fan Pub include that the target sequences are necessarily only coupled by hybridization, that when they are captured by hybridization the strands from the sample are necessarily double-stranded in the coupled portion, and that there were many elements in 22

33 between the target sequence and the solid support); and see id. at 72:14-18, 181:8-15 (further supporting Dr. Fu s stated bases for non-inclusion of step (a) in the Fan Pub). In fact, Dr. Fu illustrated that there are a significant number of links between the target sequence to be interrogated by the probes and the solid support. See Ex. 2013; Ex at 175:23-177:17. Likewise, Dr. Fu agreed that there is never a single-stranded target sequence attached to the solid support because the hybridization process converts a single strand to a double strand. Id. at 181:24-182:6. Having agreed that this element is not in the Fan Pub, Dr. Fu concedes that it does not disclose at least step (a) of Claim 1. That Dr. Fu correctly made this concession is no surprise. As previously explained by Patent Owner (Paper 12 at 12-14), the specification is clear that the attached target sequences are coupled to the first solid support with sufficient affinity to withstand denaturation of the hybridization between two polynucleotide sequences. Ex at 21:16-28, 14:11-16, 17:36-38, 68:64. In fact, the specification lists a number of mechanisms for achieving this strong coupling, none of which are hybridization. Id. at 15:48-16; see also id. at Figures 1 and 3-6. However, Ariosa s Petition relies on an intricate coupling mechanism from the Fan Pub that forms a double-stranded portion between the poly(a) tail of mrna and a poly(t) bead from the Fan Pub held together solely by hybridization to meet step (a) of Claim 1. Paper 1 at As Ariosa s experts 23

34 conceded, this poly(a) poly(t) coupling cannot withstand denaturation conditions. Ex at 182:7-183:5 (discussing Ex. 2013); Ex at 146:19-148:25. Dr. Ward s testimony is equally unhelpful to Ariosa. Dr. Ward conceded that in rendering his opinion, he treated the term immobilized (as in step (f)) and the term attached (as in step (a)) as synonymous. Ex at 107:3-13. However, different terms in a claim are presumed to have different meanings. Innova/Pure Water, Inc. v. Safari Water Filtration Sys., 381 F.3d 1111, (Fed. Cir. 2004). Moreover, Dr. Ward s testimony supports the reasoning behind Dr. Fu s concession. Ex at 113: The Board should credit Dr. Fu s correct testimony that the Fan Pub does not teach step (a) of claim 1. As such, the Fan Pub cannot anticipate Claim 1, or any claim that depends from it. C. The Fan Pub does not disclose step (b) of Claim 1 Step (b) of Claim 1 recites contacting said target sequences with a probe set comprising more than 100 different single-stranded probes... wherein each of said more than 100 different probes has identical universal priming sites. Ex at 68:50-56 (emphases added). The recitation of more than 100 different single-stranded probes was an important claim limitation added during patent prosecution. See Ex at 6-7. The Fan Pub s more 10 than [sic] does not disclose this limitation. 24

35 1. The Fan Pub s more 10 than [sic] probes does not anticipate more than 100 different single-stranded probes Ariosa cites two paragraphs of the Fan Pub 15 and 43 as allegedly disclosing more than 100 different single-stranded probes. Paper 1 at 16. Paragraph 15 of the Fan Pub does not disclose any number of probes. In addition, it is directed to a single-oligo protocol, so is not relevant to this element in step (b) of Claim 1. Ex at 142:22-143:23, 156:12-14, 169:6-14. Paragraph 43 of the Fan Pub discloses a plurality of target probes wherein plurality means at least two, with more 10 than [sic] being preferred. Ex The Petition provides no explanation how a disclosure of more than 10 teaches the claim element of more than 100 different single-stranded probes. Where the prior-art teachings overlap the subject matter of the challenged claims, it is the Petitioner s burden to demonstrate that the claimed subject matter was disclosed in the prior art with sufficient specificity to constitute an anticipation of the challenged claims. Dynamic Drinkware LLC, v. National Graphics, Inc., IPR , Paper 7 at 12 (PTAB, Jan. 29, 2015) (citing Atofina v. Great Lakes Chem. Corp., 441 F.3d 991, 999 (Fed. Cir. 2006)). The absence of any evidence or argument from Ariosa regarding 43 shows that they did not demonstrate that the claimed subject matter was disclosed with sufficient specificity. Therefore, Ariosa did not carry its burden to demonstrate that the subject matter claimed in the 794 patent is disclosed by 43 in the Fan Pub. Id. 25

