SomaLogic, Inc.

Patent Trials and Appeals Board

May 26, 2020

2020000910 (P.T.A.B. May. 26, 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.
14/401,791 11/17/2014 Glenn Sanders 0057.51PCT-US 8928
125354 7590 05/26/2020
Swanson & Bratschun, L.L.C.- SomaLogic, Inc.
8210 SouthPark Terrace
Littleton, CO 80120
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
05/26/2020 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):
efspatents@sbiplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte GLENN SANDERS, STEPHAN KRAEMER,
EVALDAS KATILIUS and EDGAR OLIVAS
____________

Appeal 2020-000910
Application 14/401,791
Technology Center 1600
____________

Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1,2 under 35 U.S.C. § 134(a) involving claims to a
method for detecting a target molecule that may be present in a test sample.
The Examiner rejected the claims as indefinite, as failing to comply with the
written description requirement, and as obvious. We have jurisdiction under
35 U.S.C. § 6(b). We reverse the written description and indefiniteness
rejections, and affirm the obviousness rejection.

1 We use the word Appellant to refer to “applicant” as defined in 37 C.F.R.
§ 1.42(a). Appellant identifies the real party in interest as SomaLogic, Inc.
Appeal Br. 3.
2 We have considered and herein refer to the Specification of Jan. 4, 2017
(“Spec.”); Non-Final Office action of Aug. 31, 2018 (“Non-Final Act.”);
Appeal Brief of Apr. 30, 2019 (“Appeal Br.”); Examiner’s Answer of Sept.
16, 2019 (“Ans.”); and Reply Brief of Nov. 18, 2019 (“Reply Br.”).
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Statement of the Case
Background
“Aptamers may be DNA or RNA” and perform functions including
“binding of the target, catalytically changing the target, reacting with the
target in a way that modifies or alters the target or the functional activity of
the target, covalently attaching to the target (as in a suicide inhibitor), and
facilitating the reaction between the target and another molecule” (Spec.
¶ 42).
“The present invention relates generally to methods . . . designed to
improve the performance of multiplexed aptamer-based assays” (Spec. ¶ 2).
“Specifically, materials and methods are provided for the reduction or
elimination of background signal.” Id. “The aptamer comprising the first
releasable first tag that has a specific affinity for a target molecule is
immobilized on a solid support in solution prior to equilibration binding
with the test sample.” (Spec. ¶ 9).
The Claims
Claims 74, 76–94, and 96–106 are on appeal. Claim 74 is
representative and is reproduced below with bracketed letters added to
identify certain phrases:
74. A method for detecting a target molecule that may be present in a
test sample comprising:
[a] exposing an aptamer having specific affinity for the target
molecule to a first solid support, wherein the aptamer
comprises a first tag and the first solid support comprises a
first capture element, and wherein the first tag has affinity
for the first capture element;
[b] allowing the first tag to interact with the first capture
element to immobilize the aptamer on the first solid
support;
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[c] washing the first solid support with one or more solutions
that dissociate aggregated aptamers;
[d] contacting the immobilized aptamer with a test sample,
wherein an aptamer-target affinity complex is formed if the
target molecule is present in the test sample;
[e] removing one or more components not immobilized on the
first solid support;
[f] attaching a second tag to the target molecule in the
aptamer-target affinity complex, wherein the second tag
has an affinity to a second capture element;
[g] releasing the aptamer-target affinity complex from said
first solid support;
[h] exposing the released aptamer-target affinity complex to a
second solid support comprising a second capture element
and allowing the second tag to interact with said second
capture element to immobilize the aptamer-target affinity
complex on the second solid support;
[i] removing one or more components not immobilized on the
second solid support
[j] eluting the aptamer from the second solid support with one
or more buffered solutions comprising a chaotropic salt;
[k] detecting the presence of said target molecule in the test
sample by detecting the aptamer of said aptamer-target
affinity complex; and
[l] wherein the target molecule is a protein.

The Rejections
A. The Examiner rejected claims 80, 102, and 106 as unpatentable under
35 U.S.C. § 112(b) for being indefinite (Ans. 3–7).
B. The Examiner rejected claims 74, 76–94, and 96–106 as unpatentable
under 35 U.S.C. § 112(a) as failing to comply with the written description
requirement (Ans. 7–16).
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C. The Examiner rejected claims 74, 76–94, and 96–106 as unpatentable
under 35 U.S.C. § 103(a) for their obviousness over the combination of
applicant’s admissions, Schneider,3 Lee,4 Zichi,5 and Nakamura6 (Ans. 17–
28).

