Lennart Bjorkesten et al.

Patent Trials and Appeals Board

Mar 3, 2020

14128379 - (D) (P.T.A.B. Mar. 3, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
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.
14/128,379 12/20/2013 Lennart Bjorkesten 253664 (34428-0034) 2505
29052 7590 03/03/2020
EVERSHEDS SUTHERLAND (US) LLP
999 PEACHTREE STREET, N.E.
SUITE 2300
ATLANTA, GA 30309
EXAMINER
GROSSMAN, ANDREA S
ART UNIT PAPER NUMBER
1641
NOTIFICATION DATE DELIVERY MODE
03/03/2020 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
patentdocket@eversheds-sutherland.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte LENNART BJORKESTEN, SOFIA EDLUND, and
ASA HAGNER-MCWHIRTER
____________

Appeal 2018-007155
Application 14/128,379
Technology Center 1600
____________

Before DONALD E. ADAMS, ERIC B. GRIMES, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal1 under 35 U.S.C. § 134(a) involving claims to a
method for identification of specific target biomolecules in a sample in a
detection procedure. The Examiner rejected the claims as obvious and as
reciting non-statutory subject matter. We have jurisdiction under 35 U.S.C.
§ 6(b). We reverse.

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. Appellant identifies the Real Party in Interest as GE
Healthcare Bio-Sciences AB (see Appeal Br. 2).
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Statement of the Case
Background
Western blotting is an analytic technique that “uses gel
electrophoresis to separate native or denatured proteins by the length of the
polypeptide . . . or by the 3-D structure of the protein . . . [t]he proteins are
then transferred to a membrane . . . where they are probed (detected) using
antibodies specific to the target protein” (Spec. 1:11–17)
Due to possibilities of increased signal amplification and to
avoid negative effects on target specific affinity related to
primary antibody conjugation, [the membrane probing]
traditionally takes place in a two-step process (using a primary
target specific antibody and a secondary labeled antibody
specific for the primary antibody), although there are now one-
step detection methods available for certain applications.
(Id. 1:22–26). The one-step method “allows the process to occur faster” but
“requires a probe antibody which both recognizes the protein of interest and
contains a detectable label” (id. 1:27–29).
“The present invention uses several probes, preferably antibodies,
directed against the same or different epitopes of the same target protein.
These antibodies may be more or less specific. Since the method of the
invention combines the signals from the different antibodies, specific signal
can be discriminated from unspecific ones” (Spec. 4:26–29).
The Claims
Claims 1, 3, 4, 9–19, 21, 22, and 24–28 are on appeal. Independent
claim 1 is representative and reads as follows:
1. A method for identification of specific target
biomolecules in a sample in a detection procedure, comprising:
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probing a gel or membrane with at least two probes that
are directed against and specifically bind to a same target
biomolecule to form bands or spot patterns on the gel or
membrane;
obtaining image sample patterns corresponding to the
bands or spot patterns;
overlaying the image sample patterns with each other;
generating image data by applying an algorithm that uses
pixel-wise multiplication to enhance overlapping features and
diminish non-overlapping features of the bands or spot patterns
in the overlayed image sample patterns;
scaling the image data using a root function; and
differentiating the bands or spot patterns corresponding
to specific binding of the probes to the target biomolecule in the
sample from non-specific binding of the probes to other
biomolecules in the sample using the scaled image data.
Appeal Br. 18.
The Issues
A. The Examiner rejected claims 1, 3, 4, 9, 10, 13, 19, 21, 22, and 26
under 35 U.S.C. § 103(a) as obvious over Leimgruber2 and Morris3 (Ans. 6–
9).
B. The Examiner rejected claims 11 and 12 under 35 U.S.C. § 103 as
obvious over Leimgruber, Morris, and Berth4 (Ans. 9–10).