36 The Petition s claim chart cites to 28 of the Fu declaration and 30 of the Ward declaration to try to support Ariosa s argument that this element is disclosed in the Fan Pub. Paper 1 at Ariosa s citations to the Fu and Ward declarations cannot fix the Petition because the Petition may not be supplemented by incorporating by reference statements from expert declarations. 37 C.F.R. 42.6(a)(3). Further, the Fu declaration simply cites to 43 of the Fan Pub and, without any analysis, concludes that a person of ordinary skill would have understood that a probe set of 100 or more single stranded probes would be used. Ex Similarly, the Ward declaration cites 43 and 106 of the Fan Pub and, without any analysis or explanation, asserts that performing 2,000 different assays on 96 samples, or 192,000 [different assays] on the same sample... would require more than 100 different probes. Ex ; Ex at 122:8-23. These statements from the Fu and Ward declarations provide no explanation or analysis and are entitled to no weight. 37 C.F.R (a). However, Dr. Ward did explain during cross-examination that a multiplexed assay for at least 100 target sequences operates differently from a multiplexed assay for at least 10 target sequences. Ex at 82:24-83:15, 85:8-86:9. Given Dr. Ward s testimony, Ariosa should have explained how a multiplexed assay that uses more than 10 probes would have been expected to operate the same as an assay that uses more than 100 probes. Osram Sylvania, Inc. v. Am. Induction 26

37 Techs., Inc., 701 F.3d 698, (Fed. Cir. 2012). But Ariosa did not provide any such explanation, and Ariosa thus failed to carry its burden to demonstrate that the claimed subject matter was disclosed in the Fan Pub with sufficient specificity. Dynamic Drinkware, IPR , Paper 7 at The Fan Pub does not disclose each of said more than 100 different probes has identical universal priming sites Step (b)(i) of Claim 1 recites wherein each of said more than 100 different probes has identical universal priming sites. Ex at 68:54-56 (emphasis added). The Fan Pub does not disclose more than 100 different single-stranded probes having identical universal priming sites. Ariosa and its expert declarations do not even attempt to explain how the Fan Pub discloses 100 different singlestranded probes having identical universal priming sites. Paper 1 at 16-17; Ex ; Ex At most, Ariosa and its experts cite, without comment or explanation, 44 of the Fan Pub. However, 44 contemplates embodiments that are clearly distinct from this element of Claim 1: different assays or different multiplexing analysis may utilize a plurality of universal priming sequences. Ex (emphasis added). Thus, 44 contemplates embodiments in which the probes contain nonidentical sequences. Further, 44 is silent regarding the number of different probes. Thus, 44 does not disclose more than 100 different single-stranded probes having identical universal priming sites. Ariosa does not explain how 44 27

38 might be assembled with other teachings in the Fan Pub to teach this claim element. Since 44 contemplates embodiments distinct from Claim 1, 44 does not teach 100 different single-stranded probes having identical universal priming sites with sufficient specificity to anticipate Claim 1. See Atofina, 441 F.3d at 999. D. The Fan Pub does not disclose all elements of Claim 1 as arranged in the claim To be anticipatory, a reference must unequivocally disclose the claimed [invention] or direct those skilled in the art to the [invention] without any need for picking, choosing, and combining various disclosures not directly related to each other. Net MoneyIN, 545 F.3d at 1371 (quoting In re Arkey, 455 F.2d 568, 587 (C.C.P.A. 1972)). Anticipation is not established by combining parts of separate protocols. Id. ( it was error for the district court to find anticipation by combining different parts of the separate protocols in the [reference] simply because they were found within the four corners of the document ). The Fan Pub and the 810 application are separate documents that disclose several different gene expression profiling assays, including single-oligo, twooligo, and three-oligo protocols. 3 Ex at 42:21-43:10, 53:21-25; Ex at 32:21-33:1, 36:7-19; Ex , 41. Each of these protocols has separate and distinct methodologies. Ex at 142:10-14, 65:7-17; Ex at 42:20-43:3, 45:2-7, 50:23-51:6, 130:25-131:7, 149:5-13; Ex , 32-35, 37. Ariosa 3 These protocols are described, infra, at Sections V.E and VI.C.1. 28