Brian A. Young et al.

Patent Trials and Appeals Board

Aug 19, 2019

13834830 - (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.
13/834,830 03/15/2013 Brian A. Young 920006-224297 1750
23643 7590 08/19/2019
Barnes & Thornburg LLP (IN)
11 S. Meridian Street
Indianapolis, IN 46204
EXAMINER
ZEMAN, MARY K
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,
and ESLEY M. HEIZER JR.1
__________

Appeal 2017-010083
Application 13/834,830
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 relating to
analysis of nucleotide sequence data, which have been rejected as being
directed to patent-ineligible subject matter and provisionally rejected for
obviousness-type double patenting. We have jurisdiction under 35 U.S.C.
§ 6(b). We affirm.

1 Appellants identify the Real Party in Interest as Battelle Memorial
Institute. Appeal Br. 2.
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STATEMENT OF THE CASE
“Polymorphic tandem repeats of nucleotide sequences . . . can be used
in human or other organism identification.” Spec. ¶ 2. “Tandem repeats can
be used directly in human identity testing, such as in forensics analysis.” Id.
“Forensic DNA analysis is about to cross a threshold where DNA
samples will begin to be analyzed routinely by massively parallel
sequencing (MPS).” Id. ¶ 4. However, the data files created by MPS are too
big to be easily transmitted or stored, or to be “human-readable in any
practical sense.” Id. ¶ 5. “Thus, other human readable forms of the raw data
from MPS workflows are needed.” Id.
The Specification discloses “a new computer file format useful for
storing, exchanging, and/or preserving evidence regarding nucleotide
sequence data, including short tandem repeat (STR) profiling data,
particularly when the data originates from a massively parallel sequencing
(MPS) instrument or workflow.” Id. ¶ 32. The disclosed file format is
referred to as the “FASTF” file format. Id.
The Specification also describes a method of “creating FASTF files
containing summary nucleotide sequence data,” and states that the “FASTF
summary-format file” is “immensely more compact” than the FASTF raw-
format file. Id. ¶ 40. “[T]he F_CS algorithm 404 generates the FASTF
summary-format file 402 from the FASTF raw-format file 102.” Id. ¶ 42; see
also ¶¶ 42–45 (describing in more detail the operation of the F_CS
algorithm, which corresponds to the steps of claim 1, below).
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Claims 1–20 and 43–70 are on appeal. Claim 1 is illustrative and
reads as follows:
1. A method comprising:
receiving a first text-based computer file including one or
more records, each of the one or more records comprising
nucleotide sequence data generated by a read of a massively
parallel sequencing (MPS) instrument;
determining, for each of the one or more records of the
first text-based file, whether a portion of the nucleotide
sequence data of the record represents a short tandem repeat
(STR) associated with a locus;
placing each portion of the nucleotide sequence data
determined to represent an STR associated with a locus into one
of a number of locus-specific lists;
determining, for each of the locus-specific lists, a number
of occurrences within the locus-specific list of identical
nucleotide sequence data representing a unique STR; and
generating a second text-based computer file including
one or more records, each of the one or more records
corresponding to a unique STR for which the number of
occurrences of identical nucleotide sequence data representing
the unique STR exceeded an abundance threshold.
Claim 45, the only other independent claim, is directed to computer-
readable storage media comprising instructions that cause a processor to
carry out the steps of claim 1.
The claims stand rejected as follows:
Claims 1–20 and 43–70 under 35 U.S.C. § 101 as being directed to
subject matter ineligible for patenting (Ans. 2);
Claims 1–20 and 43–70, provisionally, for obviousness-type double
patenting based on claims 1–20 of application 13/952,761 (Ans. 8); and
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Claims 1–20 and 43–70, provisionally, for obviousness-type double
patenting based on claims 1–20 of application 14/489,198 (Ans. 9).
I
The Examiner has rejected all of the claims on appeal on the basis that
“the claimed invention is directed to a judicial exception (i.e., a law of
nature, a natural phenomenon, or an abstract idea) without significantly
more.” Ans. 2. The Examiner finds that, in the claimed process, genetic
information is received and then steps of mathematical operations and data
generation are carried out. Id. at 2–3. The Examiner concludes that the steps
of claims 1 and 45 are “mathematical concepts involving the manipulation of
data.” Id. at 3.
