Sorgev.Kawashima et al.Download PDFPatent Trial and Appeal BoardDec 27, 201613886234 (P.T.A.B. Dec. 27, 2016) Copy Citation -1- BoxInterferences@uspto.gov Filed: 27 December 2016 Tel: 571-272-9797 UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD JOSEPH A. SORGE, Junior Party, (Patent 8,383,343) v. ERIC H. KAWASHIMA, LAURENT FARINELLI, and PASCAL MAYER, Senior Party, (Application 13/886,234) Patent Interference No. 106,019 (Technology Center 1600) Before: RICHARD E. SCHAFER, SALLY GARDNER LANE, and DEBORAH KATZ, Administrative Patent Judges. LANE, Administrative Patent Judge. Judgment - Bd.R. 127(a) -2- In view of the Decision on Priority and other Motions (Paper 165), it is 1 ORDERED that judgment on priority as to Count 1 (Declaration 2 (Paper 1, p.4), the sole count of the interference, is entered against junior party 3 JOSEPH A. SORGE; 4 FURTHER ORDERED that claims 1-13 of junior party patent 5 8,383,343 which claims correspond to Count 1, are CANCELLED; 35 USC 6 135(a);1 7 FURTHER ORDERED that the parties are directed to 35 USC 135(c) 8 and to Bd. R. 205 regarding the filing of settlement agreements; 9 FURTHER ORDERED that a copy of this judgment shall be entered 10 into the administrative record of the involved junior party patent and the involved 11 senior party application; and 12 FURTHER ORDERED that a party seeking judicial review timely 13 serve notice on the Director of the United States Patent and Trademark Office; 14 37 C.F.R. §§ 90.1 and 104.2. See also Bd. R. 8(b). Attention is directed to Biogen 15 Idec MA, Inc., v. Japanese Foundation for Cancer Research, 785 F.3d 648, 16 654–57 (Fed. Cir. 2015) (determining that pre-AIA § 146 review was eliminated 17 for interference proceedings declared after September 15, 2012). 18 1 Any reference to a statute is to statute that was in effect on March 15, 2013 unless otherwise indicated. See Pub. L. 112-29, § 3(n), 125 Stat. 284, 293 (2011). -3- cc (via e-mail): Attorney for Sorge: Daniel A. Lev dlev@pierceatwood.com Gary A. Walpert gwalpert@pierceatwood.com Attorney for Kawashima: Brenton R. Babcock 2brb@knobbe.com Brenden Gingrich 2bsg@knobbe.com David P. Kujawa 2dpk@knobbe.com Edward R. Reines edward.reines@weil.com 1 BoxInterferences@uspto.gov Filed: 27 December 2016 Tel: 571-272-9797 UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD JOSEPH A. SORGE, Junior Party, (Patent 8,383,343) v. ERIC H. KAWASHIMA, LAURENT FARINELLI, and PASCAL MAYER, Senior Party, (Application 13/886,234) Patent Interference No. 106,019 (Technology Center 1600) Before RICHARD E. SCHAFER, SALLY GARDNER LANE, and DEBORAH KATZ, Administrative Patent Judges. LANE, Administrative Patent Judge. Decision – Priority and Other Motions – Bd. R. 121(a) 2 I. Introduction 1 We have before us for decision a single substantive motion from junior party 2 Sorge. (Sorge Motion 1, Paper 35). Sorge Motion 1 seeks to change the 3 correspondence of claims to the count. See Bd. R. 208(a) (2). Kawashima filed an 4 opposition to the Sorge Motion. (Kawashima Opposition 1, Paper 89) and Sorge 5 filed a reply to that opposition. (Sorge Reply1, Paper 141). Kawashima was 6 authorized to file (Order, Paper 150), and did file, responses to the additional 7 statements of material facts in the Sorge reply. (Kawashima Responses, Paper 8 151).1 9 In addition Sorge filed a motion seeking the exclusion of certain evidence 10 relied upon in Kawashima Opposition 1. (Sorge Motion to Exclude, Paper 147). 11 Kawashima opposed (Kawashima Opposition to Motion to Exclude, Paper 152) 12 and Sorge replied. (Sorge Reply to Kawashima Opposition to Motion to Exclude, 13 Paper 153). 14 We deny the Sorge motion to change claim correspondence and dismiss as 15 moot the Sorge motion seeking exclusion of evidence. Because the earliest 16 conception date alleged by Sorge in its priority statement is after Kawashima’s 17 earliest accorded benefit date and Sorge did not attack that accorded benefit, we 18 enter judgment on priority against Sorge. 19 20 1 The parties’ requests for oral argument were considered but the Board has determined that no oral argument is necessary. (Sorge Request, Paper 146 and Kawashima Request, Paper 145). 3 II. Findings of fact 1 The record supports the following findings of fact, as well as the other 2 findings of fact set forth elsewhere in this decision, by a preponderance of the 3 evidence. 4 Parties 5 1. Junior party Sorge is involved in the interference on the basis of its 6 patent 8,383,343, issued 26 February 2013, from application 10/391,090, filed 18 7 March 2003. 8 2. Sorge indicates that its real party in interest is Catalyst Assets, LLC. 9 (Real Party Notice, Paper 4). 