A. 35 U.S.C. § 112(b)
The test for indefiniteness requires “that a patent’s claims, viewed in
light of the specification and prosecution history, inform those skilled in the
art about the scope of the invention with reasonable certainty.” Nautilus,
Inc. v. Biosig Instruments, Inc., 572 U.S. 898, 911 (2014).
Claim 80
The Examiner finds the
term “about” in claim 80 is a relative term which renders the
claim(s) indefinite. The term “about” is not defined by the
claim(s), the specification does not provide a standard for
ascertaining the requisite degree, and one of ordinary skill in
the art would not be reasonably apprised of the scope of the
invention.
(Ans. 5).
Appellant “maintains that in the context of a wash solution -- a pH of
about 11 is clearly specific enough that a person of the art would not be
confused. As detailed in the Specification, the washes are performed ‘with a
solution buffered to pH 11.’ (See e.g. paragraph [0082] of the
Specification)” (Appeal Br. 12).

3 Schneider et al., US 7,855,054, B2, issued Dec. 21, 2010.
4 Lee et al., US 2013/0142732 A1, published June 6, 2013.
5 Zichi et al., US 7,947,447 B2, issued May 24, 2011
6 Nakamura et al., US 2009/0170219 A1, published July 2, 2009.
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We agree with Appellant. The Federal Circuit has “rejected the
proposition that claims involving terms of degree are inherently indefinite.”
Sonix Tech. Co. v. Publ’ns Int’l, Ltd., 844 F.3d 1370, 1377 (Fed. Cir. 2017).
We note that the Specification not only exemplifies pH 11 for washing
(Spec. ¶ 82), but also discloses elution at pH 10 (Spec. ¶ 19) and elution at
“elevated pH” (Spec. ¶ 65). Thus, the term “about” in context of the pH
would provide reasonably certainty limiting the pH to elevated pH values
that function in either the washing or the eluting of the aptameric complex.
Claims 102 and 106
The Examiner finds “[c]laim 102 is indefinite with respect to just
what constitutes the metes and bounds of ‘specific binding affinity.’ As
presently worded, it would appear that one aptamer may have ‘specific
affinity’ for an infinite number of targets” (Ans. 7). The Examiner finds
“Claim 106 is indefinite with respect to what constitutes the metes and
bounds of ‘specific affinity’ (found at line 2) versus ‘affinity’ (found at line
9)” (id.).
Appellants contend that “[a]s provided in paragraph [0042], the
‘specific binding affinity’ of an aptamer for its target means that the aptamer
binds to its target with a much higher degree of affinity than it binds to
other, non-target, components in a mixture or sample” (Appeal Br. 13)
(emphasis added).
We agree with Appellants. The Specification teaches that:
It is recognized that affinity interactions are a matter of degree;
however, in this context, the “specific binding affinity” of an
aptamer for its target means that the aptamer binds to its target
with a much higher degree of affinity than it binds to other,
non-target, components in a mixture or sample.
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(Spec. ¶ 42). Therefore, “specific binding affinity” is expressly and clearly
defined by the Specification. See Helmsderfer v. Bobrick Washroom Equip.,
Inc., 527 F.3d 1379, 1381 (Fed. Cir. 2008) (“A patentee may act as its own
lexicographer and assign to a term a unique definition.”) To the extent that
an aptamer may have affinity for multiple different targets, that goes to the
breadth of the claim, not its definiteness. However, even “undue breadth is
not indefiniteness.” In re Johnson, 558 F.2d 1008, 1016 n.17 (CCPA 1977).
We find that the phrase “specific binding affinity” as interpreted in light of
the Specification provides reasonable certainty.
As to claim 106, the terms “specific affinity” and “affinity” refer to
different claim elements. The term “specific affinity” refers to the
interaction of an aptamer for a target while the term “affinity” refers to the
interaction of a tag used for target capture with a solid support containing the
tag partner. Thus, claim 106 provides reasonable certainty as to the meaning
of both of these terms, particularly in light of the Specification (see, e.g.,
Spec. ¶¶ 11, 42). See In re Miller, 441 F.2d 689, 693 (CCPA 1971)
(indicating “breadth is not to be equated with indefiniteness.”).