The Examiner also finds that the “claims are directed to [a] process
that can be performed mentally using a pen and paper.” Id. at 12. The
Examiner notes that “the Federal Circuit has . . . ‘treated analyzing
information by steps people go through in their minds, or by mathematical
algorithms, without more, as essentially mental processes within the
abstract-idea category.’” Id. (quoting Elec. Power Grp., LLC v. Alstom S.A.,
830 F.3d 1350, 1354 (Fed. Cir. 2016)). The Examiner finds that the steps of
claim 1 amount to collecting information, analyzing information by
mathematical algorithms, and presenting results. Id. The Examiner
concludes that “the claims are still considered to be drawn to an abstract
idea.” Id.
The Examiner also finds that the claims do not amount to significantly
more than the judicial exception because they merely recite “the additional
element of nonspecific computer systems. . . . The computer systems utilized
by the method claims are not a specific or particular machine executing
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specific algorithms, but are generic computer systems executing generically
described actions.” Id. at 5–6. The Examiner finds that “[t]he recitation of
the MPS is merely denoting a source of the received data, and is not an
active limitation of the claim itself. . . . This element fails to rise to the level
of significantly more than the judicial exception.” Id. at 6–7.
The Examiner concludes that “the limitations of the claims,
individually, and in ordered combination, do not rise to the level of
significantly more than the judicial exception(s) identified above, and the
claims are not patent eligible subject matter.” Id. at 8.
Appellants argue that the claims are drawn to a specific process and
“stand no risk of preempting the broad fields” cited by the Examiner. Appeal
Br. 6–8. Appellants also argue that the “claims are not directed to a judicial
exception because they provide an improvement of an existing technology.”
Id. at 8. Specifically, “[u]sing MPS to sequence DNA produces a huge
amount of data” and the claimed method “pars[es] through these massive
amounts of data and simplif[ies] this data into a format that both adequately
summarizes all of the information contained in the data and is reasonably
accessible to a human being.” Id. at 8–9.
Finally, Appellants argue that the claimed subject matter “is not
similar to the subject matter previously found by courts to be abstract ideas;
namely, claims like those in Bilski and Alice that merely implemented long-
standing business methods on a computer.” Id. at 10. Rather, Appellants
argue, “[t]he claims recite solutions that are rooted in sequencing technology
in order to solve a problem specifically arising out that technology.” Id.
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
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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, 67 (1972)). In contrast, patent-eligible inventions include
physical and chemical processes, such as “molding rubber products”
(Diamond v. Diehr, 450 U.S. 175, 191 (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
statutory does not become nonstatutory simply because it uses a
mathematical formula.” Diehr, 450 U.S. at 176; see also id. at 191 (“We
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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
(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
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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) “determining, for
each of the one or more records of the first text-based file, whether a portion
of the nucleotide sequence data of the record represents a short tandem
repeat (STR) associated with a locus,” (b) “placing each portion of the
nucleotide sequence data determined to represent an STR associated with a
locus into one of a number of locus-specific lists,” and (c) “determining, for
each of the locus-specific lists, a number of occurrences within the locus-
specific list of identical nucleotide sequence data representing a unique
STR.” Claim 1.
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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 steps of (a) “determining” whether portions of nucleotide
sequence data represent STRs associated with a locus, (b) “placing” portions
of nucleotide sequence data into lists, and (c) “determining” a number of
occurrences of identical nucleotide sequence data representing STRs within
a list, can be carried out by simply observing the occurrence of particular
sub-sequences (portions) of nucleotide sequence data, noting those
occurrences in a set of lists, and counting the number of occurrences noted
within each list. These steps can be carried out mentally, and therefore claim
1 recites an abstract idea.
Revised Guidance Step 2(A), Prong 2
A claim that recites an abstract idea might still be patent-eligible if
“the claim as a whole integrates the recited judicial exception into a practical
application of the exception”; i.e., if 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
individually and in combination to determine whether they integrate the
exception into a practical application.” Id. at 54–55.
