Brian A. Young et al.

Patent Trials and Appeals Board

Aug 19, 2019

13952761 - (D) (P.T.A.B. Aug. 19, 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.
13/952,761 07/29/2013 Brian A. Young 920006-225960 7502
23643 7590 08/19/2019
Barnes & Thornburg LLP (IN)
11 S. Meridian Street
Indianapolis, IN 46204
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
08/19/2019 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):
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, ANGELA T. MINARD-SMITH,
ESLEY M. HEIZER JR., DANIEL M. BORNMAN, MARK E. HESTER,
and BOYU YANG1
__________

Appeal 2018-008599
Application 13/952,761
Technology Center 1600
__________

Before ERIC B. GRIMES, JOHN G. NEW, and RYAN H. FLAX,
Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to an
allelotyping method, which have been rejected as being directed to patent-
ineligible subject matter. We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.

1 Appellants identify the Real Party in Interest as Battelle Memorial
Institute. Appeal Br. 2.
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STATEMENT OF THE CASE
Short tandem repeats, or “STR loci[,] exist in multiple states, called
alleles.” Spec. ¶ 24. Alleles differ from each other by nucleotide sequence
and sometimes by sequence length. Id. “Allelotyping is the process of
identifying the one or more alleles present at a particular STR locus in a
given sample.” Id. “The FBI and other law enforcement agencies around the
world have selected about twenty-four specific STR loci for use in forensic
DNA analysis applications.” Id. “The present disclosure relates to methods
of allelotyping loci.” Id.
Claims 1–3, 5–14, 21, and 22 are on appeal. Claim 1 is the only
independent claim and reads as follows:
1. An allelotyping method comprising:
amplifying one or more nucleotide sequences
corresponding to a particular locus using a PCR amplification
process to produce an amplified sample, wherein the amplified
sample produced comprises the one or more nucleotide
sequences that correspond to the particular locus and one or
more erroneous nucleotide sequences that do not correspond to
the particular locus, wherein the one or more erroneous
nucleotide sequences are introduced during the PCR
amplification process;
using a massively parallel sequencing (MPS) instrument
to read the one or more nucleotide sequences and the one or
more erroneous nucleotide sequences of the amplified sample
and to generate a plurality of text strings quantifying the reads
of the one of the nucleotide sequences and the one or more
erroneous nucleotide sequences of the amplified sample;
comparing the plurality of text strings to one another
using a text string matching routine to determine an abundance
count for each text string included in the plurality of text
strings;
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distinguishing each text string quantifying one of the
nucleotide sequences from each text string quantifying one of
the erroneous nucleotide sequences based upon their relative
abundance counts; and
determining one true allele for the particular locus by
identifying the text string having a highest abundance count
from among the plurality of text strings.

DISCUSSION
The Examiner has rejected claims 1–3, 5–14, 21, and 22 under
35 U.S.C. § 101 on the basis that “the claimed invention is directed to non-
statutory subject matter.” Ans. 6. “[T]he judicial exception[s] of the claim
are the steps for analyzing the sequence data to quantify and determine an
abundance count, and the final indication that the sequence with the greater
counts is determined to be the true allele.” Id.
The Examiner finds that
the two physical steps of the claims . . . amplifying a sequence
and using MPS to sequence the amplified sequence . . . are well
known and often used, and [are] considered conventional steps
for obtaining sequence data. See for example Dollive[2] . . .
who provide guidance for PCR conditions and the use of Roche
454 instrument in the identification and quantitation of
sequences from a sample.
Id.
The Examiner concludes that “the instant claims are drawn only to an
abstract process that only manipulates data and, therefore, are not directed to
statutory subject matter” and “[n]o additional steps are recited in the

2 Dollive et al., A tool kit for quantifying eukaryotic rRNA gene sequences
from human microbiome samples, 13 GENOME BIOLOGY R60 (2012).
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instantly claimed invention that would amount to significantly more than the
judicial exception.” Id. at 8–9.
Appellants argue that the “claims provide an improvement to existing
technology. Specifically, the claims are directed toward a non-abstract
process for more efficiently and accurately allelotyping DNA.” Appeal Br.
6. Appellants further argue that, “[i]n the field of sequencing and PCR, the
claimed methods provide a real solution to a real challenge (namely,
identifying errors introduced by the sequencing and amplification process).”
Id. at 7.
Appellants argue that the
steps of “amplifying . . . using a PCR amplification process”
and “using [an MPS] instrument to read” concretely and
meaningfully tie the claimed method to a particular
technological field. The claims amount to significantly more
than merely “manipulating data” because it, among other
things, includes the concrete steps of “amplifying” and “using
[an MPS] instrument to read.”
Id. at 8 (alterations in original).
Appellants also argue that “the claims are similar to the claims found
patent-eligible in Diamond v. Diehr, 450 U.S. 175, 177–78 (1981)” in that
“the steps of Appellant’s claims are not an attempt to claim the abstract idea
of ‘data manipulation.’ The steps of ‘amplifying’ and ‘using [an MPS]
instrument’ provide meaningful limits that apply any ‘data manipulation’
found in the claims to improve the existing technological process of
nucleotide sequencing using PCR.” Id. at 8–9 (alteration in original).
We agree with Appellants that the Examiner has not shown that the
claimed method is ineligible for patenting. An invention is patent-eligible if
it claims a “new and useful process, machine, manufacture, or composition
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of matter.” 35 U.S.C. § 101. However, the Supreme Court has concluded
that “[l]aws of nature, natural phenomena, and abstract ideas” are not
patentable under 35 U.S.C. § 101. See, e.g., Alice Corp. v. CLS Bank Int’l,
573 U.S. 208, 216 (2014).
To determine if a claim falls into an excluded category, we apply a
two-step framework, described in Mayo and Alice. Id. at 217–18 (citing
Mayo Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 75–77
(2012)). We first determine what the claim is “directed to.” See Alice, 573
U.S. at 219 (“On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4
in petitioners’ application explain the basic concept of hedging.”).
Patent-ineligible abstract ideas include certain methods of organizing
human activity, such as fundamental economic practices (Alice, 573 U.S. at
219–20; Bilski, 561 U.S. at 611), mathematical formulas (Parker v. Flook,
437 U.S. 584, 594–95 (1978)), and mental processes (Gottschalk v. Benson,
409 U.S. 63, 69 (1972)). In contrast, patent-eligible inventions include
physical and chemical processes, such as “molding rubber products”
(Diamond v. Diehr, 450 U.S. 175, 192 (1981)); “tanning, dyeing, making
water-proof cloth, vulcanizing India rubber, smelting ores” (id. at 182 n.7
(quoting Corning v. Burden, 56 U.S. 252, 267–68 (1854))); and
manufacturing flour (Benson, 409 U.S. at 69 (citing Cochrane v. Deener, 94
U.S. 780, 785 (1876))).
In Diehr, the claimed method employed a mathematical formula, but
the Supreme Court held that “[a] claim drawn to subject matter otherwise
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statutory does not become nonstatutory simply because it uses a
mathematical formula.” Diehr, 450 U.S. at 176; see also id. at 192 (“We
view respondents’ claims as nothing more than a process for molding rubber
products and not as an attempt to patent a mathematical formula.”). The
Supreme Court noted, however, that a claim “seeking patent protection for
that formula in the abstract . . . is not accorded the protection of our patent
laws, . . . and this principle cannot be circumvented by attempting to limit
the use of the formula to a particular technological environment.” Id. (citing
Benson and Flook); see, e.g., id. at 187 (“It is now commonplace that an
application of a law of nature or mathematical formula to a known structure
or process may well be deserving of patent protection.”).
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, and “examine the elements of the
claim to determine whether it contains an ‘inventive concept’ sufficient to
‘transform’ the claimed abstract idea into a patent-eligible application.”
Alice, 573 U.S. at 221 (quotation marks omitted). “A claim that recites an
abstract idea must include ‘additional features’ to ensure ‘that the [claim] is
more than a drafting effort designed to monopolize the [abstract idea].’” Id.
(quoting Mayo, 566 U.S. at 77 (alterations in original)). “[M]erely
requir[ing] generic computer implementation[] fail[s] to transform that
abstract idea into a patent-eligible invention.” Id.
Supplementing the above-discussed instruction of the Supreme Court,
the PTO recently published revised guidance on the application of § 101.
2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50
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(Jan. 7, 2019) (“Revised Guidance”). Under that guidance, when following
Alice’s step one, we first determine whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract
ideas (i.e., mathematical concepts; certain methods of organizing
human activity such as a fundamental economic practice; or mental
processes); and
(2) additional elements that integrate the judicial exception into a
practical application (see MPEP § 2106.05(a)–(c), (e)–(h)).
See 84 Fed. Reg. at 54–55. Only if a claim (1) recites a judicial exception and
(2) does not integrate that exception into a practical application, do we then
determine, turning to Alice’s step two, whether the claim:
(3) adds a specific limitation beyond the judicial exception that is not
a “well-understood, routine, conventional activity” in the field (see
MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of
generality, to the judicial exception.
See 84 Fed. Reg. at 56.
Revised Guidance Step 2(A), Prong 1
Following the Revised Guidance, we first consider whether the claims
recite a judicial exception. Claim 1 recites the steps of (a) “distinguishing
each text string quantifying one of the nucleotide sequences from each text
string quantifying one of the erroneous nucleotide sequences based upon
their relative abundance counts,” and (b) “determining one true allele for the
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particular locus by identifying the text string having a highest abundance
count from among the plurality of text strings.” Claim 1.
The Revised Guidance identifies “mental processes—concepts
performed in the human mind (including an observation, evaluation,
judgment, opinion)”—as abstract ideas. 84 Fed. Reg. at 52 (footnote
omitted); see also Mayo, 566 U.S. at 71 (“[M]ental processes[] and abstract
intellectual concepts are not patentable, as they are the basic tools of
scientific and technological work.”).
Here, the “distinguishing” and “determining” steps of claim 1 can be
carried out by simply observing the number of occurrences of each text
string in a set of text strings (“distinguishing each text string . . . based upon
their relative abundance counts”) and identifying the text string with the
highest number of occurrences (“determining . . . the text string having a
highest abundance count from among the plurality of text strings”). These
steps can be carried out mentally, and therefore claim 1 recites an abstract
idea.
Revised Guidance Step 2(A), Prong 2
Although claim 1 recites an abstract idea, it is still patent-eligible if
“the claim as a whole integrates the recited judicial exception into a practical
application of the exception”; i.e., whether the claim “appl[ies], rel[ies] on,
or use[s] the judicial exception in a manner that imposes a meaningful limit
on the judicial exception.” 84 Fed. Reg. at 54. This analysis includes
“[i]dentifying whether there are any additional elements recited in the claim
beyond the judicial exception(s)” and “evaluating those additional elements
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individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
Additional elements that may indicate that a judicial exception is
integrated into a practical application include: (a) an additional element that
reflects an improvement in a technology or technical field or (b) an
additional element that uses a judicial exception in conjunction with a
particular machine that is integral to the invention. Id. at 55.
We conclude that both of these additional elements are present in the
appealed claims, and their presence indicates that the recited mental steps
have been integrated into a practical application. First, the Specification
states that “[a] typical MPS process starts with a DNA sample, which is
typically amplified using PCR. . . . The parallel nature of MPS results in
numerous replicates of the nucleotide sequence of each allele.” Spec. ¶ 25.
“However, both the PCR pre-amplification process and the sequencing
process itself have non-trivial error rates. . . . These sequence errors may act
to obscure the nucleotide sequences of the ‘true’ alleles.” Id.
The Specification states that the claimed method “may be used to
determine the one or more ‘true’ alleles for each locus of a sample analyzed
by an MPS instrument.” Id. ¶ 27. That is, “while the MPS workflow results
in many unique nucleotide sequences for a particular locus, one or two of
these nucleotide sequences will be the ‘true’ alleles for that particular locus.”
Id. ¶ 35. “[I]dentifying the text string having a highest abundance count from
among the plurality of text strings,” as recited in claim 1, determines the true
allele(s) for a locus “because despite the non-trivial error rates, PCR and
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MPS workflows exhibit sufficient fidelity to generate correct sequences in
abundance.” Id.
In short, the mental steps of “distinguishing each text string . . . based
upon their relative abundance counts” and “determining . . . the text string
having a highest abundance count from among the plurality of text strings”
improve the technology or technical field of allelotyping, based on amplified
and sequenced nucleic acids, by more accurately distinguishing between a
true allele and erroneous sequences.
In addition, claim 1 requires the steps of “amplifying one or more
nucleotide sequences corresponding to a particular locus using a PCR
amplification process” and “using a massively parallel sequencing (MPS)
instrument” to read the nucleotide sequences in the amplified sample. Claim
1 therefore expressly requires using an MPS instrument.
The Revised Guidance states that “exemplary considerations are
indicative that an additional element . . . may have integrated the exception
into a practical application” include “an additional element [that]
implements a judicial exception with, or uses a judicial exception in
conjunction with, a particular machine or manufacture that is integral to the
claim.” 84 Fed. Reg. at 55.
Here, claim 1 uses the recited mental steps of “distinguishing each
text string . . . based upon their relative abundance counts” and “determining
. . . the text string having a highest abundance count from among the
plurality of text strings” in conjunction with a particular machine;
specifically, an MPS instrument. The MPS instrument is integral to the claim
because it is expressly recited as being used to read the nucleotide sequences
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generated in the preceding PCR amplification step, and that are used in the
subsequent steps of the claimed method.
The facts of this case are similar to those of SiRF Technol., Inc. v.
Int’l Trade Comm’n, 601 F.3d 1319 (Fed. Cir. 2010).3 In SiRF, the claims
were directed to a method of determining the position of a GPS receiver. Id.
at 1331–32. The court held that a GPS receiver was “integral to each of the
claims at issue.” Id. at 1332. “It is clear that the methods at issue could not
be performed without the use of a GPS receiver; indeed without a GPS
receiver it would be impossible . . . to determine the position of the GPS
receiver whose position is the precise goal of the claims.” Id.
The SiRF court also concluded that
the presence of the GPS receiver in the claims places a
meaningful limit on the scope of the claims . . . [because it]
play[s] a significant part in permitting the claimed method to be
performed, rather than function solely as an obvious mechanism
for permitting a solution to be achieved more quickly, i.e.,
through the utilization of a computer for performing
calculations. We are not dealing with a situation in which there
is a method that can be performed without a machine.
Id. at 1332–33.