10 3. Senior party Kawashima is involved in the interference on the basis of 11 its application 13/886,234, filed 02 May 2013. 12 4. Kawashima indicates that its real party in interest is Illumina, Inc., and 13 its wholly owned subsidiary is Illumina Cambridge Limited. (Real Party Notice, 14 Paper 8). 15 Count 16 5. The count, count 1, is claim 1of the Sorge involved patent or claim 2 17 of the Kawashima involved application, each of which reads: 18 A process that can be used to identify in a nucleic acid sample the presence 19 or absence of nucleic acid sequence differences, wherein each said difference is 20 with respect to one or more reference sequences, the process comprising: 21 22 a) fragmenting nucleic acids in said sample; 23 24 b) linking adapter sequences to the nucleic acid fragments generated in step 25 a); 26 27 c) binding said nucleic acid fragments to a solid support to form bound 28 nucleic acid fragments, and amplifying said bound nucleic acid fragments; and 29 4 1 d) identifying nucleic acid sequences within said amplified nucleic acid 2 fragments. 3 4 (Declaration, Paper 1, p. 4; Kawashima Clean Copy of Claims, Paper 10; Sorge 5 involved patent, Ex 2041). 6 7 6. The following claims are designated as corresponding to count 1 8 Sorge: 1-13 9 Kawashima: 2-15 10 (Declaration, Paper 1, p. 4). 11 Claims relevant to Sorge Motion 1 12 7. Sorge moves to have its claims 4-6 and 13 designated as not 13 corresponding to count 1. 14 8. Sorge claim 4, which Kawashima copied and is Kawashima claim 5, 15 is directed to the process of count 1 “wherein there are a plurality of solid supports 16 which each immobilizes separation elements which bind said nucleic acid 17 fragments to the solid supports” and “the solid supports are beads or a nylon or 18 nitrocellulose membrane having an oligonucleotide capable of hybridizing to the 19 adapter sequences attached to the nucleic acid fragments.” (’343 patent, Ex 2041; 20 Kawashima Clean Copy of Claims, Paper 10, Kawashima Opposition 1, Paper 89, 21 p.7 fn. 2). 22 9. Sorge claim 5 specifies that “the beads [of claim 4] are agarose or 23 cellulose or paramagnetic beads.” (’343 patent, Ex 2041). 24 10. Sorge claim 6, which Kawashima copied and is Kawashima claim 6, 25 is directed to the process of count 1 “wherein sequence differences are identified in 26 5 at least 10,000 nucleic acid fragments”. (’343 patent, Ex 2041; Kawashima 1 Opposition 1, Paper 89, p. 7 fn. 2). 2 11. Sorge claim 13 is directed to the process of count 1 “wherein the 3 identifying of nucleic acid sequences in step (d) includes hybridizing, sequencing 4 primers to the bound and amplified fragments and ligating the sequencing primers 5 to oligonucleotides which are also hybridized to the bound and amplified 6 fragments”. (’343 patent, Ex 2041). 7 Benefit and priority 8 12. The parties were accorded benefit of the following applications: 9 Sorge 10 11 US 09/338,855, filed 23 June 1999 12 13 Kawashima 14 15 US 13/828,047, filed 14 March 2013, 16 17 US 12/148,133, filed 16 April 2008, 18 now patent 8,476,044 19 20 US 10/449,010, filed 02 June 2003, 21 now patent 7,985,565 22 23 US 09/402,277, filed 30 September 1999 24 25 PCT/GB98/00961, filed 01 April 1998 (published as WO9844151 on 8 October 26 1998) 27 28 UK 9713236.9, filed 23 June 1997 29 30 UK 9713238.5, filed 23 June 1997 31 6 1 UK 9706528.8, filed 01 April 1997 2 3 UK 9706529.6, filed 01 April 1997 4 5 (Declaration, Paper 1, p.5). 6 13. In its Priority Statement (Sorge Priority Statement, Paper 32), Sorge 7 alleges an earliest conception date of 09 May 1997, a date after Kawashima’s 8 earliest accorded benefit date of 01 April 1997. 9 14. Sorge was authorized, but choose not, to file a motion attacking the 10 benefit accorded to Kawashima. (Order Setting Times, Paper 24, p.3; Sorge 11 Notice, Paper 75). 12 Related proceedings 13 15. The same parties are involved in related interference 106,020. 14 16. Interference 106,020 involves Sorge patent 8,263,338 and the same 15 Kawashima application as is involved here. (106,020, Declaration, Paper 1). 16 17. The count in interference 106,020 differs from the present count in at 17 least that it includes the phrase “whereby there is enrichment of subsets of the 18 nucleic acid fragments” with reference to the amplifying of step c). 19 18. Prior to the declaration of interference Sorge requested reexamination 20 of its involved patent and the patent involved in 106,020. (Sorge Notice of Related 21 Proceedings, Paper 5 and in Interference 106,020 Sorge Notice of Related 22 Proceedings, Paper 5). 