Jon Sorenson et al.

Patent Trials and Appeals Board

Nov 21, 2019

13731506 - (D) (P.T.A.B. Nov. 21, 2019)

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.
13/731,506 12/31/2012 Jon Sorenson 067191-5091-US01 2137
43850 7590 11/21/2019
Morgan, Lewis & Bockius LLP (SF)
One Market, Spear Street Tower, Suite 2800
San Francisco, CA 94105
EXAMINER
CLOW, LORI A
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
11/21/2019 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):
donald.mixon@morganlewis.com
sfipdocketing@morganlewis.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte JON SORENSON, SUSAN TANG, PATRICK MARKS, and
CHEN-SHAN CHIN
__________

Appeal 2018-004559
Application 13/731,5061
Technology Center 1600
__________

Before JOHN E. SCHNEIDER, RACHEL H. TOWNSEND, and
DAVID COTTA, Administrative Patent Judges.

TOWNSEND, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for determining a consensus base call at a given location j in a
template sequence and an apparatus for carrying out that method. The
claims have been rejected as being directed to patent-ineligible subject
matter. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.

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 Pacific
Biosciences of California, Inc. (Appeal Br. 4.)
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STATEMENT OF THE CASE
Automated sequencing systems are known. (Spec. ¶3.) The
Specification states that
the quality of the sequence information must be carefully
monitored, and may be compromised by many factors related to
the biomolecule itself or the sequencing system used, including
the composition of the biomolecule (e.g., base composition of a
nucleic acid molecule), experimental and systematic noise,
variations in observed signal strength, and differences in
reaction efficiencies.
(Id.) Appellant’s invention is directed at a method to ultimately improve the
quality of sequence data involving analysis of replicate sequence
information. (Id. 3–4, 6, 15.)
Claims 57–61, 63, 65, 67, 68, and 71–79 are on appeal. Claim 57 is
representative and reads as follows:
57. A method for determining a consensus base call at a given
location j in a template sequence that represents a nucleic acid
molecule, the method comprising:
a) obtaining a plurality of reads for the template sequence
using a nucleic acid sequence measurement platform;
b) identifying a base in the set {A, C, G, T} for location j
in the template sequence that maximizes a summation of a joint
probability function summed across the plurality of reads of the
nucleic acid molecule, the joint probability function
comprising, for each respective read in the plurality of reads, a
product of
(A) a forward path probability P that is a
summation of a first set of probabilities, each probability
in the first set of probabilities for a different candidate
sequence for the template sequence in a plurality of
candidate sequences for the template sequence given (i)
the respective read, (ii) the respective candidate
sequence, and (iii) an error model H associated with the
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plurality of reads, wherein the forward path probability
samples position j-1 of each candidate sequence in the
plurality of candidate sequences, and
(B) a backward path probability Q that is a
summation of a second set of probabilities, each
probability in the second set of probabilities for a
different respective candidate sequence in the plurality of
candidate sequences given (i) the respective read, (ii) the
respective candidate sequence, and (iii) the error model
H, wherein the backward path probability samples
position j+1 of each candidate sequence in the second
plurality of candidate sequences; and
c) deeming the base identified in b) as the consensus base
call at the given location j in the template sequence for the
nucleic acid molecule, wherein the obtaining a) and identifying
b) are performed on a suitably programmed computer.
(Appeal Br. 28.)