3 SiRF was decided before the Supreme Court’s Mayo and Alice decisions,
and relies on the machine-or-transformation test of In re Bilski, 545 F.3d 943
(Fed. Cir. 2008). However, while that test was rejected as “the sole test for
deciding whether an invention is a patent-eligible ‘process,’” the Supreme
Court nonetheless characterized it as “a useful and important clue, an
investigative tool, for determining whether some claimed inventions are
processes under § 101.” Bilski v. Kappos, 561 U.S. 593, 604 (2010). The
machine-or-transformation test remains useful, therefore, in determining
whether a claim element integrates a judicial exception into a practical
application by using it in conjunction with a particular machine.
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The facts of this case are similar because, as discussed above, claim 1
expressly requires using an MPS instrument to read the nucleotide sequences
of a PCR-amplified sample, so that those sequences can be analyzed to
determine a true allele for a particular locus. The recited MPS instrument
therefore “play[s] a significant part in permitting the claimed method to be
performed, rather than function solely as an obvious mechanism for
permitting a solution to be achieved more quickly.” Id. at 1333.
And nucleic acids cannot be sequenced mentally or by using pen and
paper; “[w]e are not dealing with a situation in which there is a method that
can be performed without a machine.” Id. at 1333. SiRF therefore supports
our conclusion that claim 1 integrates the recited mental steps into a
practical application by using them in conjunction with an MPS instrument.
In summary, we conclude that, even though claim 1 recites an abstract
idea, as a whole it integrates that idea into a practical application. Therefore,
the claimed method, as a whole, is not “directed to . . . [a] patent-ineligible
concept.” Alice, 573 U.S. at 217. We reverse the rejection of claim 1, and
dependent claims 2, 3, 5–14, 21, and 22, under 35 U.S.C. § 101.

REVERSED