Ex Parte Gjerde

Patent Trial and Appeal Board

May 22, 2013

12002242 (P.T.A.B. May. 22, 2013)

UNITED STATES PATENT AND TRADEMARKOFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/002,242 12/13/2007 Douglas T. Gjerde P026.210 7128
55130 7590 05/22/2013
PHYNEXUS, INC.
3670 CHARTER PARK DRIVE
SAN JOSE, CA 95136
EXAMINER
BASS, DIRK R
ART UNIT PAPER NUMBER
1779
MAIL DATE DELIVERY MODE
05/22/2013 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
PATENT TRIAL AND APPEAL BOARD
____________

Ex parte PHYNEXUS, INC.
(Application 12/002,242)
____________

Appeal 2012-004507
from Technology Center 1700
____________

HEARD: 16 May 2013
____________

Before RICHARD TORCZON, JAMES C. HOUSEL and DONNA M. PRAISS,
Administrative Patent Judges.

TORCZON, Administrative Patent Judge.

DECISION ON APPEAL
The appellant (PhyNexus) seeks relief from the final rejection of claims 1-9,
13 and 19-28. We AFFIRM.
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OPINION
INTRODUCTION
The claimed invention
PhyNexus filed an application entitled "Method for extracting an analyte",1
naming Douglas T. Gjerde as the inventor. The specification "relates to a method
for extracting an analyte from a liquid sample, wherein the process is characterized
by a plurality of steps[; in] particular, …a pre-elution wash step that can affect the
efficiency of the extraction."2 Claims 1 and 27 are the only independent claims.3
Claim 1 defines the invention as:
A method of extracting a protein from a sample solution, comprising
the steps of:
(a) passing a buffered sample solution containing a protein through a
pipette tip column,
wherein said pipette tip column is comprised of a bed of
extraction medium, and
whereby said protein adsorbs to the extraction medium;
(b) passing a buffered wash solution through the pipette tip column;
(c) optionally, repeating step (b) one or more times;
(d) removing the wash solution by passing an un-buffered pre-elution
solution through the pipette tip column; and
(e) passing a desorption solvent through the pipette tip column to elute
the protein,
wherein the pH of the desorption solvent is 5 or lower.
Optional step (c) is not limiting.4

1 Spec. 1 at 1.
2 Id. at 1:9-11.
3 Br., Apdx. A. In this opinion all references to the claims refer to the claims as
they appear in the claims appendix of the appeal brief. Cf. Ans. 4, item (7).
4 In re Johnston, 435 F.3d 1381, 1384 (Fed. Cir. 2006).
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For contested step (d), PhyNexus defines "pre-elution wash" as "a solution
applied to the extraction column after the sample loading [into the column] and
prior to the desorption [from the bed of extraction medium] step that removes
residual ions or buffer that would otherwise react or interact with the elution buffer
reducing its effectiveness."5 This pre-elution wash step may occur at any time
prior to elution as long as it removes ions or buffer that would interfere with
elution.6
Claim 27 defines an automated method essentially the same as the method of
claim 17 except that "substantially" appears before "removing" in step (d) and the
limitation "wherein the method is performed on a plurality of pipette tip columns
simultaneously" is added at the end.
The rejections
The examiner finally rejected all claims as having been obvious from the
combined disclosures of published applications, each naming Mr. Gjerde as a co-
inventor, as follows8:
Claims 1-9, 13 and 19-26 with Gjerde's 3759 and 36210 publications and
Claims 27 and 28 with Gjerde's 375, 362 and 48811 publications.

5 Spec. 4:3-5.
6 Interactive Gift Express, Inc. v. Compuserve, Inc., 256 F.3d 1323, 1342-43 (Fed.
Cir. 2001) (holding no order required).
7 Br. 11.
8 Final Rej. 2-3, citing 35 U.S.C. 103.
9 D.T. Gjerde & C.T. Hanna, Low dead volume extraction column device,
US 2004/0072375 A1 [375 publication or 375 Pub.].
10 D.T. Gjerde & C.T. Hanna, Open channel solid phase extraction systems and
methods, US 2004/0224362 A1 [362 publication or 362 Pub.].
11 D.T. Gierde [sic] & C.T. Hanna, Method and device for extracting an analyte,
US 2004/0142488 A1.
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PhyNexus does not contest the availability of these published applications as
prior art; instead, PhyNexus challenges the examiner's obviousness analysis in
terms of claim 1.12 Accordingly, we treat claim 1 as representative of the claims
on appeal.
FACTS AND FINDINGS
375 publication
[1] This reference "relates to a device and method for the capture of analytes by
solid phase extraction with a column device and collection of the analytes into a
controlled volume of solvent."13
[2] The analyte may be a protein.14
[3] Proteins are often eluted using a low (pH 2.5-4) solvent.15
[4] The reference discloses a method for extracting an analyte from a sample
solution using an extraction column of the invention.16
[5] The upper end of a column body may be attached to a pump to aspirate fluid
through the lower end of the column body.17
[6] The method involves the steps of (1) introducing a sample solution
containing an analyte into the extraction bed at the lower end of the extraction
column so that the extraction media adsorbs the analyte, (2) discharging the
sample solution, (3) introducing a desorption solvent into the column to elute

12 Br. 4 & 8; see also Br. 11 (basing argument for claims 27 and 28 on claim 1).
C.W. Zumbiel Co. v. Kappos, 702 F.3d 1371, 1378 n.2 & 1381 n.4 (Fed. Cir. 2012)
(treating claims together where argument is the same).
13 375 Pub. ¶0002.
14 Id.; also ¶¶0042, 0097-99 & claim 31.
15 Id. at ¶¶0097-98 & 0158.
16 Id. at ¶0037.
17 Id.
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the analyte from the extraction media and (4) discharging the analyte-
containing desorption solvent.18
[7] Gas may be used to purge the column before desorption.19
[8] The reference teaches that:20
An optional wash step between the extraction and desorption steps can
also improve the purity of the final product. Typically water or a
buffer is used for the wash solution. The wash solution is preferably
one that will remove unwanted contaminants with a minimal
desorption of the analyte of interest.
We note that water alone would not be considered a "solution".
[9] A small elution volume is preferred for greater analyte concentration.21
[10] In one example where the analyte is a protein,22 the reference teaches:23
Alternatively [to purging with gas], the bed may be washed with
10 μL of aqueous 0.1 % TFA. This solution is ejected from the
column and the protein is desorbed and deposited into the [vial].
[11] By "TFA", the reference means "trifluoroacetic acid".24
We note that aqueous 0.1% TFA is an un-buffered aqueous solution.
[12] As a difference from the claimed invention, the examiner finds this reference
does not appear to teach step (d) ("removing the wash solution by passing an
un-buffered pre-elution solution through the pipette tip column") explicitly.

18 Id. & claim 25.
19 Id. at ¶0075.
20 Id. at ¶0156; see also ¶0039 & claim 27.
21 Id. at ¶¶0053, 0062 & 0157; see also claim 28.
22 Id. at ¶0218.
23 Id. at ¶0220. Alternatively, 1% heptafluorobutyric acid may be used instead of
TFA. ¶0221.
24 Id. at ¶0218.
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362 publication
[13] This reference relates to methods for performing solid-phase extractions in
an open-channel device (an extraction capillary) for analytes including
polypeptides (proteins).25
[14] This reference teaches methods for adsorbing an analyte from a sample
solution to an extraction surface, substantially removing the sample solution
and eluting the adsorbed analyte with a desorption solution.26
[15] This reference teaches that it may be desirable to reduce the amount of
desorption solution used in eluting the analyte from the column to increase
analyte concentration in the desorption volume.27
[16] Removal of the sample solution before elution is not always necessary, but it
is usually desirable because doing so reduces contaminants and facilitates
control of the desorption solution.28
[17] The sample solution may be replaced by either a gas or a liquid.29
[18] A person having ordinary skill in the art would know how to select and use
an appropriate wash solution that would remove contaminants with minimal
loss or damage to the adsorbed analyte.30
[19] Multiple wash steps might be desirable.31
[20] The reference gives the example of using a deuterium oxide (D2O) wash
solution before using a deuterated elution solvent.32

25 362 pub. ¶0002.
26 Id. at ¶0047.
27 Id. at ¶¶0011-13.
28 Id. at ¶0056.
29 Id.
30 Id. at ¶¶0059 & 0092.
31 Id. at ¶0060.
32 Id.
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We note the reference does not indicate that the D2O solution is buffered and
so a person having ordinary skill in the art would understand that it need not be
buffered.
[21] Gas purging of the column may be performed before or after the wash step
to eliminate residual solutions in the column prior to elution.33
[22] A person having ordinary skill in the art would know that some analytes may
be allowed to become substantially dry (e.g., a nucleic acid) while other
analytes (e.g., proteins) should remain hydrated.34
[23] Anywhere from 20% to substantially all of the residual solution in the
column may be removed, with the determination of the appropriate amount
being left to the person having ordinary skill in the art.35
[24] Eliminating liquid from the column prior to elution contributes to the
concentration of the analyte in the desorption solvent.36
[25] A person having ordinary skill in the art would have known how to select
and use an appropriate buffer for the solution used to extract the analyte.37
Gjerde declarations38
[26] During examination, PhyNexus filed two declarations from Douglas T.
Gjerde under 37 C.F.R. § 1.132.

33 Id. at ¶0060.
34 Id. at ¶0061.
35 Id. at ¶0062.
36 Id. at ¶0067.
37 Id. at ¶¶0090-91.
38 Gjerde submitted additional figures with its reply brief and a demonstrative
exhibit for the oral argument. These exhibits do not appear to have been
considered by the examiner and are not evidence in the case, but will be treated as
adjuncts to counsel's argument.
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We note that neither declaration is cited in the evidence appendix to the
brief.39
[27] The first, filed in 2009 [the 2009 declaration], is essentially fact testimony
regarding the development of the invention.40
[28] The second, filed in 2010 [the 2010 declaration], is essentially expert
testimony regarding how Dr. Gjerde as one skilled in the art would have
understood the combined references.41
[29] Dr. Gjerde is the inventor for the application on appeal.42
[30] Dr. Gjerde's curriculum vitæ states education and extensive experience in
relevant fields.43
We find Dr. Gjerde qualified to testify as an expert in this art.
We find the fact testimony is not corroborated.
We find Dr. Gjerde's expert testimony does not identify a basis for his
testimony beyond the cited patents.
We find the declarations to be unclear whether Dr. Gjerde had a direct or
indirect financial interest in the outcome of the examination when the declarations
were filed.
[31] Dr. Gjerde testifies that the presently claimed invention was developed to
address a problem with his existing pipette columns in which residual neutral-
pH wash solution diminished the effectiveness of the subsequent low-pH
desorption solvent, particularly when the elution volume was low.44

39 Br., Apdx. B: "(None)".
40 Decl. under 37 C.F.R. § 1.132 at 2-3, ¶¶5-15 (dated 23 Oct. 2009).
41 Decl. under 37 C.F.R. § 1.132 at 2, ¶¶5-8 (dated 12 Oct. 2010).
42 2009 decl. 1; 2010 decl. 1, ¶2.
43 2010 decl., attachment.
44 2009 decl. 3, ¶12; 2010 decl. 1, ¶4.
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[32] Dr. Gjerde testifies that the 362 publication addresses open channels with
surrounding extraction surfaces, not extraction beds.45
[33] Dr. Gjerde testifies that the invention was not obvious to him based on the
proposed combination because he was not yet aware of the problem to be
solved.46
[34] Dr. Gjerde testifies that after purging the channel, "there is no buffer
remaining in the channel to interfere with efficient elution[ s]o the problem of
residual buffering capacity and the solution of passing an un-buffered pre-
elution solution through the channel are not relevant to the open channel
format"47 of the 362 publication.
To the extent that Dr. Gjerde's testimony assumes an improper analysis, we
accord the testimony little or no weight. For example:
We find that Dr. Gjerde's testimony on his subjective understanding of
the cited publications and of the problem he faced has little or no relevance.
We find that Dr. Gjerde's testimony regarding the differences in
operation between the 375 and 362 publications misses the point of the
examiner's reasoning, which is not predicated on a literal combination of the
two methods or on a modification of the 362 publication method, and thus is
entitled to little weight.

45 2010 decl. 2, ¶¶5-6.
46 Id., ¶7.
47 Id., ¶8.
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ANALYSIS
The declarations
PhyNexus filed its appeal brief in April 2011.48 At that time, an appellant
was required to include with the brief any declaration cited in the brief. Any
declaration not included could not be considered.49 The examiner also does not list
the declarations as evidence.50 Both the examiner and PhyNexus discuss the
declarations in the appeal briefing. There is no indication in the record that the
rule was waived. By operation of the rule governing this briefing, we cannot
consider the declarations as part of the evidence before us.
Alternatively, the declarations are entitled to little weight. Dr. Gjerde has at
least a personal interest in the patentability of the invention. Interested testimony
is entitled to less weight particularly, as here, when the fact testimony lacks
corroboration and the expert testimony lacks basis. More importantly, however,
the testimony (both factual and expert) stems from a misapprehension of the
relevant law and the examiner's reasoning. As explained below, the inventor's
avowed subjective purpose and the differences between an open channel and an
extractive bed are not very relevant to the rejection. For example, a person having
ordinary skill in the art would not have been aware of Dr. Gjerde's avowed purpose
when reading the references and thus would have read them simply for what they
literally taught or suggested.

48 Br. 1.
49 37 C.F.R. § 41.37(t) (2010) ("The evidence section shall include: * * *
(5) Affidavits and declarations. Affidavits and declarations, if any, and attachments
to declarations, before the examiner and which are relied upon by appellant in the
appeal. An affidavit or declaration otherwise mentioned in the appeal brief which
does not appear in the evidence section will not be considered."); cf. Fed. R. App.
P. 30(a)(1).
50 Ans. 4, item 8.
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Obviousness
A claimed invention is not patentable if the differences between it and the
prior art are such that the claimed invention as a whole would have been obvious to
a person having ordinary skill in the art.51 The test is objective: the particular
motivation or avowed purpose of the inventor is not controlling.52
The examiner has explained that a person having ordinary skill in the art
would have had reason to practice the claimed method based on the disclosures of
the 375 and 362 publications alone, i.e., without knowledge of or regard to the
purpose Dr. Gjerde avows in his declarations. The examiner held in the final
rejection:53
At the time of invention, it would have been obvious to one
skilled in the art to include the pre-elution wash step of Gjerde '362
with the analyte extraction method of Gjerde [375] in order to purge
any excess buffered wash solution from the column which may affect
sample recovery during the elution phase.
The examiner's reasoning contemplates modifying the 375 method, which included
everything except the pre-elution wash step by adding another pre-elution wash as
the 362 publication suggests.
Both references share the concern in the present application of producing a
high concentration of protein analyte in a small elution volume. Both recognize
the need for eliminating sample solution and contaminants prior to elution. The
362 publication explains that more than one wash or combined washing and
purging might be desirable to achieve this goal. Those in the art knew that proteins
ordinarily should remain hydrated so complete gas purging would not be desirable
with proteins. Incomplete purging would leave some volume of liquid that might

51 35 U.S.C. 103.
52 KSR Int'l v. Teleflex Inc., 550 U.S. 398, 419-20 (2007).
53 Final Rej. 3.
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contain contaminants. An un-buffered wash, such as aqueous 0.1% TFA, could be
safely used for at least some proteins prior to elution. Similarly, an un-buffered
D2O wash solution is sometimes desirable just before elution.
While the references do not expressly state that the first wash can introduce
contaminants that will interfere with the desorption solvent, the art did know that
more than one wash step might be needed to get rid of all of the contaminants that
might interfere with elution. A second wash would displace the first wash. The art
also exemplified the use of un-buffered wash solutions that were appropriate to use
for proteins or in preparation for deuterated elution solvents. Using a known un-
buffered protein-safe or D2O wash solution for the second wash satisfies the claim.
HOLDING
PhyNexus has not shown prejudicial error in the rejection of claim 1 or,
through want of separate argument, of any of the other pending claims.
Accordingly, final rejection of claims 1-9, 13 and 19-28 is—
AFFIRMED
bar

For the appellant: SUE S. KALMAN, PhyNexus, Inc., of San Jose, California.