The following ground of rejection by the Examiner is before us on
review:
Claims 57–61, 63, 65, 67, 68, and 71–79 under 35 U.S.C. § 101 as
being directed to patent ineligible subject matter.
DISCUSSION
35 U.S.C. § 101 defines patent-eligible subject matter. The Supreme
Court has carved out exceptions to what would otherwise appear to be
within the literal scope of § 101. Alice Corp. v. CLS Bank Int’l, 573 U.S.
208, 216 (2014). These exceptions include claims “directed to” an abstract
idea. Id. at 217. This appeal involves the abstract idea exception to patent
eligibility under section 101.
The Supreme Court has established a two-step framework for
“distinguishing patents that claim laws of nature, natural phenomena, and
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abstract ideas from those that claim patent-eligible applications of those
concepts.” Id. “First, we determine whether the claims at issue are directed
to” a patent-ineligible concept. Id. If so, “we consider the elements of each
claim both individually and ‘as an ordered combination’ to determine
whether the additional elements ‘transform the nature of the claim’ into a
patent-eligible application.” Id. (quoting Mayo Collaborative Servs. v.
Prometheus Labs., Inc., 566 U.S. 66, 78–79 (2012)).
The PTO issued the 2019 Revised Patent Subject Matter Eligibility
Guidance (“Guidance”), indicating how the PTO would now analyze patent
eligibility under the Supreme Court’s two-step framework. 84 Fed. Reg.
50–57 (January 7, 2019). Applying the Guidance, we agree with the
Examiner that the pending claims are directed to patent ineligible subject
matter.
The Examiner explains that the claims are not drawn to nucleic acid
sequencing but to “‘determining a consensus base call at a given location j in
a template sequence that represents a nucleic acid molecule.’” (Final Action
9.) The Examiner finds that the claims involve data analysis that “is
abstract, as it involves mathematical manipulation of [gathered] nucleic acid
sequence data.” (Id. at 9–10; see also id. at 3 (“the instant claims include
limitations directed to the abstract ideas which are the recitation of
mathematical calculations and/or relationships recited in the claims.”).) The
abstract ideas/judicially excepted subject matter specifically identified by the
Examiner are in step (b) of claim 57: the step of “identifying a base in the set
. . . .” This step involves “maximiz[ing] a summation of a joint probability
summed across the plurality of reads of the nucleic acid molecule” where the
joint probability function for each read comprises a “product of ‘(A) a
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forward path probability P that is a summation of a first set of probabilities .
. . ’; [and] ‘(B) a backward path probability Q that is a summation of a
second set of probabilities. . . ’.” (Final Action 3.)
The Examiner finds that the claims “do not include additional
elements that are sufficient to amount to ‘significantly more’ than the recited
judicial exceptions because the additional elements or combination of
elements,” include a data gathering step (obtaining a plurality of reads for
the template sequence) that is routine and conventional in the art and
because the “deeming the base” step is “merely ‘applying’ the judicial
exception [and] does not provide significantly more.” (Id. at 5.)
Appellant argues claims 57–61, 63, 65, 67, 68, and 71–79 together.
We designate claim 57 as representative.
STEP 2A, Prong One:
Under the Guidance, in determining what concept a claim is “directed
to” in step one of the Supreme Court’s two-step framework, we first look to
whether the claim recites any judicial exceptions, such as a mathematical
concept (including mathematical relationships, mathematical formulas or
equations, and mathematical calculations) or a mental process (including
observation, evaluation, and judgment). Guidance at 52, 54 (Step 2A, Prong
One). As the Examiner correctly observed, claim 57 recites mathematical
calculations, including sums and products, i.e., “(b) identifying a base in the
set . . . for location j in the template sequence that maximizes a summation
of a joint probability function summed across the plurality of reads. . . the
joint probability function comprising . . . a product of . . . (A) . . . and (B)”,
“(A) a forward path probability P that is a summation of a first set of
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probabilities . . .” and “(B) a backward path probability Q that is a
summation of a second set of probabilities . . . .”
In addition, we note that claim 57 also recites mental processes,
namely “identifying a base in the set” and “deeming the base identified in b)
as the consensus base call.” That is the “deeming” step is a process that,
under its broadest reasonable interpretation, covers performance of the
limitation in the mind. Similarly, the “identifying” step is a process that,
under its broadest reasonable interpretation, covers a visual observation.
Appellant does not dispute that the claim recites mathematical
calculations, conceding, in fact, that claim 57 “concerns the handling of a
plurality of sequence reads for template sequence and the computation of a
joint probability junction.” (Appeal Br. 17 (emphasis added).) Appellant
argues instead that the claim as a whole is not an abstract idea because it
includes data acquisition via “multiple reads for the very same template” that
“sets it apart from other alignment problems” (id. at 14), that the best call
analysis for position j is dependent on positions j+1 and j-1 in contrast to the
prior art independent analysis (id. at 14–15), and the best call analysis “takes
into consideration the error mode of a given sequencing technology used to
obtain the plurality o[f] reads” (id. at 15–17). We will address the foregoing
in the subsequent analysis.
STEP 2A, Prong Two:
Having made the determination that claim 57 recites judicial
exceptions of mathematical concepts and mental processes, under the
Guidance, we next examine whether there are additional elements beyond
the recited judicial exceptions that integrate those exceptions into a practical
application. Under the Guidance, this is referred to as the “Prong Two”
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inquiry under “Step 2A.” Guidance at 54–55. That is, under the Prong Two
analysis we look to whether the claim as a whole “appl[ies], rel[ies] on, or
use[s] the judicial exception in a manner that imposes a meaningful limit on
the judicial exception.” Id.
In performing this analysis, we are mindful that “a claim is not patent
eligible merely because it applies an abstract idea in a narrow way.” BSG
Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1287 (Fed. Cir. 2018). Thus,
for example, the Supreme Court in Parker v. Flook, 437 U.S. 584 (1978),
found the use of a novel mathematical algorithm in a process for adjusting
alarm limits, which limits signal inefficiency or danger when exceeded, in
catalytic conversion of hydrocarbons patent ineligible. Mayo, 566 U.S. at 80
(discussing Flook, 437 U.S. at 585–87). The process included “the steps of:
(1) measuring the current level of the variable, e.g., the temperature; (2)
using an apparently novel mathematical algorithm to calculate the current
alarm limits; and (3) adjusting the system to reflect the new alarm-limit
values.” Id.2 In light of this, we do not find persuasive Appellant’s
argument that because claim 57 is “directed to the specific technological
process of nucleic acid sequencing,” it is directed to patent eligible subject
matter (Appeal Br. 20).