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In addition to the data-analysis steps that can be carried out mentally
or with pen and paper, discussed above, claim 1 recites an initial step of
receiving a file that includes “records comprising nucleotide sequence data
generated by a read of a massively parallel sequencing (MPS) instrument”
and a final step of generating a file that includes records, each of which
corresponds to an “STR for which the number of occurrences of identical
nucleotide sequence data representing the unique STR exceeded an
abundance threshold.” Claim 1.
The Revised Guidance provides exemplary considerations that might
indicate that a judicial exception has been integrated into a practical
exception. 84 Fed. Reg. at 55. As relevant here, those considerations include
“[a]n additional element [that] reflects an improvement in the functioning of
a computer, or an improvement to other technology or technical field” and
“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.” Id.2
Appellants argue that the claims “provide an improvement of an
existing technology.” Appeal Br. 8. Specifically, Appellants argue that
sequencing DNA using MPS produces a huge amount of data, and the
claimed method allows “parsing through these massive amounts of data and
simplifying this data” into a summarized format. Id. at 8–9. Appellants also

2 The considerations also include an additional element that “applies or uses
a judicial exception to effect a particular treatment or prophylaxis for a
disease or medical condition” or that “effects a transformation or reduction
of a particular article to a different state or thing.” Id. Those considerations
are not relevant to the claims on appeal.
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argue that the “claims are clearly limited by the MPS instrument, which is
recited in each and every claim,” and which “is a particular piece of
scientific equipment specifically designed for the sequencing of nucleotides
(e.g., DNA) present in a sample.” Reply Br. 8.
We conclude that the claims neither effect an improvement to a
technical field nor require the use of a particular machine that is integral to
the claims. Specifically, the claimed method does not improve the field of
DNA sequencing because it makes no change, let alone improvement, in the
method by which nucleotide sequence data are generated. Nor does it require
carrying out DNA sequencing using an MPS instrument. The first step of the
claimed method simply requires receiving a computer file that includes
certain data. The fact that those data are nucleotide sequence data that were
generated using a massively parallel sequencing (MPS) instrument changes
nothing about the DNA sequencing process itself.
And the claimed process does not require actively using an MPS
instrument. We agree with the Examiner that the recitation of “nucleotide
sequence data generated by a read of a massively parallel sequencing (MPS)
instrument” (claim 1) “merely denot[es] a source of the received data.” Ans.
6. At best, this limitation requires receiving a certain type of data for use in
the claimed method, but “collecting information, including when limited to
particular content (which does not change its character as information), [is]
within the realm of abstract ideas.” Elec. Power Grp., 830 F.3d at 1353
(emphasis added).
Finally, the Revised Guidance indicates that a judicial exception
might have been integrated into a practical exception if “an additional
element applies or uses the judicial exception in some other meaningful way
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beyond generally linking the use of the judicial exception to a particular
technological environment, such that the claim as a whole is more than a
drafting effort designed to monopolize the exception.” 84 Fed. Reg. at 55.
In addition to the mental steps, claim 1 recites the “receiving” step
discussed above, which merely recites a type and source of data for use in
the claimed method.
The claimed method also includes a step of “generating a second text-
based computer file including one or more records, each of the one or more
records corresponding to a unique STR for which the number of occurrences
of identical nucleotide sequence data representing the unique STR exceeded
an abundance threshold.” Claim 1. This step simply requires comparing two
numbers (“the number of occurrences of identical nucleotide sequence data
representing [a] unique STR” and “an abundance threshold”) and presenting
the results of the comparison (including a record for an STR when its
number of occurrences exceeds the abundance threshold). The comparison
aspect of this step, however, is simply another part of the claimed process
that can be carried out mentally, and is therefore an aspect of the recited
abstract idea. And the recitation of “generating a second text-based computer
file including one or more records” is simply presenting the results of the
data analysis performed in the other steps of the method. Electric Power
Group is on point here: “[M]erely 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.” 830 F.3d at 1354.
