Ex Parte Sane et al

Patent Trial and Appeal Board

Apr 19, 2018

13688133 (P.T.A.B. Apr. 19, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
13/688, 133 11128/2012 Aditya P. Sane
41504 7590 04/23/2018
ROCHE I KILPATRICK TOWNSEND & STOCKTON LLP
Mailstop: IP Docketing - 22
1100 Peachtree Street
Suite 2800
Atlanta, GA 30309
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
88883-00891 OUS-858503 1869
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
04/23/2018 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):
ipefiling@kilpatricktownsend.com
pair_roche@firsttofile.com
KTSDocketing2@kilpatrick.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ADITYA P. SANE, RONALD T. KURNIK, and
JONATHAN M. BALDANZA
Appeal2017-006762 1
Application 13/688, 133
Technology Center 1600
Before RICHARD M. LEBOVITZ, RICHARD J. SMITH, and
DAVID COTTA, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal involves claims directed a "method of automatically
removing a step discontinuity in data representing a Polymerase Chain
Reaction (PCR) growth process," as recited in claim 1. The Examiner
rejected the claims under 35 U.S.C. § 101 as subject matter ineligible for a
patent and under 35 U.S.C. § 112, second paragraph, as indefinite.
1 The Appeal Brief ("Appeal Br.") identifies Roche Molecular Systems, Inc.
as the real-party-in-interest. Appeal Brief ("App. Br.") 3.
Appeal2017-006762
Application 13/688, 133
Appellants appeal the rejections under 35 U.S.C. § 134(a). We have
jurisdiction under 35 U.S.C. § 6(b ). The rejections are reversed.
STATEMENT OF THE CASE
Claims 1-11 and 13-21 stand rejected by the Examiner under 35
U.S.C. § 101 because the claimed invention was found by the Examiner to
be directed to patent ineligible subject matter. Examiner's Answer ("Ans.")
3; Appeal Br. 3, 10.
Claims 1-11 and 13-21 stand rejected by the Examiner under 35
U.S.C. § 112(b) or 35 U.S.C. § 112 (pre-AIA), second paragraph, as being
indefinite for failing to particularly point out and distinctly claim the subject
matter which the inventor or a joint inventor regards as the invention. Ans.
7, 30.
Independent claim 1 is representative of the claimed subject matter
and is reproduced below:
1. A method of automatically removing a step
discontinuity in data representing a Polymerase Chain Reaction
(PCR) growth process, the method comprising:
detecting, with a PCR system, intensity values of signals
generated using a biological and/or chemical reaction sample
undergoing the PCR growth process, at a plurality of
growth cycles of the PCR growth process;
receiving, by a computer system communicatively
coupled to the PCR system, a dataset representing the PCR
growth process, the dataset including a plurality of data points,
each data point having a pair of coordinate values, wherein the
pair of coordinate values correspond to a cycle number of the
PCR growth process and an intensity value of a signal generated
using the biological and/or chemical reaction sample and
detected by the PCR system after a growth cycle corresponding
to the cycle number;
calculating, by the computer system, a first approximation
2
Appeal2017-006762
Application 13/688, 133
of a curve that fits the dataset by applying a first non-linear
regression process to a first non-linear function to determine
parameters of the first non-linear function, said parameters
including a first step discontinuity parameter that represents a
magnitude of the step discontinuity, the first non-linear function
including the first step discontinuity parameter multiplying a step
function;
calculating, by the computer system, a second
approximation of a curve that fits the dataset by applying a
second regression process to a second non-linear function to
determine parameters of the second non-linear function, said
parameters of the second non-linear function including a second
step discontinuity parameter that represents the magnitude of the
step discontinuity, the second non-linear function including the
second step discontinuity parameter multiplying a step function,
wherein the second nonlinear function is different from the first
non-linear function;
determining, by the computer system, an information
coefficient for each of the first and second approximations, each
information coefficient indicating an accuracy of a fit of the
corresponding approximation to the dataset;
selecting, by the computer system, one of the
approximations based on the information coefficient, the
selected approximation providing a best fit to the dataset;
determining, by the computer system, a confidence
interval of the step discontinuity parameter for the selected
approximation;
if the confidence interval does not include the value zero,
replacing, by the computer system, a portion of the dataset with
the selected approximation with the corresponding step
discontinuity parameter set to zero, wherein the method is
implemented in a computer system having a processor; and
determining, by the computer system, a quantity of a target
molecule in the biological and/or chemical reaction sample by
determining a cycle threshold (Ct) value using the dataset.
3
Appeal2017-006762
Application 13/688, 133
REJECTION UNDER§ 101
Claim 1 is directed to a method in which the quantity of a target
molecule in a sample subjected to a PCR reaction is determined
("determining, by the computer system, a quantity of a target molecule in the
biological and/or chemical reaction sample by determining a cycle threshold
(Ct) value using the dataset."). The determination is made by a computer
system, beginning with "detecting, with a PCR system, intensity values of
signals generated using a biological and/or chemical reaction sample
undergoing the PCR growth process, at a plurality of growth cycles of the
PCR growth process." The subsequent steps comprise calculations
performed on a dataset representing the PCR growth process that culminate
in determining the quantity of target molecule in the sample. We refer to
these calculation steps collectively as an "algorithm."
Independent claim 13 is directed to computer-readable medium
including the code for performing the same steps of claim 1. Independent
claim 1 7 is directed to a PCR system comprising "a kinetic PCR analysis
module" that performs the same steps of claim 1. The question of patent
eligibility for all three independent claims tum on the same issue.
The Examiner rejected the claims under 35 U.S.C. § 101 as being
directed to patent ineligible subject matter. Ans. 3. The Examiner found
that the recited steps for performing PCR are conventional and that "[ w ]hat
is left of the claims are instructions generally drawn to analysis of PCR data"
which are "abstract steps" and an "abstract process." Id. at 4, 6. The
Examiner stated:
In the instant case, the claims are directed to only the
manipulation of data as described above. The method steps
themselves are considered to be an abstract idea because they do
4
Appeal2017-006762
Application 13/688, 133
not purport to improve the functioning of the computer itself,
there is no specific or limitation recitation of improved computer
technology, nor do they effect an improvement in any other
technology or technical field.
Id. at 6.
The Examiner further found that no additional steps are recited in the
claims "that would amount to significantly more than the judicial
exception." Id. at 6. The Examiner stated:
Furthermore, if a claim is directed essentially to a method of
calculating, using a mathematical formula, even if the solution is
for a specific purpose, the claimed method is non-statutory. In
other words, patenting abstract ideas cannot be circumvented by
limiting the use of the idea to particular technological
environment.
Id. at 7.
We do not agree with the Examiner's analysis and reverse the
rejection.
The claims at issue in this appeal comprise steps in which
mathematical calculations are performed on a dataset obtained from a PCR
reaction. Steps involving mathematical calculations using algorithms are
considered by the Supreme Court to be "abstract ideas" in the context of
determining whether a claim is a judicial exception to 35 U.S.C. § 101.
Thus, the rejected claims, as found by the Examiner involve the
implementation of an "abstract idea" on a computer system. However, as
held by the Federal Circuit in McRO, Inc. v. Bandai Namco Games America
Inc., 837 F.3d 1299 (2016):
We do not assume that such claims are directed to patent
ineligible subject matter because "all inventions at some level
embody, use, reflect, rest upon, or apply laws of nature, natural
phenomena, or abstract ideas."
5
Appeal2017-006762
Application 13/688, 133
Prometheus Labs., Inc., - U.S.--, 132 S. Ct. 1289, 1293,
182 L.Ed.2d 321 (2012) ("Mayo"); see also In re TL! Commc 'ns
LLC Patent Litig., 823 F.3d 607, 611 (Fed. Cir. 2016) ("TL!
Commc 'ns"). Instead, "the claims are considered in their entirety
to ascertain whether their character as a whole is directed to
excluded subject matter." Internet Patents Corp. v. Active
Network, Inc., 790 F.3d 1343, 1346 (Fed. Cir. 2015). If the
claims are not directed to an abstract idea, the inquiry ends. If the
claims are "directed to" an abstract idea, then the inquiry
proceeds to the second step of the Alice framework.
In step two we consider whether the claims contain an "inventive
concept" sufficient to "transform the nature of the claim into a
patent-eligible application." Alice, 134 S. Ct. at 2355 (quotation
omitted). To do so we look to both the claim as a whole and the
individual claim elements to determine whether the claims
contain "an element or combination of elements that is 'sufficient
to more than a patent upon the [ineligible concept] itself.' "Id.
(quoting Mayo, 132 S. Ct. at 1294) (alteration in original).
McRO, 837 F.3d 1299, 1311-12.
Two cases that are oft-cited in a Section 101 analysis are Diamond v.
Diehr, 450 U.S. 175 (1981) and Parker v. Flook, 437 U.S. 584 (1978).
In Diehr, the claims were directed to a method of operating a rubber-
molding press to mold a compound by curing it in a mold cavity.
Application of Diehr, 602 F.2d 982, 983-84 (CCPA 1979) ("Application of
Diehr"; lower court decision; Diehr did not reproduce the claims, but
Application of Diehr did.) The temperature in the mold during the rubber-
molding process was constantly determined and provided to a digital
computer. Id. The computer calculated the Arrhenius equation for the
reaction time during the cure to determine when the compound was cured
and to automatically open the press when cure was accomplished. Id.
6
Appeal2017-006762
Application 13/688, 133
Although the claim recited a mathematical algorithm and an abstract
idea, the Arrhenius equation, the Court held that the claim was eligible for a
patent.
[W]hen a claim containing a mathematical formula implements
or applies that formula in a structure or process which, when
considered as a whole, is performing a function which the patent
laws were designed to protect ( e. g., transforming or reducing an
article to a different state or thing), then the claim satisfies the
requirements of § 101.
Diehr, 450 U.S. at 192-93.
In Flook, the claims were found to be ineligible for a patent. In Flook,
the claim was directed to a "method for updating the value of at least one
alarm limit on at least one process variable involved in a process comprising
the catalytic chemical conversion of hydrocarbons." Flook, 437 U.S. at
596-97 (Appendix to Opinion). The steps comprised determining a new
alarm base using a mathematical algorithm, using the alarm base to update
an alarm limit, and then adjusting the alarm limit to the update value. Id.
The Court found the claim to be unpatentable under Section 101. The Court
held:
The process itself, not merely the mathematical algorithm, must
be new and useful. Indeed, the novelty of the mathematical
algorithm is not a determining factor at all. Whether the
algorithm was in fact known or unknown at the time of the
claimed invention, as one of the "basic tools of scientific and
technological work," it is treated as though it were a familiar
part of the prior art.
Flook, 437 at U.S., 591-92.
Further, the Court stated:
7
Appeal2017-006762
Application 13/688, 133
Respondent's process is unpatentable under§ 101 not because it
contains a mathematical algorithm as one component, but
because, once that algorithm is assumed to be within the prior
art, the application, considered as a whole, contains no patentable
invention. Even though a phenomenon of nature or mathematical
formula may be well known, an inventive application of the
principle may be patented. Conversely, the discovery of such a
phenomenon cannot support a patent unless there is some other
inventive concept in its application.
Flook, 437 U.S. at 594.
In reaching this determination, the Court found that the "post-solution
activity" in adjusting the alarm was insufficient to establish patent eligibility
to the claim because the claim as a whole was not "an inventive application
of the principle." Id. Rather, the Court found:
The chemical processes involved in catalytic conversion of
hydrocarbons are well known, as are the practice of monitoring
the chemical process variables, the use of alarm limits to trigger
alarms, the notion that alarm limit values must be recomputed
and readjusted, and the use of computers for "automatic
monitoring alarming." Respondent's application simply provides
a new and presumably better method for calculating alarm limits.
Flook, 437 U.S. at 595.
The question in this appeal is whether there is an "inventive"
application of the algorithms used to determine the concentration of target
molecules in the sample. As in Flook, the claimed PCR process is well-
known and conventional; accordingly, patent eligibility cannot reside in the
steps of carrying it out. However, the algorithm is being used in the claimed
invention to provide an improvement to the PCR process in the same way
the algorithm improved rubber molding in Diehr. Thus, Appellant does not
rely on the novelty of the algorithm, itself, to establish patent eligibility, but
rather on the process as a whole in which the algorithm is used to improve
8
Appeal2017-006762
Application 13/688, 133
the claimed PCR process. As explained in the Specification, the application
of the algorithm to PCR overcame a difficulty experienced in prior art
methods:
Embodiments of the invention remove a jump discontinuity in
fluorescence of real-time polymerase chain reaction data. The
presence of the discontinuity may cause incorrect result
calculation and is hence recommended to be removed.
Depending on the initial copy number of the target, the
discontinuity in the fluorescence may be absent at high
concentration levels. The confidence region of an eight
parameter nonlinear model is used to accurately estimate the
data. The method overcomes difficulties in prior methods for
removal of the discontinuity at all concentration levels.
Spec. ,-r 11.
The disclosed and recited steps in the algorithm are applied to PCR
technology to determine the concentration of the amplified target molecule
in the sample. The method, therefore, is an improvement to PCR technology
because it provides for more accurately determining the quantity of the
target molecule in the sample. Appeal Br. 20. An improvement to an
"existing technological process" was found in McRO to confer patent
eligibility on the claims. McRO, 837 F.3d at 1315. See also Enfzsh, LLC v.
Microsoft Corp., 822 F.3d 1327, 1336 (Fed. Cir. 2016) ("the claims at issue.
. . are not directed to an abstract idea within the meaning of Alice. Rather,
they are directed to a specific improvement to the way computers operate,
embodied in the self-referential table."); Appeal Br. 22.