2 We note that claim 65 recites an apparatus that includes memory with one
or more programs stored therein and one or more processors that execute the
program(s) where the program(s) include instructions to carry out the
method steps as set forth in claim 57. We note that the Supreme Court has
stated that “simply implementing a mathematical principle on a physical
machine, namely a computer, was not a patentable application of that
principle.” Id. at 84 (citing Gottschalk v. Benson, 409 U.S. 63, 71 (1972).)

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In contrast to Flook, the Supreme Court in Diamond v. Diehr, 450
U.S. 175 (1981), found the overall physical and chemical process for
molding precision synthetic rubber “patent eligible because of the way the
additional steps of the process integrated the equation into the process as a
whole.” See e.g., Mayo, 566 U.S. at 80 (discussing Diehr, 450 U.S. at 177–
79); Recognicorp, LLC v. Nintendo Co. Ltd., 855 F.3d 1322, 1326 (Fed. Cir.
2017) (“In confirming patentability, the Supreme Court focused not on the
presence of a mathematical formula but on the subject matter of the claims
as a whole. [Diehr, 450 U.S.] at 192.”). The process included “installing
rubber in a press, closing the mold, constantly determining the temperature
of the mold, constantly recalculating the appropriate cure time through the
use of the formula and a digital computer, and automatically opening the
press at the proper time.” Mayo, 566 U.S. at 80–81. The Court stated: “[A]
claim containing a mathematical formula” satisfies § 101 when it
“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).” Diehr, 450 U.S. at 192. Outside of the math, Diehr was
directed to a process that was directed to otherwise eligible subject matter,
an industrial process for the molding of rubber products. Id. at 192–93; see
Thales Visionix Inc. v. United States, 850 F.3d 1343, 1348 (Fed. Cir. 2017)
(“In terms of the modern day Alice test, the Diehr claims were directed to an
improvement in the rubber curing process, not a mathematical formula.”).
Unlike the process performed in Diehr, the process in Appellant’s
claim 57 does not involve additional elements beyond the recited
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mathematical concepts and mental processes to transform or reduce an
article into a different state or thing.
Contrary to Appellant’s argument, we do not find claim 57 provides
specific mechanisms that are significantly more than the abstract ideas
(Appeal Br. 25; Reply Br. 3–4). We find that there is only one limitation
that is not one of the identified abstract ideas, namely step “a) obtaining a
plurality of reads for the template sequence using a measurement platform.”
However, this is a pre-solution data gathering step (see MPEP § 2106.05(g)
(“[a]n example of pre-solution activity is a step of gathering data for use in a
claimed process.”)), that does not apply any of the abstract ideas in a
meaningful way, but instead simply “generally link[s] the use of a judicial
exception to a particular technological environment or field of use.”
Guidance, 84 Fed. Reg. at 55 (citing MPEP § 2016.05(h)); see also In re
Grams, 888 F.2d 835, 840 (Fed. Cir. 1989) (“The presence of a physical step
in the claim to derive data for the algorithm will not render the claim
statutory.”). Moreover, we note that Appellant’s Specification indicates that
“[e]ssentially any technology capable of generating sequence data from
biomolecules may be used to generate the replicate sequence reads.” (Spec.
¶ 39.)
Appellant’s arguments that the best call analysis is dependent on
positions j+1 and j-1 (Appeal Br. 14–15), and that the best call analysis
“takes into consideration the error mode of a given sequencing technology”
(id. at 15–17), unlike the prior art, does not establish that there are additional
elements beyond the recited judicial exceptions that integrate those
exceptions into a practical application. Appellant’s arguments simply
indicate that the mathematics (which is the specific mechanism for
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determining the consensus base call) involved in the claimed method are an
improved algorithm that improves the accuracy of the consensus base call at
a given location j in a template base sequence. (See Appeal Br. 13–17, 25;
see also Reply Br. 3–5.) In this respect, this case is like Flook. In Flook, the
“only difference between the conventional methods of changing alarm limits
