Bio-Rad Laboratories, Inc.

Patent Trials and Appeals Board

Dec 7, 2021

2021001718 (P.T.A.B. Dec. 7, 2021)

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.
15/973,243 05/07/2018 Duc DO QLI352DIV 8771
152796 7590 12/07/2021
Kolisch Hartwell, P.C.
Bio-Rad Laboratories, Inc.
520 SW YAMHILL STREET, SUITE 300
Portland, OR 97204
EXAMINER
CHUNDURU, SURYAPRABHA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
12/07/2021 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):
abney@khpatent.com
docketing@khpatent.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DUC DO, CLAUDIA LITTERST, and
DIANNA MAAR1
Appeal 2021-001718
Application 15/973,243
Technology Center 1600
Before DONALD E. ADAMS, ERIC B. GRIMES, and
ULRIKE W. JENKS, Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
digital assay method, which have been rejected as obvious. We have
jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Bio-Rad Laboratories, Inc.
Appeal Br. 4. “Appellant” refers to “applicant” as defined in 37 C.F.R.
§ 1.42.
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Application 15/973,243

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STATEMENT OF THE CASE
“In an exemplary digital assay, a sample is separated into a set of
partitions, generally of equal volume, with each containing, on average, less
than about one copy of the analyte.” Spec. 2:2–5. A Poisson distribution
gives “[t]he probability of finding exactly 0, 1, 2, 3, or more copies in a
partition, based on a given average concentration of analyte.” Id. at 2:8–10.
“Each partition can be tested to determine whether . . . [it] contains at least
one copy of the analyte. . . . The positive fraction or the negative fraction
then may be utilized to determine the concentration of the analyte in the
partitions, such as with Poisson statistics.” Id. at 2:14–21.
“The present disclosure provides a digital assay system . . . for assay
of one or more targets in a set of partitions containing a generic reporter of
target amplification.” Id. at 3:10–12. “A generic reporter . . . binds without
substantial specificity to a product of a reaction.” Id. at 15:3–4. “For
example, the generic reporter may be a photoluminescent dye that binds to
nucleic acid relatively nonspecifically.” Id. at 15:11–12.
The Specification “describes use of the digital assay system . . . with a
generic reporter to distinguish amplification of a target from at least one
amplification byproduct.” Id. at 49:10–12. “[I]f the target has a different
length and/or amplification efficiency than each byproduct that is amplified,
partitions containing amplified target can be distinguished from those with
amplified primer dimer based on a distinguishable signature.” Id. at 49:17–21.
Claims 1 and 3–11 are on appeal. Claim 1, reproduced below, is
illustrative:
1. A method of performing a digital assay, the
method comprising:
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forming partitions each including a portion of a same
mixture, the mixture containing a target and also containing a
generic reporter that is sensitive to amplification of the target,
wherein only a subset of the partitions each contain at least one
copy of the target;
amplifying the target and at least one byproduct in the
partitions, wherein the byproduct includes a primer dimer;
collecting amplification data from the generic reporter for
a plurality of the partitions, wherein partitions exhibiting
detectable amplification of the target, partitions exhibiting
detectable amplification of the byproduct, and partitions
exhibiting detectable amplification of neither the target nor the
byproduct are distinguishable from one another in the data; and
determining a level of the target using the amplification
data.
OPINION
Claims 1 and 3–11 stand rejected under 35 U.S.C. § 103 as obvious
based on Colston2 and Nakano.3 Final Action4 4. The Examiner finds that
Colston teaches a method of performing a digital assay comprising each of
the steps of claim 1, including “amplifying the target and at least one
byproduct (reference nucleic acid, endogenous or exogenous template) in the
partitions,” but “did not specifically teach that the byproduct is a primer
dimer.” Id. at 4, 6.
The Examiner finds that Nakano teaches
a polymerase chain reaction in partitions (water-in-oil
emulsions) wherein the water-in-oil emulsion based
amplification of a template DNA using a primer pair . . .