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Revised Guidance Step 2(B)
Finally, the Revised Guidance directs us to consider whether claim 1
includes “additional elements . . . [that] provide[] ‘significantly more’ than
the recited judicial exception.” 84 Fed. Reg. at 56. The Revised Guidance
states that an additional element that “simply appends well-understood,
routine, conventional activities previously known to the industry, specified
at a high level of generality, to the judicial exception, . . . is indicative that
an inventive concept may not be present.” Id.
Here, as discussed above, the only steps recited in claim 1, other than
those that can be carried out mentally or with pen and paper, are (a)
“receiving a first text-based computer file” that includes records comprising
nucleotide sequence data generated using an MPS instrument and (b)
“generating a second text-based computer file” that includes records
corresponding to STRs that occurred in an abundance above a threshold.
These limitations recite conventional computer functions—receiving
and generating text-based computer files—at a high level of generality. They
do not, for example, require any unconventional method of acquiring
nucleotide sequence data. The first step of claim 1 only requires that the data
in the received computer file was generated using massively parallel
sequencing; it does not require carrying out the MPS process in any
particular way.
Claim 1 also does not require using any unconventional method to
generate the second text-based computer file. The Specification states that
[a]fter the number of occurrences of each unique STR
within each locus-specific list is determined, the F_CS
algorithm 404 will select which nucleotide sequence data to
write to the summary file 402. This determination is made
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based on some abundance threshold. . . . For each unique STR
that is to be included in the summary file 402, the F_CS
algorithm 404 will create one record in the summary file 402.
Spec. ¶ 45. Thus, neither the claim language nor the Specification requires
using anything more than a conventional computer function to generate the
second text-based computer file.
Even considered as an ordered combination, therefore, claim 1 as a
whole requires receiving a text-based computer file, searching the records in
that file for certain data and noting the search result in a list, then counting
the number of items in the list, comparing that number to a threshold, and
outputting the result as a second text-based computer file. Claim 1 does not
recite any unconventional method for carrying out these functions, and
therefore is not “directed to improvements in the way computers and
networks carry out their basic functions.” SAP Am., Inc. v. InvestPic, LLC,
898 F.3d 1161, 1168 (Fed. Cir. 2018). “[T]he focus of the claims is not any
improved computer or network, but the improved mathematical analysis” of
nucleotide sequence data. Id.
We therefore conclude that claim 1 “simply appends well-understood,
routine, conventional activities previously known to the industry, specified
at a high level of generality, to the judicial exception.” Revised Guidance, 84
Fed. Reg. at 56. Claim 1 does not recite additional elements that provide
significantly more than the judicial exception, and thus the claim as a whole
is patent-ineligible.
Appellants’ Arguments
Appellants argue that the “claims stand no risk of preempting the
broad fields of ‘analyzing genetic data’ and ‘us[ing] “forensic metadata”. . .
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to identify a unique individual’ because the claims are actually directed to a
much more specific process.” Appeal Br. 6. See also id. at 8:
Appellant respectfully submits that the claims in the present
application would not preempt the entire field of “analyzing
genetic data,” nor would they preempt the field of
“determin[ing] a unique sequence element,” nor would they
preempt any general mathematical algorithm or even
“generating a second text-based computer file.”
This argument is unpersuasive. “While preemption may signal patent
ineligible subject matter, the absence of complete preemption does not
demonstrate patent eligibility.” Ariosa Diagnostics, Inc. v. Sequenom, Inc.,
788 F3d 1371, 1379 (Fed. Cir. 2015). Where “claims are deemed only to
disclose patent ineligible subject matter under the Mayo framework, . . .
preemption concerns are fully addressed and made moot.” Id. Here, for the
reasons discussed above, we conclude that the claims on appeal are directed
to patent-ineligible subject matter under the Mayo framework. Preemption
concerns are fully addressed by that conclusion.
Appellants also argue that “claims are not directed to a judicial
exception because they provide an improvement of an existing technology.”
Appeal Br. 8. Specifically, “DNA sequencing is a tangible (i.e., non-
abstract) process that presents tangible challenges. Using MPS to sequence
DNA produces a huge amount of data.” Id. Appellants argue that the “claims
address the technical challenge of organizing and simplifying massive
amounts of genetic data generated by MPS into a form that is accessible by a
human being. The claims recite solutions that are rooted in sequencing
technology in order to solve a problem specifically arising out that
technology.” Id. at 10.
