Ex Parte Young et al

Patent Trial and Appeal Board

Jul 16, 2018

14489198 (P.T.A.B. Jul. 16, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/489,198 09/17/2014 Brian A. Young
23643 7590 07/18/2018
Barnes & Thornburg LLP (IN)
11 S. Meridian Street
Indianapolis, IN 46204
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.
920006-229539 1022
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
07/18/2018 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):
INDocket@btlaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte BRIAN A. YOUNG, ESLEY M. HEIZER JR.,
ANGELA T. MINARD-SMITH, NANCY J. McMILLAN,
GOKHAN YA VAS, and DANIEL M. BORNMAN
Appeal2017-007443 1
Application 14/489,198
Technology Center 1600
Before FRANCISCO C. PRATS, JAMES A. WORTH, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
PRATS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims to methods
involving the use of a massively parallel sequencing instrument to read the
nucleotide sequences of amplified nucleic acids. The Examiner rejected the
claims as being directed to subject matter ineligible for patenting.
We have jurisdiction under 35 U.S.C. § 6(b )(1 ).
We reverse.
1 Appellants state that the "real party in interest is Battelle Memorial
Institute, by virtue of an assignment recorded in the Patent Office at patent
record reel 034113, beginning at frame 0104." Appeal Br. 2.
Appeal2017-007443
Application 14/489,198
STATEMENT OF THE CASE
The sole rejection before us for review is the Examiner's rejection of
claims 1-10 and 12-19 as being directed to subject matter not eligible for
patenting. Final Act. 4--8; Ans. 2-5.
Claims 1 and 12, the independent claims on appeal, are illustrative
and reads as follows:
1. A method comprising:
amplifying one or more nucleotide sequences in a sample
using a PCR amplification process to produce an amplified
sample;
using a massively parallel sequencing (MPS) instrument
to read the one or more nucleotide sequences of the amplified
sample and generate one or more text strings based on the
amplified sample;
selecting a first plurality of text strings from the one or
more text strings read by the MPS instrument, wherein each of
the selected first plurality of text strings represent a nucleotide
sequence that-corresponds to a first target locus in the amplified
sample;
comparing the selected first plurality of text strings to
one another to determine an abundance count for each unique
text string included in the selected first plurality of text strings;
identifying a first number of unique text strings included
in the selected first plurality of text strings as representing noise
responses; and
determining a method detection limit (MDL) as a
function of the abundance counts for the first number of unique
text strings identified as representing noise responses.
12. A method comprising:
amplifying one or more nucleotide sequences in a sample
using a PCR amplification process to produce an amplified
sample;
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Application 14/489,198
using a massively parallel sequencing (MPS) instrument
to read the one or more nucleotide sequences of the amplified
sample and generate one or more text strings based on the
amplified sample;
selecting a first plurality of text strings from the one or
more text strings read by the MPS instrument, wherein each of
the selected first plurality of text strings represent a nucleotide
sequence that corresponds to a first target locus in the amplified
sample;
comparing the selected first plurality of text strings to
one another to determine an abundance count for each unique
text string included in the selected first plurality of text strings;
and
outputting a graphical display, wherein the graphical
display comprises a first plurality of graphical elements that
each correspond to one of the unique text strings included in the
selected first plurality of text strings and that each represent the
abundance count determined for the corresponding unique text
string.
Appeal Br. 10, 14.
STANDARD OF REVIEW
As stated inJn re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden ... of presenting a
prima facie case of unpatentability ....
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
DISCUSSION
The Examiner's Prima Facie Case
In concluding that Appellants' claims are directed to subject matter
ineligible for patenting, the Examiner found that the processes recited in the
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rejected claims "are directed towards a judicial exception, i.e. an abstract
idea." Ans. 4.
In particular, the Examiner reasoned, the claimed processes involve
"obtaining sequence information and resolving the obtained sequence
information in order to determine potential target sequences of interest. As
such, the instant claims are drawn only to an abstract process that only
manipulates data and, therefore, are not directed to statutory subject matter."
Id.
The Examiner then addressed "[t]he second part ... of the two step
analysis [which] is to determine whether any element or combination of
elements, in the claim is sufficient to ensure that the claim as a whole
amounts to significantly more than the judicial exception." Id. at 5. As to
that analysis, the Examiner determined that "[ n Jo additional steps are recited
in the instantly claimed invention that would amount to significantly more
than the judicial exception." Id.
In that regard, the Examiner asserted that the claims "provide[] for the
additional elements of performing PCR and massive parallel sequencing of
the PCR product to obtain sequence information about the sample[;]
however these steps are well known and considered conventional steps of
obtaining sequence information about a sample." Id. at 3.
Analysis
35 U.S.C. § 101 states that "[w]hoever invents or discovers any new
and useful process, machine, manufacture, or composition of matter, or any
new and useful improvement thereof, may obtain a patent therefor, subject to
the conditions and requirements of this title."
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The Supreme Court has "long held that this provision contains an