2 Colston Jr., et al., US 2010/0173394 A1, published July 8, 2010.
3 Michihiko Nakano et al., “Single-molecule PCR using water-in-oil
emulsion,” J. Biotechnol. 102:117–124 (2003).
4 Office Action mailed March 26, 2020.
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detected a non-specific product in some emulsions (Fig. 4, lane
8) in addition to target specific product containing emulsions,
which were considered as primer-dimer products.
Id. at 6.
The Examiner concludes that it would have been obvious “to modify
the method of Colston et al. with the inclusion of detecting non-specific
byproduct comprising primer-dimer as taught by Nakano et al. to improve
the method of detecting specific target nucleic acid.” Id. The Examiner finds
that a person of ordinary skill in the art would have expected that “the
combination would result in distinguishing background non-specific
products over the specific template amplification products because Nakano
et al. explicitly taught that the emulsion based PCR could detect both non-
specific and target specific products that would distinguish between the
background noise over the specific target amplicons.” Id. at 6–7.
Appellant argues that “the Examiner has failed to establish prima
facie obviousness of claim 1” because “there would have been no motivation
or reasonable expectation of success for the proposed modification of
Colston with Nakano.” Appeal Br. 12. Appellant argues that Colston “relates
to droplet-based assays,” in which “amplification of a target is performed in
droplets [i.e., partitions] of an emulsion, and an amplification signal is
detected from the droplets while the droplets are intact.” Id. at 13. Thus,
Appellant argues, Colston “does not disclose or suggest distinguishing the
occurrence of two different amplification reactions in the same set of
partitions, such as amplification of a target and a byproduct including a
primer dimer, as recited in claim 1.” Id. at 14.
Appellant argues that “Nakano demonstrates amplification of a
specific target (SV515) and an apparent primer dimer using separate
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emulsions, not the same set of droplets.” Id. at 17–18. Appellant also argues
that Nakano “distinguish[ed] the specific target and the primer dimer from
one another by size through gel electrophoresis . . . after breaking the
emulsions (i.e., fusing the droplets thereof).” Id. at 18.
Appellant argues that Colston “fails to disclose or suggest any way to
distinguish amplification products of different sizes while the amplification
products remain in droplets of an emulsion” and, therefore, “the skilled
person would have had no motivation to modify Colston with Nakano, to
achieve the claimed invention.” Id.
We agree with Appellant that the Examiner has not persuasively
shown that it would have been obvious to modify Colston, based on Nakano,
in the manner required by claim 1. “An examiner bears the initial burden of
presenting a prima facie case of obviousness.” In re Huai-Hung Kao, 639
F.3d 1057, 1066 (Fed. Cir. 2011). “Motivation to combine is
a factual determination as to whether there is a known reason a skilled
artisan would have been motivated to combine elements to arrive at a
claimed combination.” Arctic Cat, Inc. v. Bombardier Recreational Prods.,
Inc., 876 F.3d 1350, 1359 (Fed. Cir. 2017).
Colston describes an assay method that includes the steps of:
(A) preparing a sample . . . for analysis, (B) separating
components of the samples by partitioning them into droplets or
other partitions, each containing only about one component
(such as a single copy of a nucleic acid target . . . ), (C)
amplifying or otherwise reacting the components within the
droplets, (D) detecting the amplified or reacted components . . .
and/or (E) analyzing the resulting data.
Colston ¶ 138. Colston defines a reporter as “a compound or set of
compounds that reports a condition, such as the extent of a reaction” and
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states that “[e]xemplary reporters for nucleic acid amplification assays may
include a probe and/or an intercalating dye (e.g., SYBR Green, ethidium
bromide, etc.).” Id. ¶ 180.
Colston states that “[s]ignals . . . may be detected from the droplets.
The signals may include test signals, calibration signals, control signals,
reference signals, or any combination thereof.” Id. ¶ 1044. “[T]est signals
and control signals may indicate respectively whether amplification of a test
nucleic acid target and a control nucleic acid target occurred in individual
droplets.” Id.
Nakano discloses a “PCR method utilizing a water-in-oil (W/O)
emulsion that included numerous droplets of reaction mixture in bulk oil