and that described in respondent’s application rest[ed] in the second step––
the mathematical algorithm or formula.” 437 U.S. at 585–86. In Flook, the
court found that the claimed subject matter “simply provides a new and
presumably better method for calculating alarm limit values” and, thus, was
not directed to patent eligible subject matter. Id. at 595 (explaining “‘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
nonstatutory.’”). The court found that the use of that method to adjust an
alarm limit did not render the method patent eligible. Id. We conclude that,
like Flook, the claimed method is to a “new and presumably better”
algorithm, and the only difference between the claimed method and
conventional methods lies in the algorithms used. As in Flook, the judicially
excepted subject matter generates information: here the probability of
correctness of the base for location j, in Flook, an alarm value. In Flook, the
information generated was used to “adjust” an alarm value. Here, the
information generated is used to select the identity of the base for location j.
In neither case does the use of the information generated by the excepted
subject matter integrate the judicially excepted subject matter into a practical
application.
Appellant’s reliance on McRO, Inc. v. Bandai Namco Games
America, Inc., 837 F.3d 1299 (Fed. Cir. 2016) (Appeal Br. 18–22, Reply Br.
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6–7) to argue its claim is not directed to an abstract idea is unavailing. In
McRO, prior to the claimed invention, character facial expressions and lip
synchronization were accomplished by human animators, with the assistance
of a computer, where animators set appropriate parameters at certain time
points, a so-called “keyframe” approach. McRO, 837 F.3d. at 1305. The
animators, using a computer, manually determined the appropriate
parameters to set for each keyframe based on the phoneme timings in a time-
aligned phonetic transcript. Id. The invention in McRO that resulted in an
improvement to the field of computer animation was removal of the human
element to the keyframe process by using rules, rather than human
animators, which automatically set the parameters. Id. at 1313. The rules in
McRO, thus, allowed the computer to produce accurate and realistic
synchronization in animated characters that could only previously be
produced by humans. The claims here do not relate to any such rules
replacing human action to allow computers to perform automatically what
previously required human interaction. That is, neither the claim, nor the
Specification provide for rules that allow for a computer to act in a way that
it could not before without human interaction.
Appellant further argues that “claim 57 would not preempt the
computer implementation of any known commercial, industrial or scientific
practice or methodology, as it incorporates a novel and non-obvious solution
to a technical problem (Appeal Br. 17, see also id. at 22–24) and thus, the
claim should be deemed directed to patent eligible subject matter. We do
not find this argument persuasive. Preemption is sufficient to render a claim
ineligible under § 101, but its absence does not require a conclusion of
patent eligibility. Athena Diagnostics, Inc. v. Mayo Collab. Servs., LLC,
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915 F.3d 743, 752 (Fed. Cir. 2019) (citing Flook, 409 U.S. at 71–72 (holding
claim involving mathematical formula invalid under § 101 that did not
preempt a mathematical formula); Ariosa Diagnostics, Inc. v. Sequenom,
Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015); In re BRCA1- & BRCA2-Based
Hereditary Cancer Test Patent Litig., 774 F.3d 755, 764 n.4 (Fed. Cir.
2014).
STEP 2B
We next turn to Step 2B to evaluate whether the claims provide an
inventive concept. Guidance at 54.
Under the Guidance, we must consider in Step 2B whether an
additional element or combination of elements: (1) “adds a specific
limitation or combination of limitations that are not well-understood,
routine, conventional activity in the field, which is indicative that an
inventive concept may be present;” or (2) “simply appends well-understood,
routine, conventional activities previously known to the industry, specified
at a high level of generality, to the judicial exception, which is indicative
that an inventive concept may not be present.” Id.
The analysis is not an evaluation of novelty or non-obviousness, but,
rather, a search for “an element or combination of elements that is ‘sufficient