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Similarly, Appellants argue that “[b]oth individually and as an ordered
combination, the steps of Appellant’s claims are novel and unconventional.”
Appeal Br. 7. Appellants argue that, “[i]n particular,” the steps of
determining a number of occurrences of sequence data representing a unique
STR and generating a second text-based computer file based on comparing
the number of occurrences to an abundance threshold “are neither taught nor
suggested by the prior art.” Id.
Appellants argue that “the claims describe a novel and nonobvious
method for organizing and simplifying massive amounts of genetic data
generated by MPS into a form that is accessible by a human being with only
a reasonable amount of analysis.” Id. at 8. Appellants argue that, compared
to a raw-format file, “the ‘second text-based computer file’ recited in claim 1
is [a] significantly more compact file . . . (e.g., on the order of kilobytes, not
gigabytes). This reduction in file size makes the second computer file both
portable and human accessible.” Id. at 9.
These arguments are also unpersuasive. Neither the claim language
nor the Specification requires any unconventional way of carrying out the
computer functions recited in the claim: receiving a file comprising data,
searching the data, compiling a list, counting the items in the list, comparing
the count to a threshold, and generating a second file comprising other data.
As Appellants themselves characterize it, the claimed method is one
that simplifies a large set of data into a smaller, more accessible form. The
claimed method might result in an improved, more useful set of data but the
improvement is in the form of the data set, not in any function of the
computer carrying out the method or in the apparatus generating the
nucleotide sequence data.
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An improved mental process of analyzing data is still a mental
process, and therefore an abstract idea without significantly more. See SAP
Am., 898 F.3d at 1168 (“[T]he focus of the claims is not a physical-realm
improvement but an improvement in wholly abstract ideas —the selection
and mathematical analysis of information, followed by reporting or display
of the results.”). See also Elec. Power Grp., 830 F.3d at 1353 (“Merely
requiring the selection and manipulation of information—to provide a
‘humanly comprehensible’ amount of information useful for users, . . . by
itself does not transform the otherwise-abstract processes of information
collection and analysis.”).
We therefore conclude that the method of claim 1 is not eligible for
patenting, and we affirm the rejection of claim 1 under 35 U.S.C. § 101.
Claims 2–13, 43, and 45–57 fall with claim 1 because they were not argued
separately. 37 C.F.R. § 41.37(c)(1)(iv).
Appellants argue that “claims 14–20, 44, and 58–64 include additional
limitations that further specify technical improvements to an existing
technology that constitute significantly more than an abstract idea or natural
phenomenon.” Appeal Br. 11. Specifically, Appellants argue that “these
claims require the ‘second text-based computer file’ to include human
readable aspects not present in the first file.” Id. Appellants also argue that
claims 66, 67, 69, and 70 “recite the[] differences in file size between the
first and second text-based computer files” that result from the claimed
process of “parsing through the massive amounts of data generated by MPS
and simplifying that data.” Id. at 13.
These arguments are not persuasive. Because claims were argued as a
group, we select claims 14 and 66 as representative. Claim 14 reads:
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The method of [claim 1, wherein generating the second text-
based computer file comprises, for each of the one or more
records, writing nucleotide sequence data representing the
corresponding unique STR to a second text line of the record],
wherein generating the second text-based computer file further
comprises, for each of the one or more records, writing a
human-readable sequence-based allele (HRSBA) designation
that is deterministic of the corresponding unique STR to a third
text line of the record.
Appeal Br. 31 (Claims Appendix). Claim 66 reads: “The method of claim 1,
wherein the file size of the second text-based computer file is at least two-
thousand times smaller than the file size of the first text-based computer
file.” Id. at 40.
Claim 14 recites including additional data—nucleotide sequence data
representing the corresponding unique STR and a human-readable sequence-
based allele (HRSBA) designation—in the second text-based computer file
of claim 1. The additional data recited in claim 14, however, are still part of
the abstract idea to which claim 1 is directed. See Ans. 15 (“[T]hese
limitations are a part of the abstract idea itself.”). Claim 14 does not add any
limitations that amount to an improvement in a technical field or otherwise
add significantly more to the abstract idea of claim 1.