Specifically, in McRO, "the claimed improvement" was to a computer
system "to produce 'accurate and realistic lip synchronization and facial
expressions in animated characters' that previously could only be produced
by human animators . . . [T]his computer automation is realized by
9
Appeal2017-006762
Application 13/688, 133
improving the prior art through "the use of rules, rather than artists, to set the
morph weights and transitions between phonemes."' McRO, 1313. In
finding the claims patent eligible, the court stated: "The claimed process
uses a combined order of specific rules that renders information into a
specific format that is then used and applied to create desired results: a
sequence of synchronized, animated characters." McRO, 1315.
Here, there is also an order of specific rules that produces an
improvement to the measurement of a PCR product in a sample. As in
Diehr where the algorithm improved the process of curing rubber, the
algorithm recited in the claims improves the process of determining the
target molecule in the PCR process, a physical and chemical process. There
is nothing that requires a method "be tied to a machine or transform an
article" to be patentable. Bilski v. Kappas, 561 U.S. 593, 610-11 (2010).
The concern underlying the exceptions to § 101 is pre-emption. Alice
Corp. Pty. Ltd. v. CLS Banklnt'l, 134 S. Ct. 2347, 2354 (2014). The
preemption concern arises when the claims are not directed to a specific
invention and instead improperly monopolize "the basic tools of scientific
and technological work." Alice, 134 S. Ct. at 2354. However, in this case,
the algorithm does not preempt other methods for determining target
quantity in a PCR sample, including other methods which use the individual
steps differently than how they are used in the claims. Consequently,
preemption is not properly invoked.
For the foregoing reasons we reverse the Section 101 rejection of
claims 1, 13, and 1 7, and claims 2-11 and 14--16, and 18-21, which depend
from them.
10
Appeal2017-006762
Application 13/688, 133
REJECTION UNDER SECTION 112, SECOND PARAGRAPH
The Examiner rejected the claims as indefinite because of the
recitation of "information coefficient" in the claims. The Examiner stated
the term is "vague and appears incomplete because there is no definition nor
detailed guidance in the present in the specification for how this value is
determined to define the metes and bounds of the term." Ans. 7.
While the Examiner stated that the term "information coefficient" is
indefinite, the Examiner also acknowledged the term "is generally
understood in the art," imposing the indefiniteness rejection because "there
is no art accepted calculation nor a single method for determining this
coefficient/value." Ans. 8. A term is not indefinite merely because there is
more than one way to calculate it, particularly where there is no evidence
suggesting that different methods of calculation produce materially different
results. The Examiner did not establish that the term is susceptible to more
than one meaning, and thus ambiguous, but rather asserted it is indefinite
simply because it can be calculated by different methods. The Examiner
states that how the information coefficient is calculated is critical to the
method, but does not provide persuasive evidence to support this assertion.
The claim does not restrict how the information coefficient is calculated and
thus, definitely conveys the breadth of the term to one of ordinary skill in the
art. Consistently, claims 7, 16, and 19 involve specific ways of calculating
the information coefficient. See Spec. i-f 45 describing this embodiment.
The Examiner also stated
Further, it is noted that the 'best fit to the dataset' is obtained
using the 'information coefficient' which indicates that this value
is somehow different and unique to approximations and best fit
11
Appeal2017-006762
Application 13/688, 133
assessments usually used in the art since an 'information
coefficient' is provided in the comparison of two non-linear
function approximations.
Ans. 8.
The Examiner is referring to the following steps of claim 1:
determining, by the computer system, an information coefficient
for each of the first and second approximations, each information
coefficient indicating an accuracy of a fit of the corresponding
approximation to the dataset;
selecting, by the computer system, one of the approximations
based on the information coefficient, the selected approximation
providing a best fit to the dataset;
The first recited step instructs the system to determine an information
coefficient and requires the coefficient to be an indication of "an accuracy of
a fit of the corresponding approximation to the dataset." The second recited
step instructs the system to use the information coefficient to select an
approximation providing a best fit to the dataset. The Examiner did not
explain why using the information coefficient to determine a best fit to the
data set renders the claim indefinite. On the face of it, the claim language
clearly instructs the system to determine the best fit. We have not been
directed to any evidence that the terms "information coefficient" or "best fit"
are ambiguous terms. To the contrary, as admitted by the Examiner (Ans.
13) and established by Appellants (Appeal Br. 31; Reply Br. 11-12) the
terms are well-known in the art and they do not introduce any lack of clarity
into the claims.
The rejection of claims 1-11and13-21under§112, second
paragraph is reversed.
REVERSED
12