to ensure that the patent in practice amounts to significantly more than a
patent upon the [ineligible concept] itself. ’” Alice, 573 U.S. at 217–218
(alteration in original). A novel and nonobvious claim directed to a purely
abstract idea is, nonetheless, patent-ineligible. See Mayo, 566 U.S. at 90.
Thus, that there is no evidence provided by the Examiner “that the process
required by the claims is the same as any process previously used in
sequence determination and conducted by similar or other means” (Reply
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Br. 5), is insufficient to establish the claim is directed to something
significantly more than the patent ineligible concept itself.
As discussed above, the collection of multiple reads is described in
Appellant’s Specification to be by any routine methodology. Appellant’s
mathematical algorithm to process the data in order to identify the base for
location j may be novel, but that by itself is insufficient to render the claim
directed to that judicial exception patent eligible for the reasons discussed
above. See Flook, 437 U.S. at 591–92 (
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,” see Gottschalk v. Benson, 409 U.S., at 67,
93 S.Ct., at 255, it is treated as though it were a familiar part of
the prior art.);
see also id. at 594–95 (“Respondent’s application simply provides a new and
presumably better method for calculating alarm limit values.”).
Furthermore, while it may be the case that the methodology improves
the accuracy of the determination of the base call at a given location j in a
template sequence (Reply Br. 6), there is no technological improvement.
There is no contention or evidence that the functioning of a computer or
other device is improved, nor is there a contention or evidence that the claim
solves a problem with a system that analyzes sequence data. Cf. Amdocs
Ltd. v. Openet Telecom, Inc., 841 F.3d 1288, 1300–02 (Fed. Cir. 2016)
(determining the claimed invention creating a distributed architecture
“entailed an unconventional technological solution (enhancing data in a
distributed fashion) to a technological problem (massive record flows [that]
previously required massive databases)” that “improve[d] the performance
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of the system itself”); Thales Visionix Inc. v. U.S., 850 F.3d 1343, 1348–49
(Fed. Cir. 2017) (determining that a system for tracking motion of an object
via a first inertial sensor on a moving object, a second inertial sensor on a
moving reference frame, and an element adapted to receive signals from the
inertial sensors and determine an orientation of the object relative to the
moving reference frame, was not directed to an abstract idea because the
system used its inertial sensors in a non-conventional manner to determine
the relative position and orientation of a moving object on a moving
reference frame). Here, the improvement relates to improved data analysis
from using a new algorithm, not new technology. As Appellant
acknowledges, Appellant’s claims are directed to “a method of calculating a
result within the context of a specific set of limiting rules,” (Reply Br. 8) i.e.,
mathematical algorithms. (See Appeal Br. 25:
As discussed above, and as set forth in the specification as
noted above, consideration of positions j-1 and j+1 of the
template sequence when calling position j of template sequence
allows for the use of more robust error models and hence more
accurate calling of the template sequence. . . .
(and noting the specific calculations required by the claim as being the
“specific mechanisms” by which the more accurate calling is
achieved).)
Because Appellant’s independent claim 57 is directed to a patent-
ineligible abstract concept, does not include additional elements that
integrate the judicial exception into a practical application, and does not add
a specific limitation beyond the judicial exception that is not “well-
understood, routine, [and] conventional,” we sustain the Examiner’s
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rejection of the claims under 35 U.S.C. § 101 as being directed to non-
statutory subject matter.
Claims 58–61, 63, 67, 68, and 71–79 have not been argued separately
and therefore fall with claims 57 and 65. 37 C.F.R. § 41.37(c)(1)(iv).
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
57–61, 63,
65, 67, 68,
71–79
101 Eligibility/Patent
Ineligible subject
matter
57–61, 63,
65, 67, 68,
71–79

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED