Ex Parte Carnevali et al

Patent Trial and Appeal Board

May 30, 2018

12770089 (P.T.A.B. May. 30, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/770,089 04/29/2010
16167 7590 06/04/2018
Kilpatrick Townsend & Stockton LLP/ Complete
Genomics, Inc.
1100 Peachtree Street, Suite 2800
Mailstop: IP Docketing - 22
Atlanta, GA 30309
FIRST NAMED INVENTOR
Paolo Carnevali
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.
92171-002110US-798099 9005
EXAMINER
SKIBINSKY, ANNA
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
06/04/2018 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
KTSDocketing2@kilpatrick.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte PAULO CARNEVALI, JONATHAN M. BACCASH,
IGOR NAZARENKO, AARON L. HALPERN, GEOFFERY NILSEN,
BRUCE MARTIN, and RADJOE DRMANIC. 1
Appeal2017-007405
Application 12/770,089
Technology Center 1600
Before DONALD E. ADAMS, JOHN E. SCHNEIDER, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
SCHNEIDER, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for analyzing polynucleotide sequences, which have been rejected as
directed to non-statutory subject matter. We have jurisdiction under 35
U.S.C. § 6(b).
We AFFIRM.
1 Appellants identify the Real Party in Interest as Complete Genomics, Inc.
Appeal Br. 3.
Appeal2017-007405
Application 12/770,089
STATEMENT OF THE CASE
"In genetic research, genetic testing, personalized medicine, and many
other applications, it is often useful to obtain a sample of genetic material,
determine a sequence of that sample, and to analyze that sequence with
respect to one or more existing references to identify sequence variations or
obtain other useful information for the sample." Spec. ,r 2. "[S]ome
techniques used for obtaining sample sequences yield a polynucleotide
sequence comprising multiple shorter sequences ( sometimes referred to as
oligomers) with predicted spatial relationships, and in some cases with
spatial relationships of variable distances." Spec ,r 3. These techniques "are
not adequate to provide high speed, low cost de novo assembly or
reassembly of short sequences comprising continuous reads that are variably
gapped." Spec. ,r 4.
The Specification describes "methods and systems for calling
variations in a sample polynucleotide sequence compared to a reference
polynucleotide sequence." Spec. ,r 6.
Claims 2, 4, 7-29, 38-61 2 are on appeal. Claim 8 is representative of
the rejected claims and reads as follows:
8. A computer-implemented method for calling
variations in a sample polynucleotide sequence with respect to a
reference polynucleotide sequence, the method comprising:
locating, by at least one computer, local areas in the
reference polynucleotide sequence where a likelihood that one
or more bases of the sample polynucleotide sequence are
changed from corresponding bases in the reference
polynucleotide sequence exceeds a likelihood threshold,
wherein the at least one computer determines the likelihood at
2 Claim 3 is also pending in the application but has been withdrawn from
consideration as directed to a non-elected species. Non-Final Act. 3.
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Application 12/770,089
least in part based on mapped mated reads of the sample
polynucleotide sequence, wherein locating the local areas likely
to have changed from the reference polynucleotide sequence
comprises:
computing reference scores using a Bayesian formulation
process, compnsmg:
for each of a plurality of base positions in the reference
polynucleotide sequence:
generating a set of initial hypotheses for the base position
by modifying a base value at that position in p alleles by all
possible I-base variations;
determining a set of mapped mated reads that are near the
base position; and
computing a reference score by computing, for each of
the initial hypotheses in the set, a probability ratio P vlP ref, where
P v is a probability of a I-base variation hypothesis, and Pref is a
probability of the base value in the reference polynucleotide
sequence, and where the set of mapped mated reads near the
base position are used during calculation of the probability ratio
at the base position; and
comparing the reference scores to the likelihood
threshold;
generating, by the at least one computer, a plurality of
sequence hypotheses for each of the local areas, each of the
plurality of sequence hypotheses including a plurality of bases
at positions in the corresponding local area, the plurality of
sequence hypotheses for a respective local area being generated
by changing bases relative to the initial hypotheses at positions
of the respective local area;
identifying, by the at least one computer, one or more
optimized sequence hypotheses of maximum probability from
the plurality of sequence hypotheses for each of the local areas
by calculating a probability estimate for each of the plurality of
sequence hypotheses, wherein the mapped mated reads are
generated independently of each other, and wherein the
probability estimates take into account all of the mapped mated
reads are calculated by
P(C 1,'f td Rds) .... d'l;;\,' ivo ······ LM P(g)P(AltdRd )C, lid)
P(i.j(}lAiiaka.~')·· = t10(1··) Mt .. t" 1;.~1·r;\iJ:jP(iiiictkdii\1.:·fi.n
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Application 12/770,089
where M is a number of mappings for each mapped mated read,
Nao represent a number of bases in the reference genome, Na
represents a number of bases in the sample genome, and N n
represents a number of mated reads; and
analyzing, by the at least one computer, the optimized
sequence hypotheses to identify a series of variation calls in the
sample polynucleotide sequence.