Similarly, claim 66 adds a limitation regarding the form (file size) of
the second text-based computer file resulting from the claimed method. That
file size, however, simply reflects the amount of data (relative to the original
data) that are recorded in the file; i.e., the amount of summarized data
resulting from the claimed method. However, requiring a particular relative
size for the second text-based file does not improve a computer function or a
technical field, or otherwise add significantly more to the abstract idea of
claim 1.
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We therefore affirm the rejection of claims 14 and 66 under 35 U.S.C.
§ 101. Claims 15–20, 44, 58–64, 67, 69, and 70 fall with claims 14 and 66.
37 C.F.R. § 41.37(c)(1)(iv).
Finally, Appellants argue that
claim 65, which recites that the method also comprises
“generating, by the massively parallel sequencing instrument,
the first text-based computer file” (which, per claim 1,
comprises nucleotide sequence data generated by a read of the
MPS instrument) . . . amount[s] to “significantly more” through
the recitation of a tangible, concrete MPS instrument (which is
not “generic computer structure”). . . . The MPS instrument
clearly ties the claims to specific machine and a specific
application. Such a limitation removes any possible preemption
concerns presented by Appellant’s claims.
Appeal Br. 12–13.
This argument is unpersuasive. Claim 65 reads: “The method of claim
1, further comprising generating, by the massively parallel sequencing
instrument, the first text-based computer file including one or more records,
each of the one or more records comprising nucleotide sequence data.”
Appeal Br. 40 (Claims Appendix) (emphasis added).
Thus, claim 65 requires only that the first text-based computer file,
comprising nucleotide sequence data, is generated by a massively parallel
sequencing instrument. Generating a text-based computer file is not a
function that is peculiar to an MPS instrument, but rather is a generic
computer function. The recited MPS instrument is therefore not integral to
the process of claim 65. Cf. Revised Guidance, 84 Fed. Reg. at 55 (“an
additional element implements a judicial exception with, or uses a judicial
exception in conjunction with, a particular machine or manufacture that is
integral to the claim” (emphasis added)).
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We therefore affirm the rejection of claim 65 under 35 U.S.C. § 101.
Claim 68 falls with claim 65. 37 C.F.R. § 41.37(c)(1)(iv).
II
The Examiner has provisionally rejected claims 1–20 and 43–70 for
obviousness-type double patenting based either on claims 1–20 of
application 13/952,761 or on claims 1–20 of application 14/489,198.
Appellants argue that
[t]he Manual of Patent Examining Procedure states that, “[i]f a
‘provisional’ nonstatutory double patenting rejection is the only
rejection remaining in an application having the earliest
effective U.S. filing date . . . compared to the reference
application(s), the examiner should withdraw the rejection in
the application having the earliest effective U.S. filing date and
permit that application to issue as a patent.” MPEP
804(I)(B)(1). The present application has the earliest effective
filing date (March 15, 2013) as compared to the two referenced
applications (both having an effective filing date of July 29,
2013).
Appeal Br. 26. Appellants argue that, therefore, we should order Examiner
to withdraw the provisional double patenting rejections. Id. at 27.
However, for the reasons discussed above, we affirm the rejection of
the claims under 35 U.S.C. § 101 as being directed to patent-ineligible
subject matter. Therefore, the provisional rejections are not the only
rejections remaining in the instant application.
Appellants have waived arguments based on the merits of the
provisional obviousness-type double patenting rejections. We therefore
affirm them. See 37 C.F.R. § 41.37(c)(1)(iv) (The Appeal Brief must contain
“[t]he arguments of appellant with respect to each ground of rejection.”);
Hyatt v. Dudas, 551 F.3d 1307, 1314 (Fed. Cir. 2008) (“In the event of such
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a waiver, the PTO may affirm the rejection of the group of claims that the
examiner rejected on that ground without considering the merits of those
rejections.”).
SUMMARY
We affirm all of the rejections on appeal.
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