important implicit exception: Laws of nature, natural phenomena, and
abstract ideas are not patentable." Alice Corp. Pty. Ltd. v. CLS Bank Intern.,
134 S. Ct. 2347, 2354 (2014).
Our reviewing court has summarized the Supreme Court's two-part
test for distinguishing between claims to patent-ineligible exceptions, and
claims to patent-eligible applications of those exceptions, as follows:
Step one asks whether the claim is "directed to one of
[the] patent-ineligible concepts." [Alice, 134 S. Ct. at 2354]. If
the answer is no, the inquiry is over: the claim falls within the
ambit of § 101. If the answer is yes, the inquiry moves to step
two, which asks whether, considered both individually and as
an ordered combination, "the additional elements 'transform the
nature of the claim' into a patent-eligible application." Id.
( quoting Mayo [ Collaborative Services v. Prometheus Labs,
Inc., 132 S. Ct. 1289, 1297 (2012)]).
Step two is described "as a search for an 'inventive
concept."' Id. (quoting Mayo, 132 S. Ct. at 1294). At step two,
more is required than "well-understood, routine, conventional
activity already engaged in by the scientific community," which
fails to transform the claim into "significantly more than a
patent upon the" ineligible concept itself. Mayo, 132 S. Ct. at
1298, 1294.
Rapid Litigation Mgmt. Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1047 (Fed.
Cir. 2016) (paragraphing added).
In the present case, Appellants persuade us that the preponderance of
the evidence does not support the Examiner's conclusion that the rejected
claims recite subject matter ineligible for patenting. In particular, even if we
were to agree with the Examiner that the rejected claims are directed to the
abstract idea of obtaining and manipulating nucleic acid sequence data,
Appellants persuade us (see Appeal Br. 7-8; Reply Br. 3) that the Examiner
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has not shown sufficiently that the additional features recited in the claims
constitute well-understood, routine, conventional activity already engaged in
by skilled artisans in the field in which this application is involved.
As seen above, in addition to the claimed "comparing," "identifying,"
and "determining" steps identified by the Examiner as constituting data
manipulation (Ans. 3), both independent claims on appeal recite the steps of
"using a massively parallel sequencing (MPS) instrument to read the one or
more nucleotide sequences of the amplified sample and generat[ing] one or
more text strings based on the amplified sample[, and] selecting a first
plurality of text strings from the one or more text strings read by the MPS
instrument." Appeal Br. 10, 14 (claims 1 and 12).
In setting out the rejection, however, the Examiner did not identify
any specific evidence, in the Specification or otherwise, to support the
assertion (Ans. 3) that the use of an MPS instrument in the manner required
by claims 1 and 12 was merely a well-understood conventional element
routinely employed by skilled artisans for analyzing sequence data, and
therefore added nothing to the elements of the claims alleged as being
directed to a judicial exception.
In that regard, we note the following assertion by the Examiner,
suggesting that Appellants' Specification provides such evidence:
The specification provides guidance that PCR can produce
copies that contain errors, however this is known by the skilled
artisan and it would be understood that variations in a set of
compiled sequences would have to be verified back to the
starting sample or that the few random differences obtained
from Massive Parallel Sequencing (MPS) represent these PCR
variant sequences.
Id. at 7.
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The Examiner however, does not cite to any particular portion of the
Specification, or evidence elsewhere in the record, to demonstrate that the
use of an MPS instrument in the manner required by claims 1 and 12 was
merely a well-understood conventional element routinely employed by
skilled artisans for analyzing sequence data. Indeed, Appellants'
Specification supports a contrary finding, suggesting that at the time this
application was filed, MPS analysis was not yet conventional or routine:
Forensic DNA analysis is about to cross a threshold
where DNA samples will begin to be analyzed routinely by
MPS (also sometimes referred to in the art as "next-generation"
or "current-generation" sequencing). The advent of routine
MPS for forensic DNA analysis will create large quantities of
nucleotide sequence data that may enable richer exploitation of
DNA in forensic applications.
Spec. ,r 5 ( emphasis added).
Thus, even if we were to agree with the Examiner that the rejected
claims involve an abstract idea, i.e., manipulation of nucleic acid sequence
data, we are not persuaded that the preponderance of the evidence on this
record supports a factual finding that other features of the claims, MPS in
particular, were well-understood, routine, conventional activities already
engaged in by skilled artisans in the field, given the absence of evidence
cited by the Examiner to support such a finding, and given the above-quoted
disclosures in Appellants' Specification. See Berkheimer v. HP Inc., 881
F.3d 1360, 1369 (Fed. Cir. 2018) ("Whether something is well-understood,
routine, and conventional to a skilled artisan at the time of the patent is a
factual determination.").
Accordingly, because the Examiner has not shown by a
preponderance of the evidence that the combination of features set forth in
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Appellants' claims is merely a recitation of an abstract idea alongside
nothing more than well-understood, routine, and conventional elements
already engaged in by skilled artisans in the field, we must reverse the
Examiner's rejection.
SUMMARY
For the reasons discussed, we reverse the Examiner's rejection of
claims 1-10 and 12-19, as being directed to a judicial exception (i.e., a law
of nature, a natural phenomenon, or an abstract idea) without significantly
more.
REVERSED
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