23 19. In the request for its patent involved in this interference Sorge asked 24 for reexamination of claims 1, 3 and 7-12 over Kawashima published benefit 25 application WO9844151 (Kawashima publication) asserting that the Kawashima 26 publication anticipates these claims. (Request for Reexamination, Ex 1048). 27 7 20. That request was granted (See Paper entered in 90/020,080 on 1 April 1 2015) but the reexamination proceeding was suspended after the grant pursuant to 2 an Order by the Board. (See Paper entered in the application on 7 April 2015 and 3 Board Order, Paper 132). 4 Testimony 5 21. Sorge relies upon the testimony of Dr. Michael L. Metzker, Ph.D. 6 (Metzker Declaration, Ex 2006 and Second Metzker Declaration Ex 2043). 7 22. Dr. Metzker has a Bachelor of Science degree in Biochemistry & 8 Biophysics and a doctorate degree in Molecular and Human Genetics. (Metzker 9 Declaration Ex 2006, ¶2). 10 23. Dr. Metzker has extensive experience with technology development in 11 DNA sequencing methods as discussed within his declaration testimony. (Metzker 12 Declaration, Ex 2006, ¶¶4-6). 13 24. Based on his education, professional and research experience as 14 discussed further in his declaration testimony (Metzker Declaration, Ex 2006, ¶¶2-15 9) and curriculum vitae (Ex 2007), we find Dr. Metzker to be qualified to testify 16 regarding the technical subject matter involved in the interference. 17 25. Dr. Metzker’s testimony shows that he considered the count and the 18 Kawashima involved application as the prior art for purposes of evaluating the 19 obviousness of Sorge claims 4-6 and 13. (Metzker Deposition Transcript, Ex 20 1011, p.155:15-21, 157:24-158:10 (objections omitted); Metzker Declaration, Ex. 21 2043, ¶¶ 23-28). 22 2 Sorge requested rehearing of the Board Order (Request, Paper 18) but later withdrew the Request. (Withdrawal of Request, Paper 164). 8 26. Dr. Metzker’s testimony does not contain a statement that he 1 considered all other known relevant prior art, including prior art identified in the 2 Kawashima proposed motions list as allegedly anticipating or rendering obvious 3 the Sorge claims (Kawashima Motions List, Paper 20),3 and determined that it 4 would not have overcome the differences between the subject matter of the count 5 and the subject matter of Sorge claims 4-6 and 13 or that the differences were not 6 merely routine or conventional in the art. 7 27. We agree with the parties that the record shows that a person of 8 ordinary skill in the art would have had a Ph.D. degree or equivalent amount of 9 education and several years of experience in the laboratory performing 10 experiments in the field of biochemistry, molecular biology, molecular genetics, or 11 a related discipline. (Sorge Motion 1, SMF4 5 and Kawashima Opposition 1 at 12 2:15-21 and Appendix 2, p.2, responding to SMF). 13 3 Consideration of whether Kawashima would be authorized to file this motion was deferred until a time after the present motions had been decided. (Order Authorizing Motions, Paper 24, p. 4). As a result of this decision the involved Sorge claims will be cancelled so there is no reason to authorize a motion attacking the patentability of these claims. 4 Statement of Material Fact. 9 III. Discussion. 1 A. Sorge Motion 1 2 Sorge moves to have claims 4-6 and 13 of its involved patent designated as 3 not corresponding to count. Sorge claim 4 and claim 6 were copied by Kawashima 4 as Kawashima claims 5 and 6 (also designated as corresponding to count 1) but it 5 does not appear that Sorge claims 5 and 13 were copied. (’343 patent, Ex 2041; 6 Kawashima Clean Copy of Claims, Paper 10; Kawashima Opposition 1, Paper 89, 7 p.7 fn. 2). 5 8 To be sufficient a motion must provide a showing, supported with 9 appropriate evidence, such that, if unrebutted, it would justify the relief sought. 10 The burden of proof is on the movant. Bd. R. 208(b). 11 A claim corresponds to the count if the subject matter of the count, treated as 12 prior art to the claim, would have anticipated or rendered obvious the subject 13 matter of the claim. Bd. R. 207(b) (2). Thus to prevail in its Motion 1 Sorge must 14 address, inter alia, the scope and content of the prior art and show how this prior 15 art would not have rendered obvious Sorge claims 4-6 and 13 in view of the count. 