Claims 2, 4, 7-29, 38---61 have been rejected under 35 U.S.C. § 101 as
directed to non-statutory subject matter.
DISCUSSION
The issue with respect to this rejection is whether a preponderance of
the evidence supports the Examiner's conclusion that claims 2, 4, 7-29, 38-
61 are directed to non-statutory subject matter.
The Examiner finds that the claimed method relies on "the abstract
ideas of performing algorithmic analysis of sequence data, comparing
sequence data, and using mathematical concepts including mathematical
algorithms and formulas. The claims are entirely drawn to a computational
algorithmic method and do not include additional steps outside of [] the
abstract idea." Non-Final Act. 4. The Examiner finds that although some of
the claims contain additional elements, "[ v ]iewed as a whole, these
additional claim element( s) do not provide meaningful limitation( s) to
transform the abstract idea into a patent eligible application of the abstract
idea such that the claim( s) amounts to significantly more than the abstract
idea itself." Id.
Appellants argue that the claims are not directed to a mere
transformation of data but to determination of a physical property of a
sample. Appeal Br. 14. Appellants argue that the claims are not directed to
a mathematical formula and that the cases cited by the Examiner are limited
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Application 12/770,089
to claims involving a mathematical formula. Appeal Br. 16-19. Appellants
contend that the claims are directed to solving a technical problem namely
how to identify variations in sample nucleotide sequences from
measurements of polynucleotide fragments from a sample organism. Appeal
Br. 19--21. Appellants also contend that the claims are directed to an
improvement of a technology or technical field. Appeal Br. 21-25.
Appellants also contend that the claims recite limitations that represent
something significantly more than abstract concepts.
Analysis
"Laws of nature, natural phenomena, and abstract ideas are not
patentable." Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S.
Ct. 1289, 1293 (2012) (citation omitted). "Groundbreaking, innovative, or
even brilliant discovery does not by itself satisfy the§ 101 inquiry." Ass 'n
for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2117
(2013).
The Supreme Court articulated a two-step test for patent eligibility
under § 101 that "distinguish[ es] patents that claim laws of nature, natural
phenomena, and abstract ideas from those that claim patent-eligible
applications of those concepts." Alice Corp. Pty. Ltd. v. CLS Bank Int 'l, 134
S. Ct. 2347, 2355 (2014) (citing Mayo, 132 S. Ct. at 1296-97) ("the
Alice/Mayo test"). "First, we determine whether the claims at issue are
directed to one of those patent-ineligible concepts. If so, we then ask,
' [ w ]hat else is there in the claims before us?"' Id. ( citation and quotations
omitted). Second, we "search for an inventive concept-i.e., 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." Id. ( quotations and alterations omitted).
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We agree with the Examiner that the claims are directed to ineligible
subject matter. Each of the recited steps, locating, computing, generating,
determining, comparing, identifying, and analyzing involve abstract ideas
and are not patent eligible. See SAP America, Inc. v. Investpic, LLC, No
2017-2081, 2018 WL 2207254, at *4 (Fed. Cir, May 15, 2018). That the
claims are directed to a certain type of data content and call for the use of a
computer does not render the claims patent eligible. Id. at *5---6.