2 Leimgruber et al., Development of improved cell lysis, solubilization and
imaging approaches for proteomic analyses, 2 Proteomics 135–44 (2002).
3 Morris et al., US 2008/0166030 A1, published July 10, 2008.
4 Berth et al., The state of the art in the analysis of two-dimensional gel
electrophoresis images, 76 Appl. Microbiol. Biotechnol. 1223–43 (2007).
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C. The Examiner rejected claims 14, 16, 17, and 28 under 35 U.S.C.
§ 103 as obvious over Leimgruber, Morris, and Tacha5 (Ans. 10–11).
D. The Examiner rejected claim 15 under 35 U.S.C. § 103 as obvious
over Leimgruber, Morris, and Uhlen6 (Ans. 11).
E. The Examiner rejected claim 18 under 35 U.S.C. § 103 as obvious
over Leimgruber, Morris, Tacha, and Uhlen (Ans. 11–12).
F. The Examiner rejected claim 24 under 35 U.S.C. § 103 as obvious
over Leimgruber, Morris, Tacha, and Czerney7 (Ans. 12–13).
G. The Examiner rejected claim 25 under 35 U.S.C. § 103 as obvious
over Leimgruber, Morris, and Pieper8 (Ans. 13–14).
H. The Examiner rejected claim 27 under 35 U.S.C. § 103 as obvious
over Leimgruber, Morris, and Bio-rad9 (Ans. 14–15).
I. The Examiner rejected claims 1, 3, 4, 9–19, 21, 22, and 24–28 under
35 U.S.C. § 101 as directed to a judicial exception (Ans. 3–5).

A. 35 U.S.C. § 103(a) over Leimgruber and Morris
The Examiner finds that Leimgruber teaches a
method for identification of a specific target biomolecule[]
(protein) in a sample in a detection procedure (Gel Blot overlay
Approach described in Fig. 2) comprising: probing a gel with a
least two probes (various anti-phosphorylation antibodies such
as antibodies to phosphoserine, phosphothreonine,
phosphotyrosine, phosphoMAPKs, and phospho-hsp27) that are
directed against and specifically bind to a same target

5 Tacha, US 2005/0186642 A1, published Aug. 25, 2005.
6 Uhlen et al., US 2008/0233660 A1, published Sept. 25, 2008.
7 Czerney et al., US 7,745,640 B2, issued June 29, 2010.
8 Pieper et al., US 7,642,089 B2, issued Jan. 5, 2010.
9 Quantity One, User Guide for Version 4.2.1, Bio-Rad Laboratories (2000)
(“Bio-rad”).
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biomolecule (phosphorylated protein) to form bands or spot
patterns on the gel or membrane (the spots are formed by the
labels which bind to the antibodies.
(Ans. 6–7). The Examiner acknowledges that “Leimgruber does not teach
the generating, scaling, or differentiating steps” (id. at 7).
The Examiner finds Morris teaches “enhancing overlapping features
and sorting out nonoverlapping features of the bands or spot patterns in the
overlaid sample patterns to generate image data by creating an average gel
image, which averages out noise (diminishes nonoverlapping features) and
reinforces real protein spots” (Ans. 7). The Examiner finds it obvious to
combine these teachings “because Leimgruber teaches using image
processing and Morris teaches methods of processing data overlays of gels
which differentiate specific protein binding” (Ans. 7–8).
The issue with respect to this rejection is: Does a preponderance of the
evidence of record support the Examiner’s conclusion that Leimgruber and
Morris render the claims obvious?
Findings of Fact
1. Leimgruber teaches a biomolecule detection method in which
proteins are transferred from two-dimensional (2-D) gels to blot
membranes. Proteins are then detected by staining with SYPRO
Ruby and the resulting 2-D protein pattern is captured using a
charge-coupled device (CCD) camera. The blots are then
probed with antibodies directed against the protein(s) or
functionalities of interest. The resulting chemiluminescent blot
image is also generated with the CCD camera and the
fluorescent SYPRO Ruby image is recaptured again without
moving the membrane. It is thereby possible to generate a direct
image overlay of the blot pattern on that of the stained protein
pattern.
(Leimgruber 135, abstract).
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2. Figure 2 of Leimgruber is reproduced below:

“Figure 2. Gel/blot overlay approach. A schematic of the chemiluminescent
Western blot image overlay on the fluorescent protein stain” (Leimgruber
139, col. 1).
3. Leimgruber teaches:
The anti-hsp27 antibody was obtained from Santa Cruz (Santa
Cruz, CA, USA) and the antiphosphoprotein antibodies were
from Zymed (San Francisco, CA, USA), Upstate Biochemicals
(Lake Placid, NY, USA) and Cell Signaling Technologies
(Beverly, MA, USA) (mixtures of antibodies to phosphoserine,
phosphothreonine, phosphotyrosine, phospho-MAPKs,
phospho-hsp27).
(Leimgruber 137, col. 1).
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4. Figure 5 of Leimgruber is reproduced below:

“Figure 5. Effects of inhibitor treatment on the phosphorylation of hsp27
and an unknown protein. U937 treatments are indicated for each row and
the antibodies used for protein detection are indicated at the top of each
column” (Leimgruber 141).
5. Morris teaches
a method and computer program product for detecting and
quantifying protein spots, including: generating an average gel
image by taking a pixel-by-pixel average of the intensities of a
plurality of aligned gel images; detecting spots on the average
gel image using pinnacle detection; and quantifying spots on
individual gels using the maximum intensity within fixed
neighborhoods surrounding pinnacle locations found in the
average gel image.
(Morris, abstract; see Morris ¶ 23).
Principles of Law
“Inherency . . . may not be established by probabilities or
possibilities. The mere fact that a certain thing may result from a given set
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of circumstances is not sufficient.” MEHL/Biophile Int’l. Corp. v.
Milgraum, 192 F.3d 1362, 1365 (Fed. Cir. 1999).
Analysis
Appellant contends “the Examiner provides no evidence that any two
of the phosphoserine, phosphothreonine, phosphotyrosine, phospho-
MAPKs, and phospho-hsp27 antibodies specifically bind to a same
biomolecular species, and therefore has not made a prima facie case
showing that Leimgruber teaches Appellant's claimed at least two probes”
(Appeal Br. 13).
The Examiner responds that Leimgruber “provides evidence that the
anti-phosphorylated antibodies bind to hsp-27, thereby providing evidence
that both probes (i.e. at least two of the antibodies to phosphoserine,
phosphothreonine, phosphotyrosine, phosphoMAPKs, and phospho-hsp27)
bind to the same target” (Ans. 21–22). The Examiner finds “based on this
evidence, it is likely that the antibodies to phospho-hsp27 and at least one of
the antibodies to phosphoserine, phosphothreonine, and phosphotyrosine
bind to hsp-27, thereby indicating two probes are able to bind to the same
phosphorylated protein” (id. at 22).
We agree with Appellant because the Examiner is not arguing that it
would have been obvious to use two antibodies to the same target protein but
rather is arguing that Leimgruber’s assay teaches antibodies that inherently
do so. However, the Examiner expressly states that Leimgruber’s antibodies
“likely” bind the same target protein, not that these antibodies necessarily
bind the same target protein. The rejection therefore does not apply the
correct requirement for an inherency teaching. Inherency does not require
that the missing descriptive material be present “more likely than not,” but
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rather that it “is ‘necessarily present.”’ Trintec Indus., Inc. v. Top-U.S.A.
Corp., 295 F.3d 1292, 1295 (Fed. Cir. 2002) (quoting In re Robertson, 169
F.3d 743, 745 (Fed. Cir. 1999)). More specifically, under the principles of
inherency, the fact that a certain result or characteristic may occur or be
present in the prior art is not sufficient to establish the inherency of that
result or characteristic. See In re Rijckaert, 9 F.3d 1531, 1534 (Fed. Cir.
1993). Because there is no evidence that the antibodies of Leimgruber
necessarily bind the same target protein, and consequently no evidence of
inherency, and the Examiner has not provided a reasoned basis for
modifying Leimgruber’s method to include such antibodies, there is no
prima facie case of obviousness.
Conclusion of Law
A preponderance of the evidence of record does not support the
Examiner’s conclusion that Leimgruber and Morris render the claims
obvious.

B.–H. 35 U.S.C. § 103
The Examiner does not rely upon any of the additional cited
references to teach two antibodies binding to the same target protein (see
Ans. 9–15), but rather relies upon these references to address elements of the
dependent claims. Having reversed the obviousness rejection of claim 1 for
failing to necessarily teach the use of two antibodies to the same target
protein for the reasons given above, we also find that the further
combinations do not address this issue and therefore do not render the
rejected claims obvious for the same reasons.

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I. 35 U.S.C. § 101
The Examiner finds the claims “directed to a method for identification
of specific target biomolecules in a sample in a detection procedure” but are
“directed to an abstract idea, because all steps except for probing are mere
data manipulation and data analysis” (Ans. 3–4). The Examiner finds the
“additional elements (the probing and obtaining steps) are nothing more than
routine generic measurement steps using two probes against an analyte on a
gel or membrane and obtaining an image” (id. at 4).
Appellant contends the “focus of the claims, when read in light of the
specification, is on a particular method for increasing the specificity of target
protein identification in protein immunoblots and quantitative comparisons”
(Appeal Br. 6). Appellant contends the inventors “discovered a particular
solution to this problem—using two probes directed against the same or
different epitopes of a target biomolecule to obtain signals which are then
processed according to a specific sequence of steps that enhances signals
from the true target biomolecule” (id. at 7).
Appellant also contends the Examiner did not “establish or provide
any rational explanation as to why the claimed subject matter as a whole
(e.g., as an ordered combination) is routine and conventional activity and
does not amount to significantly more than the alleged judicial exceptions of
data manipulation, mathematical steps, and data analysis” (Appeal Br. 10).
Principles of Law
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include
implicit exceptions: “[l]aws of nature, natural phenomena, and abstract
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ideas” are not patentable. See, e.g., Alice Corp. v. CLS Bank Int’l, 573 U.S.
208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court’s two-step framework, described in Mayo
and Alice. Id. at 217–18 (citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75–77 (2012)). In accordance with that framework,
we first determine what concept the claim is “directed to.” See Alice, 573
U.S. at 219.
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, where “we must examine the
elements of the claim to determine whether it contains an ‘inventive
concept’ sufficient to ‘transform’ the claimed abstract idea into a patent-
eligible application.” Alice, 573 U.S. at 221 (quotation marks omitted). “A
claim that recites an abstract idea must include ‘additional features’ to
ensure ‘that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea].’” Id. (quoting Mayo, 566 U.S. at 77).
“[M]erely requir[ing] generic computer implementation[] fail[s] to transform
that abstract idea into a patent-eligible invention.” Id.
The United States Patent and Trademark Office published guidance
on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent
Subject Matter Eligibility Guidance (“Guidance”).10 Under the Guidance, in
determining what concept the claim is “directed to,” we first look to whether
the claim recites:
(1) any judicial exceptions, including certain groupings
of abstract ideas (i.e., mathematical concepts, certain methods

10 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg.
50–57 (January 7, 2019).
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of organizing human activity such as a fundamental economic
practice, or mental processes) (Guidance Step 2A, Prong 1);
and
(2) additional elements that integrate the judicial
exception into a practical application (see MPEP
§§ 2106.05(a)–(c), (e)–(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look to
whether the claim contains an “‘inventive concept’ sufficient to ‘transform’”
the claimed judicial exception into a patent-eligible application of the
judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82).
In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial
exception that are not “well-understood, routine and
conventional in the field” (see MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine,
conventional activities previously known to the industry,
specified at a high level of generality, to the judicial exception.
(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54–56.
Analysis
Applying the Revised Guidance to the facts on this record, we find
that Appellant’s claims 1, 3, 4, 9–19, 21, 22, and 24–28 are directed to
patent-eligible subject matter. Because the same issues are present in each
of the claims, we focus our consideration on representative claim 1. The
same analysis applied below to claim 1 also applies to the other rejected
claims.
A. Guidance Step 1
We consider whether the claimed subject matter falls within the four
statutory categories set forth in § 101, namely “[p]rocess, machine,
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manufacture, or composition of matter.” 2019 Guidance 53–54; see
35 U.S.C. § 101. Claim 1 recites a “method” thus, fall within the “process,”
category. Consequently, we proceed to the next step of the analysis.
B. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any
judicial exception to patent eligibility is recited in the claim. The Revised
Guidance identifies three judicially-excepted groupings identified by the
courts as abstract ideas: (1) mathematical concepts, (2) certain methods of
organizing human behavior such as fundamental economic practices, and (3)
mental processes.
Claim 1 recites limitations that reasonably fall within the
“mathematical concept” grouping listed in the Revised Guidance. “[C]laims
focused on ‘collecting information, analyzing it, and displaying certain
results of the collection and analysis’ are directed to an abstract idea.” SAP
America, Inc. v. InvestPic, LLC, 898 F.3d 1161, 1167 (Fed. Cir. 2018).
Here, claim 1 collects image pattern data, analyzes that data with an
algorithm and scales the data using a root function, and then uses the data to
differentiate band or spot patterns. The Specification teaches:
A more detailed example of an algorithm for the purpose
described above for two antibodies is:
Pt(n) = SQRT( P1(n) . P2(n) ) where
Pt(n) is the signal intensity in an image pixel (n)
representing the target protein Western pattern.
P1(n) is corresponding value from an image representing
the Western pattern from the first Ab.
P2(n) is corresponding value from an image representing
the Western pattern from the second Ab.

