Ex Parte Seul

Patent Trial and Appeal Board

Sep 13, 2017

14675981 (P.T.A.B. Sep. 13, 2017)

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
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/675,981 04/19/2015 Michael Seul BIOINV-PRFL 2734
93599 7590
Eric P. Mirabel, JD, LLM
3783 Darcus Street
Houston, TX 77005
09/15/2017 EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
09/15/2017 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):
emirabel @ come ast. net
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte MICHAEL SEUL1
Appeal 2017-007955
Application 14/675,981
Technology Center 1600
Before DEMETRA J. MILLS, ERIC B. GRIMES, 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 a method
of identifying alleles in nucleic acid samples, which have been rejected as
indefinite and directed to nonstatutory subject matter. We have jurisdiction
under 35 U.S.C. § 6(b).
We affirm the rejection for indefmiteness.
STATEMENT OF THE CASE
“[Tjhere is a need for a method of increasing the efficiency of
selecting nucleic acid samples which include rare alleles (SNPs) from a
1 Appellant identifies the Real Party in Interest as Bioinventors &
Entrepreneurs Network LLC. (Appeal Br. 3.)
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Application 14/675,981
plurality of nucleic acid samples, using pooling of the samples followed by
analysis of the pools.” (Spec. 3.)
Claims 1—20 are on appeal. Claim 1 is illustrative and reads as
follows (emphasis added):
1. A process of identifying alleles at a plurality of polymorphic sites for at
least two nucleic acid samples, wherein the alleles of interest at particular
polymorphic site are identified by a marker tag, the process comprising:
(a) for each of the alleles of interest:
(i) determining a value, d, representing a first maximum number of samples
to be combined together, by finding first that the probability of at least one
of d nucleic acid samples in any combination having at least one allele of
interest does not exceed a predetermined probability threshold, wherein said
alleles of interest are known to occur in the population at a specified
frequency;
(ii) if d of said allele of interest exceeds a preset upper limit, dmax, then
setting the value d for said allele equal to dmax,
(b) further limiting the first maximum number of samples to be combined
together by grouping the said alleles of interest by their determined values of
d, such that said alleles of interest having values of d within designated
limits are placed into the same group(s);
(c) for alleles of interest in at least one of the groups:
(i) pooling aliquots from a number dgrp of the nucleic acid samples wherein
dgrp is set equal to the smallest d value of at least one of the alleles of
interest in said group, to form a plurality of sample pools;
(ii) associating particular said alleles of interest in different sample pools
with a source tag identifying the different sample pools;
(iii) pooling aliquots from one or more of the different sample pools to form
one or more combined pools wherein the total number of samples in each
combined pool does not exceed dmaX; and
(iv) associating particular said desired alleles in combined pools each with a
marker tag identifying the different alleles present (at said specific
polymorphic sites) in the combined pools,
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(d) determining if any alleles of interest are in any combined pool by
identifying the associated marker tags in the combined pools, and further
determining:
(i) whether the marker tags at the specific polymorphic sites are identical or
different, and identifying the source tags to identify the sample pool(s)
where samples including any alleles of interest bearing one of said identified
marker tags originated; and
(ii) if said marker tags are different, and if d for an identified sample pool
exceeds 1, thereby raising ambiguity in identifying the nucleic acid
sample(s) having the identified alleles, then making at least some of the
ambiguous identifications unambiguous.
The claims stand rejected as follows:
Claims 1—20 under 35 U.S.C. § 112, second paragraph, as indefinite
(Ans. 2) and
Claims 1—20 under 35 U.S.C. § 101 as being directed to patent-
ineligible subject matter (Ans. 4).
I
The Examiner has rejected all of the claims on appeal as indefinite.
The Examiner concludes that three limitations recited in the claims make
them indefinite: (1) “a predetermined probability threshold,” (2) “a preset
upper limit, dmax,” and (3) “making . . . unambiguous.” (Ans. 2—3.)
Regarding “a predetermined probability threshold,” the Examiner
reasons that the claims do not define the term and “the specification does not
provide a standard for ascertaining the requisite degree.” {Id. at 2.) The
Examiner also reasons that “since the value must be a predetermined
probability threshold there is an implication that the outcome of the process
is already known to establish this value.” {Id.) The Examiner concludes that
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Application 14/675,981
the scope of the claims is unclear because there is no specific guidance on
how the threshold is predetermined and it “may appear to be dependent on
the starting material being analyzed.” {Id. at 3.)
Appellant argues that “predetermined probability threshold” simply
means “a predetermined discretionary threshold, and its specific value need
not be stated in the claim, as the method works with any value between 0
and 1, but not equal to either 0 or 1, and the choice of a specific value, in
that range, is discretionary.” (Appeal Br. 13.) Appellant also argues that,
according to the Specification’s description of the invention, “it is not the
outcome which is used in setting the probability threshold, but rather the
frequency of one or more alleles in the population, where those allele
frequencies are known.” {Id. at 14.)