phase. These droplets . . . functioned as micro-reactors.” Nakano 117,
Abstract. Nakano describes experiments using two different template DNAs,
pUC19 and pSV515, “which was constructed by inserting the replication
origin of the Simian Virus 40 (SV40) into pUC19.” Id. at 118, right col.
In its experiment using pSV515 as a template, Nakano found that,
“[a]s shown in Fig. 4, two samples . . . were amplified among eight samples
when a single molecule (average) of template DNA was used. These results
suggest that this method can be essentially applied to various template
DNAs, although non-specific product was observed in very few cases (lane
8).” Id. at 120–121. Regarding the latter result, Nakano states:
We believe that the product in Fig. 4, lane 8 is a non-specific
product. The production mechanism for this non-specific
product was not yet identified. However, primer dimers are a
well-known cause of non-specific products. We therefore
consider the non-specific product in lane 8 in Fig. 4 to be a
primer–dimer.
Id. at 123, left col.
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The Examiner reasons that it would have been obvious “to modify the
method of Colston et al. with the inclusion of detecting non-specific
byproduct comprising primer-dimer as taught by Nakano et al. to improve
the method of detecting specific target nucleic acid.” Final Action 6. The
evidence of record, however, does not support this conclusion.
Nakano discloses that one of the “main cause[s] for difficulty in
single-molecule PCR is interference of the primer–dimers.” Nakano 122,
bridging sentence. Nakano states, however, that its “W/O emulsion method
solves this problem, because the increased concentration of the initial
template DNA improves the specificity of PCR.” Id. at 122, right col.
Nakano concludes that its “results indicate that primer–dimer formation is
suppressed in this W/O emulsion system.” Id. at 123, left col.
Like Nakano, Colston’s method also includes “partitioning [samples]
into droplets or other partitions, each containing only about one component
(such as a single copy of a nucleic acid target (DNA or RNA) or other
analyte of interest), . . . amplifying or otherwise reacting the components
within the droplets, [and] detecting the amplified or reacted components.”
Colston ¶ 138. As the Examiner has acknowledged (Final Action 6), Colston
does not state that its method results in a primer dimer byproduct.
For its part, Nakano discloses that primer dimer formation is one of
the main causes of difficulty in single-molecule amplification of nucleic
acids. Thus, Nakano does not provide a reason for a skilled artisan to modify
Colston’s method so as to intentionally produce a primer dimer byproduct,
whereas claim 1 requires “amplifying the target and at least one byproduct in
the partitions, wherein the byproduct includes a primer dimer.”
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Nakano also does not support a conclusion that Colston’s method
inherently produces a primer dimer byproduct. “Inherency is established in
the context of obviousness when the limitation at issue necessarily must be
present, or [is] the natural result of the combination of elements explicitly
disclosed by the prior art.” Hospira, Inc. v. Fresenius Kabi USA, LLC, 946
F.3d 1322, 1329 (Fed. Cir. 2020) (internal quotations omitted).
Nakano states that “the non-specific product in lane 8 in Fig. 4,”
which was considered “to be a primer–dimer” (Nakano 123, left col.), “was
observed in very few cases” (id. at 121, right col.). Notably, this non-specific
product was observed only in one out of eight samples of pSV515 (id. at
121, Fig. 4) and in none of the samples of pUC19 (id. at 120, Fig. 2).
Nakano also states that “[s]ome smear bands are also shown in Figs. 2
and 4” but concludes that those products “are unlikely to be primer–dimers,”
and are instead “generated by non-specific interaction between the primers
and the desired products.” Id. at 122–123. Nakano states that “primer–dimer
formation is suppressed in [its] W/O emulsion system.” Id. at 123, left col.
Thus, Nakano does not support the conclusion that Colston’s droplet-
based method inherently—i.e., necessarily—results in amplification of
primer dimers along with the desired target nucleic acid.
In summary, the Examiner has not carried the initial burden of
showing that the method of claim 1 would have been prima facie obvious to
a person of ordinary skill in the art based on the disclosures of Colston and
Nakano. We therefore reverse the rejection of claim 1, and dependent claims
3–11, under 35 U.S.C. § 103.
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DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 3–11 103 Colston, Nakano 1, 3–11

REVERSED