16 KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 399 (2007), citing Graham v. John 17 Deere Co. of Kansas City, 383 U.S. 1, 17-18 (1966). A showing that an opposing 18 party does not claim or describe the subject matter of the moving party’s claim is 19 not sufficient to show the claim does not correspond to the count since the claim 20 may nevertheless have been obvious when considered in view of all known prior 21 5 Kawashima notes that were we to conclude that the subject matter of Sorge claim 4 and 6 should not be designated as corresponding to the count there potentially could be a second interference involving this subject matter since both parties claim it. Since we do not grant Sorge Motion 1 there is no need to consider whether a second interference would be appropriate. 10 art and the count. 1 We recognize that proving that subject matter is not obvious may require a 2 negative proof, i.e., that no prior art in combination with the subject matter of the 3 count could render the claimed subject matter obvious. As noted in the Standing 4 Order, a party may be able to satisfy its burden of production with testimony from 5 a knowledgeable witness certifying that the witness is unaware of any prior art that 6 would have overcome the differences between the subject matter of the count and 7 the subject matter of the claim and that the differences were not merely routine or 8 conventional in the art. (Standing Order, Paper 2, ¶208.1). 9 The opinions of an expert witness must disclose the underlying facts or data 10 upon which the opinion is based. Opinions expressed without disclosing the 11 underlying facts or data may be given little, or no, weight. (Bd. R. 158(a); 12 Standing Order, Paper 2, ¶ 158.1.1). 13 The Count 14 The count is directed to a process of identifying sequence differences, also 15 known as a single nucleotide polymorphisms (SNPs), within a nucleic acid sample 16 as compared to a reference sequence. The steps of the process comprise first 17 fragmenting the nucleic acids of the sample and then linking adapter sequences to 18 these fragments. The nucleic acid fragments are bound to a solid support and 19 amplified which allows them to be identified. 20 Dr. Metzker’s testimony 21 Sorge Motion 1 relies on Dr. Metzker’s testimony to show a lack of 22 obviousness of the subject matter of its claims 4-6 and 13. One difficulty we have 23 with this testimony is that it does not show that Dr. Metzker considered all 24 identified relevant prior art in making his determinations regarding the particular 25 11 subject matter found at claims 4-6 and 13. Instead Dr. Metzker’s testimony, when 1 addressing these claims, discusses only the count and the involved Kawashima 2 application as prior art. Dr. Metzker’s cross examination testimony is consistent 3 with our observation that he considered, as prior art, the count and the involved 4 Kawashima application in coming to his opinions regarding Sorge claims 4-6 and 5 13. (See, e.g., Metzker Deposition Transcript (Ex 1011) at p.155:15-21, p. 157:24-6 158:10 (objections omitted) stating, e.g., “…I was to look at the count and then to 7 look at Kawashima as - - as determining whether the dependent claim elements 8 were obvious or not obvious”). 9 As we noted above a party may be able to show non obviousness through a 10 statement from a knowledgeable witness certifying that the witness does not know 11 of any prior art that would have overcome the differences between the subject 12 matter of the count and the subject matter of the claim and that the differences 13 were not merely routine or conventional in the art. However, we were not directed 14 to such a statement in Dr. Metzker’s testimony nor to any other indication that Dr. 15 Metzker considered all identified relevant prior art in analyzing the obviousness of 16 Sorge claims 4-6 and 13. At the very least Dr. Metzker should have considered the 17 prior art raised in the Kawashima proposed motions list that purportedly rendered 18 obvious the Sorge claims. (Kawashima Motions List, Paper 20, p. 1 and 2). In its 19 Motion 1 Sorge does not direct us to portions of Dr. Metzker’s testimony where he 20 explains why, or even asserts that, this art, and other known prior art, in 21 combination with the subject matter of the count would not have rendered obvious 22 the subject matter of claims 4-6 and 13. 23 We note, and Sorge points out in its Reply 1, that Dr. Metzker provides a 24 general discussion of the “scope of content of the prior art at the time of the Sorge 25 12 invention” in declaration testimony prepared for the 106,020 interference (Sorge 1 Reply 1, Paper 141, p. 1:27-2:3) referring to Metzker Declaration, Ex 2006) and in 2 amended declaration testimony submitted with its Reply. (Amended Metzker 3 Declaration, Ex 1005).6 However, we have not been directed to portions of that 4 testimony that address the subject matter of Sorge claims 4-6 and 13 in particular 5 and indicate that Dr. Metzker considered other identified prior art in reaching his 6 opinions about this subject matter. Even if we were to accept that Dr. Metzker did 7 consider the prior art cited in his general discussion in accessing Sorge claims 4-6 8 and 13, Sorge does not point out where Dr. Metzker explains how this prior art 9 would not have rendered these claims obvious. 10 We discuss the particular claims below. 11 Claims 4 and 5 12 Sorge claim 4, which is the same as copied Kawashima claim 5, requires that 13 “the solid supports are beads or a nylon or nitrocellulose membrane having an 14 oligonucleotide capable of hybridizing to the adapter sequences attached to the 15 nucleic acid fragments.” (’343 patent, Ex 2041). Sorge claim 5 specifies that “the 16 beads [of claim 4] are agarose or cellulose or paramagnetic beads.” (’343 patent, 17 Ex 2041). 18 Sorge argues, and we agree, that the count does not expressly or inherently 19 6 We understand the Amended Metzker Declaration (Ex 1005) to have been prepared in response to objections by Kawashima that the Second Metzker Declaration (Ex 2043) improperly incorporated by reference portions of the Metzker Declaration prepared for interference 106,020. (Deposition of Metzker, Ex 1011, p. 116:17-118:17). In this decision we refer primarily to the testimony at Exhibits 2006 and 2043 when discussing Sorge Motion 1 since that is the evidence cited in support of the Motion. However, it appears that Exhibit 1005 only repeats testimony found within Exhibits 2006 and 2043. 13 include the limitation of using beads or a nylon or nitrocellulose membrane as the 1 solid support. Sorge acknowledges that “beads and nylon or nitrocellulose 2 membranes were known [solid supports] in the art”. (Sorge Motion 1, p. 12:8-12), 3 Sorge’s arguments rely upon the testimony of Dr. Metzker. Regarding 4 claims 4 and 5 Dr. Metzker testified as follows: 5 24. Claim 4 of the ’343 patent specifies that the solid support 6 of the Count is beads or a nylon or nitrocellulose membrane. Claim 5 7 further specifies that the beads are agarose, cellulose, or paramagnetic. 8 As discussed above, the ’234 application does not support a claim to 9 using beads or such a membrane as the solid support. By contrast, 10 Sorge demonstrated that beads and nylon or nitrocellulose membranes 11 were compatible with the enrichment methods disclosed in the ’343 12 patent. See for example ’343 patent, col. 34, ll. 58-67. At the time of 13 the Sorge invention, there were many solid support options to select 14 from such that the use of a solid support for binding nucleic acid 15 fragments in the Count would not have presented a person of ordinary 16 skill in the art with a finite and discrete number of choices. 17 18 25. In addition, using any particular solid support would not 19 have yielded predictable results. For example, the bridge amplification 20 method of the ’234 application is incompatible with the use of beads, 21 as discussed above. Therefore, it is my opinion that a person of 22 ordinary skill in the art would not have expected that the beads or a 23 nylon or nitrocellulose membrane would work with the invention of 24 the Count. 25 26 (Second Metzker Declaration, Ex 2043, ¶¶24 and 25). 27 We agree with Dr. Metzker that the Count did not present a person of 28 ordinary skill in the art with “a finite and discrete number of choices” for solid 29 supports, but this statement does not amount to an explanation of why selecting 30 14 known supports would not have been obvious. Dr. Metzker’s testimony that 1 “using any particular solid support would not have yielded predictable results” is 2 not supported by underlying facts or data other than the contention that the 3 involved Kawashima application does not disclose using these solid supports. As 4 we stated above this is not the correct standard for evaluating claim 5 correspondence. 6 Dr. Metzker’s testimony that “Sorge demonstrated that beads and nylon or 7 nitrocellulose membranes were compatible with the enrichment methods disclosed 8 in the ’343 patent” also is not persuasive. The Count does not require the feature 9 of “enriching” the bound nucleic acid fragments so the question of whether the 10 solid supports of claims 4 and 5 would work in such “enrichment methods” is not 11 the relevant inquiry. 12 Sorge argues that one skilled would not have chosen beads or a nylon or 13 nitrocellulose membrane as supports even though they were known in the art 14 because these supports suffered insurmountable signal to noise (SNR) problems. 