We agree with Appellant that the claim term “predetermined
probability threshold” is not indefinite, and simply refers to a certain
probability, chosen before reaching step (a)(i) of the claimed process
(“predetermined”). “[BJreadth is not to be equated with indefmiteness.” In
re Miller, 441 F.2d 689, 693 (CCPA 1971).
We do not agree with the Examiner’s reasoning that the claim
language implies that the value depends on knowing the outcome of the
claimed process. Claim 1 states that the value d is determined “by finding
first that the probability of at least one of d nucleic acid samples in any
combination having at least one allele of interest does not exceed a
predetermined probability threshold.” (Claim 1.) Because the
predetermined probability threshold determines a probability of a nucleic
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acid sample having an allele of interest, it does not require that the outcome
be known in advance.
Regarding “a preset upper limit, dmax,” the Examiner reasons that this
term “is not defined by the claim [and] the specification does not provide a
standard for ascertaining the requisite degree.” (Ans. 2—3.) The Examiner
concludes that the scope of the claims is unclear because there is no specific
guidance on how the upper limit is preset and it “may appear to be
dependent on the starting material being analyzed.” {Id. at 3.)
Appellant argues that the Specification describes dmax as being
“predetermined based on the ability to detect and discriminate alleles, in a
pool or pool of pools, when at a high dilution, where dilution increases with
the number of the samples in a pool and number of first reaction products in
a pooled pool.” (Appeal Br. 14.) Appellant argues that “[b]ecause the
setting is discretionary (as is true for ‘predetermined probability threshold’),
one skilled in the art does not need any more specific guidance to set it —
they use their discretion.” {Id.)
We will affirm this basis of the rejection. The Specification states that
“dmax is based on, among other things, the ability of the technology to be
able to discriminate alleles at high dilution.” (Spec. 4, emphasis added.)
Appellant points to no further guidance in the Specification regarding the
“other things” that dmax is based on. Although Appellant cites passages on
pages 25 and 46 of the Specification (Appeal Br. 14), those passages relate
to a “maximum pool size” rather than dmax.
Appellant has pointed to nothing in the Specification to indicate that
dmax is the same as a maximum pool size, and the Specification itself
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suggests that they are different. As noted above, the Specification states that
dmax is based in part on the ability of the technology to be able to
discriminate alleles at high dilution. By contrast, the Specification states
that “[t]he ‘maximum pool size’ may be determined by limitations arising
from the steps of the method.” (Spec. 25.)
Both of the independent claims (claims 1 and 18) recite “a preset
upper limit, dmax.” Because the Specification states that dmax is based on the
ability of the technology to be able to discriminate alleles at high dilution, as
well as other things that are not specified, we agree with the Examiner that
the meaning of dmax is indefinite, and therefore the scope of the claimed
method is unclear.
Regarding “making at least some of the ambiguous identifications
unambiguous,” the Examiner reasons that “making” is “unclear and
incomplete, because how this step is performed to make an ‘ambiguous
identification unambiguous’ is not defined by the claim nor clearly set forth
in the specification.” (Ans. 3.) “Review of the specification and examples
does not provide a standard for ascertaining the requisite degree or specific
steps that make something ambiguous or unambiguous.” {Id.) The
Examiner concludes that the phrase makes the scope of the claims unclear.
{Id.)
Appellant argues that the Specification defines “disambiguating” and
explains how to determine the likelihood of an ambiguity, and therefore “the
disambiguation method (in claim 1, referred to as ‘making at least some of
the ambiguous identifications unambiguous’), by repeating the method with
a lower d, as well as how to determine the value of ‘d,’ is very clearly
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Application 14/675,981
defined as an algorithm, readily understood by anyone skilled in the art.”
(Appeal Br. 15—16.)
We agree with Appellant that the Examiner has not shown that the
disputed phrase makes the scope of the claim unclear to those skilled in the
art. The last step of claim 1 states that, “if [the] marker tags are different,
and if d for an identified sample pool exceeds 1, thereby raising ambiguity
in identifying the nucleic acid sample(s) having the identified alleles, then
making at least some of the ambiguous identifications unambiguous”
(emphasis added). Thus, the claim language itself makes clear that an
“ambiguous identification” means that the results do not identify the specific
sample(s) having the identified alleles. Thus, “making at least some of the
ambiguous identifications unambiguous” means taking steps to identify the
nucleic acid sample(s) that have the identified alleles. While the claim does
not require specific steps to make ambiguous identifications unambiguous,
the claim language does make clear what functional result must be achieved
to fall within the scope of the claimed method. That makes the claim broad,
but not indefinite. See In re Miller, 441 F.2d at 693.