B. 35 U.S.C. § 112, Written Description
The Examiner finds that the claims encompass
performing a multiplexed assay where literally thousands of
different target molecules are simultaneously detected. A
review of the disclosure fails to find where applicant has
disclosed the nucleotide sequence for any aptamer, much less
thousands of aptamers, which are essential to practicing the
claimed method . . .
In addition to the above, the claimed method has been
construed as encompassing the detection of proteins that are to
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be found in thousands of different bacteria, viruses, plants, fish,
insects, etc.
(Ans. 12).
Appellant contends:
detection and quantification of the aptamers can be performed
using any suitable nucleic acid detection and quantification
method known to those in the art, including, but not limited to
DNA microarray hybridization, Q-PCR, mass spectroscopy, the
Invader assay, next generation sequencing, and the like. See e.g.
paragraphs [0056], [0089], [0091], [00134]-[00147]. These are
all well-known methods and as noted above, a patent need not
teach, and preferably omits, what is well known in the art.
(Appeal Br. 20–21).
We find the Examiner erred. As Appellant correctly points out,
“detection and quantification of the aptamers can be performed using any
suitable nucleic acid detection and quantification method known to those in
the art.” (App. Br. 20). In addition, the Specification evidences that each of
the amplification methods, target molecules, proteins, and method steps
represent references to methods, targets, and proteins well-known and
readily understood by those of ordinary skill in the art (see Spec. ¶¶ 43, 57,
89). See Falko-Gunter Falkner v. Inglis, 448 F.3d 1357, 1368 (Fed. Cir.
2006). “[T]he determination of what is needed to support generic claims to
biological subject matter depends on a variety of factors, such as the existing
knowledge in the particular field, the extent and content of the prior art, the
maturity of the science or technology, the predictability of the aspect at
issue.” Capon v. Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005).
The Examiner provides no persuasive evidence of record suggesting
that identifying aptamers to any desired target using known SELEX methods
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does not rely on well-established prior art methods. The Examiner lacks
evidence that performing sandwich-type analytical assays using aptamers
and tags differ in any way from established prior art methods. The
Examiner fails to establish that multiplexing such sandwich-type analytical
assays was not a well-established technique in the prior art.
Therefore, in light of the absence of any evidence supporting
unpredictability or lack of knowledge in the prior art in performing the
generic claim to a multiplexed aptamer-based assay, we reverse the
Examiner’s erroneous written description rejection.