15 To support this argument Sorge refers the testimony of Dr. Metzker which refers to 16 the involved Kawashima application and its failure to use such supports for 17 “enriching and identifying” SNPs of bound nucleic acid fragments. This argument 18 is not persuasive since Dr. Metzker did not indicate that he considered the prior art 19 other than the Count and the involved Kawashima application in making his 20 determination. 21 Further Dr. Metzker’s cross-examination testimony indicates that one of 22 skill in the art reading Kawashima’s disclosure would have understood that they 23 could use, e.g., agarose beads in Kawashima’s method. (Second Metzker 24 Deposition, Ex 1012, p. 241:3-23, p. 239:22-242:22, stating, e.g., one skilled in the 25 15 art “would know how to bind nucleic acids that have adapters ligated to the ends of 1 those fragments to amplify on a solid support” such as agarose beads.) In its 2 Reply 1, Sorge does not address or dispute this testimony by Dr. Metzker or 3 otherwise reply to Kawashima’s specific arguments regarding Sorge claims 4 and 4 5. 5 Sorge has not met its burden to show why claims 4 and 5 should not be 6 designated as corresponding to the Count. 7 Claim 6 8 Sorge claim 6, which is the same as copied Kawashima claim 6, is directed 9 to the process of Count 1 “wherein sequence differences are identified in at least 10 10,000 nucleic acid fragments”. (’343 patent, Ex 2041). 11 12 Regarding claim 6, Dr. Metzker testified as follows: 13 26. Claim 6 of the ’343 patent specifies that the method of 14 claim 1 (which corresponds to the Count), is used to identify sequence 15 differences in at least 10,000 nucleotide fragments. Prior to the 16 complexity reduction invention of the ’343 patent, there was no 17 practical way to identify sequence differences in samples having large 18 numbers of fragments of interest. This was because the signal from 19 the fragments of interest could not be distinguished from the noise of 20 all the other fragments in the sample. As discussed above, Kawashima 21 may indicate an aspiration to sequence up to 1,000,000 fragments 22 simultaneously using bridge amplification, and bridge amplification 23 might have been able to generate tens of thousands of colonies 24 without complexity reduction or enrichment. See ’234 application, 25 paragraph [0219]. But the reality is that neither Kawashima nor 26 anyone else was able to detect signal from tens of thousands of 27 colonies to allow a person of ordinary skill in the art to determine that 28 many sequence difference at the time, whereas Sorge demonstrated 29 16 that his complexity reduction invention enabled the identification of 1 differences across more than 10,000 fragments. See for example ’343 2 patent, Examples 1-4. 3 4 (Second Metzker Declaration, Ex 2043, ¶26). 5 The testimony that Sorge directs us to regarding claim 6 does not mention 6 any prior art other than the Kawashima involved application. Dr. Metzker 7 concedes that the Kawashima application contains disclosure of a method of 8 sequencing “up to 1,000,000 fragments simultaneously” but implies, without 9 further explanation, that Kawashima did not enable such a method. Dr. Metzker’s 10 testimony regarding claim 6 also does not address this same disclosure as it 11 appears Kawashima benefit application WO 98/44151 which Sorge asserted 12 anticipates other involved Sorge claims (Kawashima benefit application WO 13 98/44151, published 08 October 1998, Ex 2031, p. 50. FF 19). 14 Sorge argues that “[a]ccepting the Count as prior art, a POSITA would not 15 have had a reasonable expectation that sequence differences could have been 16 identified in more than 10,000 nucleic acid fragments…” and that “[t]his was 17 because the SNR prevented discriminating signals from thousands of fragments”. 18 In support of this argument Sorge directs us to the testimony of Dr. Metzker, which 19 relies upon the involved Kawashima application. According to Dr. Metzker that 20 application does not demonstrate signal differentiation in arrays of thousands of 21 nucleic fragments. Metzker Decl. ¶ 63; Ex. 2043, ¶ 26; Metzker Decl. ¶ 47. This 22 argument is not persuasive since Dr. Metzker did not indicate that he considered 23 the prior art other than the Count and the involved Kawashima application in 24 making his determination. 25 We note also that claim 6 does not require identifying the sequence 26 17 differences “simultaneously” as Dr. Metzker’s testimony suggests. Further the 1 testimony pointed out to us regarding claim 6 does not provide sufficient basis, 2 such as a full discussion of the relevant prior art, for Dr. Metzker’s opinion that 3 one skilled in the art would not have found it obvious to perform the process of the 4 count in a way to allow for identification of sequence differences “in at least 5 10,000 nucleic acid fragments.” While Dr. Metzker testified that “neither 6 Kawashima nor anyone else was able to detect signal from tens of thousands of 7 colonies”, we have not been directed to testimony or other evidence explaining 8 why the known prior art, including the Count which is not limited to any particular 9 amplification method,7 would not have rendered obvious a method that allow for 10 identification of sequence differences in at least 10,000 nucleic acid fragments. 11 In his cross examination testimony Dr. Metzker seemed to concede that prior 12 art methods were known that would allow for identification of sequence 13 differences in at least 10,000 nucleic acid fragments. For example Dr. Metzker 14 agreed that the prior art method of Winzeler (Ex 2026) discloses a method for 15 examining 10,000 sequence differences in a small genome, such as yeast. (Metzker 16 Deposition Transcript, Ex 1011 at p.159:13-160:18, in particular p.160:6-128). In 17 7 Dr. Metzker testified that the involved Kawashima application focused on the bridge amplification method of amplifying a nucleic acid sample on a solid support to create “colonies” comprising multiple copies of the same nucleic acid sequence in different sections of the solid support but the count is not limited to this method. 8 Q. Okay. And if a person of ordinary skill in the art had just Claim 1[the count], you know, knowledge of that process and they wanted to scale up, they could look at Winzeler and do it his way, correct, to get to scale up? A. Well, Winzeler was looking at the yeast genome. So he was looking at a much smaller genome. And with that small genome, he could apply this technology and scale it up to 10,000. 18 its Reply 1, Sorge argues that “[t]he other primary references, i.e., Winzeler (Ex. 1 2026) … involve arrays of oligonucleotides, not bound and amplified fragments, 2 that are directly bound to a solid support [and] even if they involve bound nucleic 3 acid sequences, they are not directed to the fragmenting, linking, or identifying 4 steps of the Count.” (Sorge Reply 1 at 3:10-20) We agree that Winzeler does not 5 appear to teach every limitation of claim 6. However, Sorge has not directed us to 6 testimony from Dr. Metzker or other evidence that addresses whether claim 6 7 would have been rendered obvious in view of both the count and other known prior 8 art which includes at least Winzeler. 9 Sorge has not met its burden of showing that claim 6 should not be 10 designated as corresponding to the Count. 11 Claim 13 12 Sorge claim 13 is directed to the process of Count 1 “wherein the identifying 13 of nucleic acid sequences in step (d) includes hybridizing, sequencing primers to 14 the bound and amplified fragments and ligating the sequencing primers to 15 oligonucleotides which are also hybridized to the bound and amplified fragments”. 16 (’343 patent, Ex 2041). 17 Regarding claim 13 Dr. Metzker testified: 18 19 27. Claim 13 of the ’343 patent depends from claim 1 and 1 requires the detection step (d) includes hybridizing sequencing 2 primers to the bound and amplified fragments and ligating the 3 sequencing primers to oligonucleotides which are also hybridized to 4 the bound and amplified fragments. As discussed above, Sorge 5 invented a number of distinct methods for detecting sequence 6 differences between nucleic acid samples, primarily using complexity 7 reduction and enrichment, and one of those involves detecting 8 sequence differences by ligating the sequencing primers to 9 oligonucleotides which are also hybridized to the bound and amplified 10 fragments. Kawashima did not copy those claims, and the ’234 11 application does not support a claim covering this distinct invention. 12 13 28. At the time of the Sorge invention, assuming that the 14 Count is prior art to claim 13, one of ordinary skill in the art would 15 not have found obvious the additional step of ligating the sequencing 16 primers to oligonucleotides that are also hybridized to the bound and 17 amplified fragments. As discussed above, ligase-based sequencing 18 was a completely separate technology from polymerase-based 19 sequencing. At the time of the Sorge invention, one of ordinary skill 20 in the art would not have been able to simply substitute the 21 polymerase-based approach of the Count with a ligase-based 22 approach. In addition, the ’343 patent disclosed how to perform 23 ligase-based sequencing in the context of its approach to identifying 24 sequence differences. ’343 patent, col. 26, ll. 5-14. By contrast, the 25 ’234 application focuses on polymerase-based sequencing-by-26 synthesis and does not support using ligation-based sequencing. It is 27 my opinion that ligation-based sequencing was unlikely to be 28 compatible the bridge amplification method of the ’234 application 29 because bridge amplification does not produce enough template 30 nucleic acid sequence for ligation-based sequencing. 31 32 (Second Metzker Declaration, Ex 2043, ¶¶27 and 28). 33 20 1 Dr. Metzker testified that while the ’338 patent disclosed how to perform 2 ligation-based sequencing with the enrichment and complexity reduction methods 3 but that the involved Kawashima application “focuses on polymerase-based 4 sequencing-by-synthesis and does not support using ligation-based sequencing”. 5 This argument is not persuasive since Dr. Metzker did not indicate that he 6 considered the prior art other than the Count and the involved Kawashima 7 application in making his determination. The question before us is not whether the 8 Kawashima application disclosed the subject matter of Sorge claim 13 but whether 9 one skilled in the art considering the Count and all relevant prior art would have 10 arrived at the subject matter of Sorge claim 13. 11 Further Dr. Metzker’s declaration testimony discusses the distinction 12 between polymerase-based methods and ligase-based methods but the Count is not 13 limited to either of these methods. On cross-examination Dr. Metzker testified that 14 the use of known ligase-based detection methods such as the known 15 Oligonucleotide Ligation Assay (OLA) was within the competency of a skilled 16 artisan at the time of the invention. (Metzker Deposition Transcript, Ex 1011 at 17 76:3-78:19; 164:3-28). In its Reply 1, Sorge does not address or dispute this 18 testimony by Dr. Metzker or otherwise reply to Kawashima’s specific arguments 19 regarding Sorge claim 13. 20 Sorge has not met its burden of showing that claim 13 should not be 21 designated as corresponding to the Count. 22 B. Motion to Exclude 23 Sorge moves that the Board exclude from evidence the certain portions of 24 the Declaration of Dr. George M. Weinstock (Ex 1025), exhibits that are said to 25 21 have been cited in Dr. Weinstock’s testimony but not in the Kawashima 1 Opposition, and a letter said to be from the owner of the patent involved in 2 interference 106,020, Catalyst Assets, regarding licensing the claimed technology 3 (Ex 1006). 4 The declaration of Dr. Weinstock (Weinstock Declaration, Ex 1025) is a 5 single declaration prepared for use, and filed in, both interferences 106,019 and 6 106,020. We did not find it necessary to rely upon the Weinstock Declaration in 7 making our determination in this interference that Sorge did not meet its burden of 8 proof on Sorge Motion 1. Further we did not rely on the other evidence Sorge 9 seeks to exclude. 10 We therefore DISMISS as moot the Sorge Motion to Exclude. 11 C. Priority 12 Sorge was authorized to file a motion attacking the Kawashima accorded 13 benefit. The parties agreed that the motion attacking benefit would have been 14 dispositive on the issue of priority. (Order Authorizing Motions, Paper 24, p. 3; 15 Paper Sorge Notice, Paper 75). Sorge choose not to file the motion and did not ask 16 for authorization to file a motion for judgment based on priority. 17 The earliest conception date alleged by Sorge in its priority statement is after 18 Kawashima’s earliest accorded benefit. (FF9 13, Sorge Priority Statement, Paper 19 32). Sorge therefore cannot prevail on priority. Cooper v. Goldfarb, 154 F.3d 20 1321, 1327 (Fed. Cir. 1998) (Priority of invention goes to the first party to reduce 21 to practice an invention of the Count unless the other party can show that it was the 22 first to conceive the invention and that it exercised reasonable diligence in later 23 9 Finding of fact. 22 reducing to practice that invention.); See also Bd. R. 204(a). 1 Judgment on priority will be entered against Sorge in a separate paper. 2 IV. Order 3 It is 4 ORDERED that Sorge Motion 1 is DENIED, 5 FURTHER ORDERED that Sorge Motion 2 is DISMISSED as moot; and 6 FURTHER ORDERED that judgment on priority against Sorge shall be 7 entered in a separate paper. 8 cc (via e-mail): Attorney for Sorge: Daniel A. Lev dlev@pierceatwood.com Gary A. Walpert gwalpert@pierceatwood.com Attorney for Kawashima: Brenton R. Babcock 2brb@knobbe.com Brenden Gingrich 2bsg@knobbe.com David P. Kujawa 2dpk@knobbe.com Edward R. Reines edward.reines@weil.com Copy with citationCopy as parenthetical citation