We affirm the rejection based on the indefmiteness of the “preset
upper limit, dmax” recited in claim 1. Claim 18, the only other independent
claim, also recites “a preset upper limit, dmax” and is therefore indefinite for
the same reason discussed above with respect to claim 1. Claims 2—17, 19,
and 20 depend from either claim 1 or claim 18 and are therefore indefinite
for the same reason as well.
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II
The Examiner has rejected all of the claims on appeal as being
directed to patent-ineligible subject matter. The Examiner reasons that
“[f]or claim 1, there are no necessary physical steps that need to be
performed with respect to obtaining the data for the alleles.” (Ans. 4.) The
Examiner concludes that “the claims as stated are drawn to simply
representing a genetic sequence of an allele with a tag and comparing the
presence of the allele/tag in a mixed sample relative to a frequency of the
allele expected in a population. As such, the instant claims are drawn only
to an abstract process that only manipulates data and, therefore, abstract
idea.” (Id. at 5.) That is, “the claims are directed to only the manipulation
of data.” (Id.)
The Examiner finds that “[n]o additional steps are recited in the
instantly claimed invention that would amount to significantly more than the
judicial exception. . . . [which] is the information of any given sequence.”
(Id. at 6.) Specifically, “[u]sing florescent labeled primers to identify a
sequence was known and conventional,” and “[tjagging a sequence and
providing it in a mixed sample for comparison/analysis . . . sets forth
considerations in evaluating data, but requires clear knowledge of the
starting materials and the alleles.” (Id.)
Appellant argues that “[t]he Examiner has ignored the bulk of the
steps in independent claims 1 and 18 which set forth the steps required to
‘obtain data for the alleles.’” (Appeal Br. 16.) Appellant argues that claim
18 similarly requires “performing a physical test.” (Id. at 17.) Appellant
argues that “[b]ecause the claimed method involves physical steps, e.g.,
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‘pooling’; determining, . . . and ‘associating’ alleles with tags . . . , it is not
merely an ‘abstract idea.’” {Id.) Appellant argues that “[o]verall, the
methods of the claims clearly are an improvement to a technology, as the
claims are to ‘identifying alleles at a plurality of polymorphic sites for at
least two nucleic acid samples,’ thereby permitting the determination of an
entire set of specific alleles for a multiplicity of samples.” {Id. at 18.)
We reverse this rejection because the Examiner has not shown that the
claimed process does not amount to significantly more than an abstract idea.
The Examiner, in fact, when responding to Appellant’s arguments,
“acknowledged that the claims [d]o recite and require physical steps for
obtaining the sequence data.” (Ans. 12.) The Examiner then cited Buell2
“in support of the assertion that pooling samples [and] assessing sequences
in a pooled sample for quick and more efficient screening were known in the
art and considered conventional.” {Id.) The Examiner also stated that
“Hamady et al. . . . provides techniques and evidence that multiple
sequences can be sequenced and characterized for a gene of interest, and
provide evidence that this could be applied to mixed samples.” {Id. at 13.3)
2 The Examiner did not provide a citation for Buell, but noted that it had
earlier been relied on as evidence supporting a prior art rejection. (Ans. 12.)
As we understand it, “Buell” refers to Barbara Buell, Stanford Business,
http://www.gsb.stanford.edu/statistical-solution-testing (1997), which was
made of record by the Examiner Jan. 22, 2016.
3 The Examiner also did not provide a citation for Hamady, but stated that
“Hamady et al. is of record.” (Ans. 13.) As we understand it, “Hamady et
al.” refers to Hamady et al., Error-correcting barcoded primers for
pyrosequencing hundreds of samples in multiplex, 5 Nature Methods 235—
237 (2008), which was made of record by the Examiner Jan. 22, 2016.
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However, the rejection does not rely on either Buell or Hamady as
evidence to show that the physical steps that are required in the claimed
method are no more than “well-understood, routine, conventional activity
previously engaged in by researchers in the field,” Mayo Collaborative
Services v. Prometheus Labs., Inc., 566 U.S. 66, 73 (2012). Rather, the
rejection is based on interpreting the claims as not requiring any physical
steps, an interpretation the Examiner has acknowledged is not accurate.
While the Examiner cited evidence in responding to Appellant’s argument
on this point, that evidence is not part of the basis for rejection and we
decline to rely on it as such. See In re Hoch, 428 F.2d 1341, 1342 n.3
(CCPA 1970) (“Where a reference is relied on to support a rejection,. . .
there would appear to be no excuse for not positively including the reference
in the statement of rejection.”). We therefore reverse the rejection under 35
U.S.C. § 101.
SUMMARY
We affirm the rejection under 35 U.S.C. § 112, second paragraph.
We reverse the rejection under 35 U.S.C. § 101.
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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