Sorgev.Kawashima et al.

Patent Trial and Appeal Board

Dec 27, 2016

10391090 (P.T.A.B. Dec. 27, 2016)

-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