Appellants contend that the claims are directed to a determination of a
physical property of a sample involving accurately identifying variations in a
sample polynucleotide sequence from measurements of polynucleotide
fragments from a sample organism. Appeal Br. 15. We are not persuaded.
Although claim 8 refers to comparing a sample polynucleotide sequence to a
reference sequence, nowhere does the claim require the sample sequence be
a fragment from a sample organism. The claim calls for comparing one
sequence with another. This is abstract data analytics and we are
unpersuaded that the type of data (sequence information) saves the claim
from abstraction.
Moreover, even if the sample sequence was from a sample organism,
this is merely limiting the data to a particular content or source. This is
insufficient to render the claimed method patentable. SAP at *5.
Appellants next argue that the claims are not directed to a
mathematical formula and that the cases where abstract ideas were found
unpatenable all relate to mathematical formulas. Appeal Br. 19. We remain
unpersauded. As discussed above, the claimed method relates to collecting
information and analyzing it. The Federal Circuit has made it clear that
claims focused on collecting and analyzing information, without
significantly more, are not patent eligible. SAP at *4.
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Id.
"Information as such is an intangible," hence abstract, and
"collecting information, including when limited to particular
content (which does not change its character as information),
[i]s within the realm of abstract ideas." Id. ( citing cases). So,
too, is "analyzing information ... by mathematical algorithms,
without more." Id. at 1354 (citing cases, including Parker v.
Flook, 437 U.S. 584 (1978), and Gottschalk v. Benson, 409
U.S. 63 (1972)). And "merely presenting the results of abstract
processes of collecting and analyzing information, without
more (such as identifying a particular tool for presentation), is
abstract as an ancillary part of such collection and analysis."
Id. ( citing cases). The claims here are directed at abstract ideas
under those principles.
Appellants argue that the claims are patent eligible because they are
directed to a specific technology, identification of variations in
polynucleotide sequences and show an improvement over other techniques.
Appeal Br. 20-25. Once again, we are unpersuaded. Even assuming the
claimed method may be innovative, it is an innovation in ineligible subject
matter. SAP at * 1. No matter how much of an advance may be represented
by the method of the claims, "the advance lies entirely within the realm of
abstract ideas .... An advance of that nature is ineligible for patenting." Id.
Appellants cite to McRO, Inc. v. Bandai Namco Games America Inc.,
837 F.3d 1299 (Fed. Cir. 2016) for the proposition that data processing rules,
such as those reflected in the present claims are patent eligible. Appeal Br.
18 and 26. We remain unpersuaded.
As the Federal Circuit has pointed out, the claims in McRO, "were
directed to the creation of something physical- namely the display of 'lip
synchronization and facial expressions."' SAP at *4. For this reason the
claims in McRO, were deemed patent eligible. Id. In the present
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application, the claims a do not produce a tangible result. All that is claimed
are the rules for data handling.
Appellants also rely on In re Abele, 684 F.2d 902 (CCPA 1982) to
support the patentability of the present claims. Appeal Br. 20. Appellants
contend that like claim 6 in Abele, the present claims are directed to solving
a physical problem and are therefore patent eligible. Appeal Br. 20.
We have considered Appellants' argument and find it unpersuasive.
In re Abele, was decided before the Supreme Court's decision in Alice and
its progeny. Subsequent decisions by the Federal Circuit make it clear that
merely limiting the particular data being analyzed is insufficient to render
the claims patent eligible. SAP at *5.
Finally, Appellants contend that the present claims recited
unconventional steps, which represent something substantially more than an
abstract idea. Appeal Br. 28. Appellants point to the fact that several of the
steps are not found in the prior art and cannot be deemed conventional. Id.
Here again, even if the claims may be novel and non-obvious, that
alone is insufficient to show that the claims are patent eligible. SAP at * 1.
As discussed above the claims, as a whole, are directed to a series of abstract
steps, and are not patent eligible. Id. This is true even for the steps which
Appellants contend are unconventional and not found in the prior art. See,
Appeal Br. 28.
We conclude that a preponderance of the evidence supports the
Examiner's conclusion that the claims are directed to non-statutory subject
matter.
SUMMARY
We affirm the rejection under 35 U.S.C. § 101.
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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
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