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(Spec. 5:11–19). While we recognize claim 1 is limited to protein analysis,
“even if a process of collecting and analyzing information is ‘limited to
particular content’ or a particular ‘source,’ that limitation does not make the
collection and analysis other than abstract.” SAP, 898 F.3d at 1168.
C. Guidance Step 2A, Prong 2
Having determined that the claims recite a judicial exception, the
Revised Guidance directs us to next consider whether the claims integrate
the judicial exception into a practical application. Guidance Step 2A, Prong
2. “[I]ntegration into a practical application” requires that the claim recite
an additional element or a combination of elements, that when considered
individually or in combination, “apply, rely on, or use the judicial exception
in a manner that imposes a meaningful limit on the judicial exception, such
that the claim is more than a drafting effort designed to monopolize the
judicial exception.” Guidance at 54.
A judicial exception is not integrated into a practical application when
the claims are drawn to the mere use of “a computer as a tool to perform an
abstract idea.” Guidance, 84 Fed. Reg. at 55.
Here, claim 1 is more similar to those held ineligible in Mayo than
they are to those held eligible in Vanda Pharm. Inc. v. West-Ward Pharm.
Int’l Ltd., 887 F.3d 1117 (Fed. Cir. 2018) because claim 1 lacks a step that
recites more than the use of the algorithm like the claims in Vanda which
“recite more than the natural relationship between CYP2D6 metabolizer
genotype and the risk of QTc prolongation. Instead, they recite a method of
treating patients based on this relationship that makes iloperidone safer by
lowering the risk of QTc prolongation.” Vanda, 887 F.3d at 1136.
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Therefore claim 1 does not recite elements that integrate the abstract
idea into a practical application that is more than the abstract idea itself.

D. Guidance Step 2B
Having determined that the judicial exception is not integrated into a
practical application, the Revised Guidance requires us to evaluate the
additional elements individually and in combination to determine whether
they provide an inventive concept, such as a specific limitation beyond the
judicial exception that is not well-understood, routine, conventional in the
field, or simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of generality, to
the judicial exception. See 84 Fed. Reg. 51.
Berkheimer mandates evidence showing the claim elements were
well-understood, routine, and conventional in the prior art is necessary to
satisfy Alice step two. See Berkheimer v. HP Inc., 881 F.3d 1360, 1369
(Fed. Cir. 2018) (noting that “[whether] something is well-understood,
routine, and conventional to a skilled artisan at the time of the patent is a
factual determination.”).
Appellant contends the Examiner “failed to establish or provide any
rational explanation as to why the claimed subject matter as a whole (e.g., as
an ordered combination) is routine and conventional activity and does not
amount to significantly more than the alleged judicial exceptions of data
manipulation, mathematical steps, and data analysis” (Appeal Br. 10).
The Examiner responds “as explained in the Non-Final rejection at 16,
the references in the 103(a) rejection show that using two probes and
obtaining an image (the additional elements in combination) are routine and
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conventional and therefore the claims are not significantly more than the
abstract idea” (Ans. 20).
In this case, the Examiner has provided no evidence that the central
step in the method of claim 1, “probing a gel or membrane with at least two
probes that are directed against and specifically bind to a same target
biomolecule”, was known in the prior art. As discussed in our analysis
above of the obviousness rejection, Leimgruber and the other cited prior art
do not disclose or demonstrate an assay where two different probes are used
that necessarily bind to the same target biomolecule in a sample, whether in
a Western blotting procedure or other procedure. Moreover, even if it were
accidentally inherent in Leimgruber that two different antibodies did bind a
single target biomolecule, it is unclear if that would be sufficient to establish
that such a use of multiple antibodies on a single protein is routine and
conventional.
Moreover, the Examiner provides no other evidence that such an
assay is well known, routine, or conventional. It is the Examiner’s burden to
establish, for the purposes of this rejection, that the elements of the claims
were routine and conventional. See MPEP § 1213.02 (“The Board’s primary
role is to review the adverse decision as presented by the Examiner, and not
to conduct its own separate examination of the claims.”).
The rejection of the claims under 35 U.S.C. § 101 is reversed.

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CONCLUSION
In summary:
Claims
Rejected
35 U.S.C. §  Reference(s)/Basis Affirmed Reversed
1, 3, 4, 9, 10,
13, 19–22, 26
103  Leimgruber,
Morris
1, 3, 4, 9, 10,
13, 19–22, 26
11, 12 103 Leimgruber,
Morris, Berth
11, 12
14, 16, 17, 28 103 Leimgruber,
Morris, Tacha
14, 16, 17, 28
15 103 Leimgruber,
Morris, Uhlen
15
18 103 Leimgruber,
Morris, Tacha,
Uhlen
18
24 103 Leimgruber,
Morris, Tacha,
Czerney
24
25 103 Leimgruber,
Morris, Pieper
25
27 103 Leimgruber,
Morris, Bio-rad
27
1, 3, 4, 9–19,
21, 22, 24–28
101  1, 3, 4, 9–19,
21, 22, 24–28
Overall
Outcome
1, 3, 4, 9–19,
21, 22, 24–28

REVERSED