C. 35 U.S.C. § 103(a)
The issue with respect to this rejection is: Does a preponderance of
the evidence of record support the Examiner’s conclusion that the Schneider,
Lee, and Zichi render the claims obvious.
Findings of Fact (“FF”)
1. Schneider teaches, regarding the preamble of claim 74, methods
“for the detection and/or quantification of one or more target molecules that
may be present in a test sample” (Schneider 2:44–46).
2. Schneider teaches a “Dual Catch Affinity Assay” which is
substantially similar to the process of claim 74 but recites a different order
for performing steps (a), (b), (d), and (e) of claim 74 and does not include
the wash step (c) (see Schneider 3:43 to 4:51). Schneider specifically
teaches:
a test sample is contacted with an aptamer that includes a
releasable first tag and has a specific affinity for a target
molecule. If the test sample contains the target molecule, an
aptamer affinity complex will form in the mixture with the test
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sample. The aptamer affinity complex is captured on a first
solid support by exposing the mixture to the first solid support.
The attachment is accomplished by contacting a first solid
support with the aptamer affinity complex and allowing the
releasable first tag included on the aptamer to associate, either
directly or indirectly, with an appropriate first capture agent that
is attached to the first solid support. . . .
The aptamer affinity complex and uncomplexed aptamer that
has associated with the probe on the solid support is then
partitioned from the remainder of the mixture, thereby
removing free target and all other uncomplexed matter in the
test sample.
(Schneider 3:43–60).
3. Schneider explains that washing is a type of partitioning,
specifically explaining that the “aptamer affinity complex is then partitioned
from the remainder of the mixture, e.g. by washing the support to remove
non-complexed aptamers” (Schneider 13:51–54).
4. Schneider teaches, regarding step (f), a “second tag (which may
be the same or different from the releasable first tag) is attached to the target
molecule of the aptamer affinity complex” (Schneider 3:65–67).
5. Schneider teaches, regarding step (g), “[f]ollowing partitioning
the aptamer affinity complex, along with any uncomplexed aptamer, is
released from the first solid support using a method appropriate to the
particular releasable first tag being employed” (Schneider 3:62–65).
6. Schneider teaches, regarding step (h), that the “aptamer affinity
complex is captured on a second solid support by allowing the second tag to
associate either, directly or indirectly, with an appropriate second capture
agent that is attached to a second solid support by exposing the released
aptamer affinity complex to the second solid support” (Schneider 4:3–8).
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7. Schneider teaches, regarding step (i), that the “aptamer affinity
complex that has associated with the probe on the solid support is partitioned
from the remainder of the mixture” (Schneider 4:8–10).
8. Schneider teaches, regarding step (j), that the “aptamers that are
complexed with the target in the aptamer affinity complex can be released
from the solid support by dissociation of the aptamer affinity complex”
(Schneider 4:11–13).
9. Schneider teaches, regarding the chaotropic salt in step (j), that
“aptamer from the aptamer affinity complex can then be released for further
processing by one or more of the following treatments: high salt” (Schneider
13:54–56).
10. Schneider teaches, regarding step (k), that the “photoaptamer
released from the catch-2 partition is detected and optionally quantified by
any suitable nucleic acid detection method, such as, for example, DNA chip
hybridization, Q-PCR, mass spectroscopy, the Invader assay, and the like”
(Schneider 13:58–62).
11. Schneider teaches, regarding step (l), that an embodiment
“where the target molecule is a protein or polypeptide” (Schneider 8:15–16).
12. Schneider does not teach an order in which steps (a) and (b) are
used for pre-immobilizing the aptamer to the solid support prior to binding
to the target and step (c) is used for washing to remove excess aptamer. Nor
does Schneider identify the specific high salt components recited in the
Specification (see Spec. ¶ 18 “[i]n one embodiment the chaotropic salt is
selected from the group consisting of sodium perchlorate, lithium chloride,
sodium chloride and magnesium chloride.”).
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13. Lee teaches, in example 3, an “Aptamer-Based Biomolecular
Detection Method” that begins with steps (a) and (b) of claim 74 by using a
streptavidin coated 96 well plate and “a biotin-modified DNA aptamer (10
nM) was incubated in the 96-well plate for 1 and a half hours” (Lee ¶ 94).
14. Lee then teaches a step (c) of claim 74 where the “plate was
then washed with the PBS buffer for 5 minutes” (Lee ¶ 94).
15. Lee teaches a step (d) of claim 74 where “analyte sample
containing PDGF-BB . . . was added to each well and incubated” (Lee ¶ 95).
16. Lee teaches a step (e) of claim 74 where “the plate was washed
with the PBS buffer for 5 minutes” (Lee ¶ 96).
17. Lee then teaches a detection step (k) of claim 74 where a
labeled aptamer complex was added and “the fluorescence signals were
measured using a microplate reader” (Lee ¶ 96).
18. Lee teaches that “an NaCl concentration [was] gradually
increased from 0 to 0.7 M (pH 6.0) for elution” (Lee ¶ 72), teaching the use
of one of the specific chaotropic salts recited by the Specification (see Spec.
¶ 18).
19. Zichi teaches the method may begin with a kit where the
“aptamer in the kit is immobilized onto a solid support used in conjunction
with the assay for testing the specimen. In various embodiments, the solid
support is designed for the detection of one or more targets of interest”
(Zichi 5:43–46).
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Principles of Law
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
Analysis
We find that the claims are obvious over the combination of
Schneider, Lee, and Zichi (FF 1–19).7 We adopt the position and fact-
finding of the Examiner. We address Appellant’s arguments below.
Appellant contends “the primary difference between the claimed
method and that of the references relied upon by the Examiner is the pre-
immobilization of aptamers on the solid support, prior to exposure to the test
solution.” (Appeal Br. 26). Appellants specifically point out that neither
Zichi nor Schneider teach a process “in which the aptamer is tagged and
bound to a solid support prior to incubation with the target molecule” (id. at
27).
Appellant acknowledges that “the Examiner cites Lee as teaching
immobilization of a biotinylated DNA aptamer to a solid support” but
contends Lee “performed an aptamer-based sandwich assay as a method for
detecting a protein in a sample. Lee does not teach or suggest the method
claimed herein” (Appeal Br. 27).
We find this argument unpersuasive because it is the combination of
Schneider, Lee, and Zichi that render the claim obvious, not any single
reference alone. “Non-obviousness cannot be established by attacking

7 We note the Board may rely on less than all of the references applied by
the Examiner in an obviousness rationale without designating it as a new
ground of rejection. In re Bush, 296 F.2d 491, 496 (CCPA 1961).
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references individually where the rejection is based upon the teachings of a
combination of references. . . . [The reference] must be read, not in
isolation, but for what it fairly teaches in combination with the prior art as a
whole.” In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir. 1986).
Here, Schneider teaches a dual catch affinity assay with aptamers that
differs from claim 1 in the order of steps (a)–(e). Schneider differs
specifically in whether the aptamer is first bound to the solid support and
then contacted with target as in claim 74, or whether the aptamer is first
contacted with target and then bound to the solid support, along with the
associated washing steps (FF 1–3). Schneider teaches steps (f)–(l) in an
order identical to that recited in claim 74.
Lee teaches an affinity assay with aptamers that is identical in order to
steps (a)–(e) of claim 74 but lacks disclosure of the remaining steps (FF 13–
18). The assays of Schneider and Lee assays share the goal of accurately
determining the presence of target molecules in test solutions and employ
comparable steps to achieve that goal (FF 1–18). As the Examiner
indicated, such an arrangement would allow target molecules to only bind to
immobilized aptamers. (Non-Final Act. 48–49).
We find that it would have been obvious to use the alternative
aptamer-target binding approach of Lee because “[w]hen a patent simply
arranges old elements with each performing the same function it had been
known to perform and yields no more than one would expect from such an
arrangement, the combination is obvious.” KSR, 550 U.S. at 417. In
addition, to the extent that Lee suggests rearranging the steps of Schneider
thereby rendering claim 74 obvious, “[t]here is no merit in [Appellant’s]
point here in the absence of any proof in the record that the order of
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performing the steps produces any new and unexpected results.” In re
Burhans, 154 F.2d 690, 692 (CCPA 1946).
Appellant contends
there is no motivation to modify the method of the ’054 patent,
based upon the combination of references cited by the
Examiner. Certainly, none of the cited prior art suggests that
pre-immobilizing the aptamer on the solid support could allow
the use of even higher plasma concentrations, such as at least
40% as demonstrated in the present application, compared to
the 10% plasma concentration demonstrated in the ’054 patent.
(Appeal Br. 28; citing Spec. ¶ 69).
We find these arguments unpersuasive because, as noted already,
“[w]hen a patent simply arranges old elements with each performing the
same function it had been known to perform and yields no more than one
would expect from such an arrangement, the combination is obvious.” KSR,
550 U.S. at 417. Not only does Lee teach binding aptamer to solid support
prior to contacting target (FF 13–18) but Zichi also evidences that a solid
support with pre-bound aptamer may be used in such analytical assays (FF
19), further demonstrating the obviousness of this approach. The ordinary
artisan would have expected that pre-binding the aptamer to the solid
support and washing away unbound aptamer would result in an assay, like
that of Lee, that “would allow for the capture of target with only those
aptamer sequences that are bound” (Non-Final Act. 48).
As to Appellant’s reliance on the comparison in the Specification
between pre-immobilization and “the process as previously described in
Gold” (Spec. ¶ 69), we find this argument unpersuasive for several reasons.
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First, Gold8 only teaches testing “stock SOMAmer solutions for 10%, 1%
and 0.03% serum” (Gold 14). Gold does not, however, teach that higher
amounts of serum are ineffective in the binding assay, nor does Appellant
identify any such teaching. Lastly, Appellant does perform a direct
comparison using the same samples, proteins, and aptamers to provide
evidentiary support that would show unexpected results. See In re Baxter
Travenol Labs., 952 F.2d 388, 392 (Fed. Cir. 1991) (“[W]hen unexpected
results are used as evidence of nonobviousness, the results must be shown to
be unexpected compared with the closest prior art.”).
In addition, pre-immobilization would have been expected to reduce
competition for the solid support. The Examiner explains “performing the
first wash step of immobilized aptamers prior to being brought into contact
with the target molecule would serve to reduce the likelihood of erroneous
complexes of aptamer being present on the surface of the solid support, and
interfering with the binding of target to the aptamers that are actually bound”
(Non-Final Act. 49). Thus, the result is expected, not unexpected. See In re
Skoner, 517 F.2d 947, 950 (CCPA 1975) (“Expected beneficial results are
evidence of obviousness of a claimed invention. Just as unexpected
beneficial results are evidence of unobviousness”).
Conclusion of Law
A preponderance of the evidence of record supports the Examiner’s
conclusion that the Schneider, Lee, and Zichi render the claims obvious.
Appellant does not argue the claims separately, so claims 76–94, and 96–106
fall with claim 74. 37 C.F.R. § 41.37 (c)(1)(iv)(2018).

8 Gold et al., Aptamer-Based Multiplexed Proteomic Technology for
Biomarker Discovery, 5 PLoS ONE e15004 1–17 (2010).
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CONCLUSION
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
80, 102, 106 112(b) Indefiniteness 80, 102, 106
74, 76–94,
96–106
112(a) Written
Description
74, 76–94,
96–106
74, 76–94,
96–106
103(a) Schneider, Zichi,
Lee, Nakamura
74, 76–94,
96–106

Overall
Outcome
74, 76–94,
96–106

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R.
§ 1.136(a)(1)(iv).
AFFIRMED