Ex Parte McMaster et al

Patent Trial and Appeal Board

Dec 7, 2016

13068727 (P.T.A.B. Dec. 7, 2016)

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.
70-002511US 6725
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
13/068,727 05/17/2011
34791 7590 12/07/2016
Quine Intellectual Property Law Group P.C.
P.O. Box 458
Alameda, CA 94501
Gary McMaster
12/07/2016 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte GARY MCMASTER, JOAN DAVIES,
YUNQING MA, and YULING LUO,1
Appeal 2014-004283
Application 13/068,727
Technology Center 1600
Before DONALD E. ADAMS, MELANIE L. MCCOLLUM, and
ROBERT A. POLLOCK, Administrative Patent Judges.
POLLOCK, Administrative Patent Judge.
DECISION ON APPEAL
Appellants appeal under 35 U.S.C. § 134(a) from the final rejection of
claims 20, 22—28, and 48. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
According to the Specification, the invention relates to “nucleic acid
extraction and quantitation from cells and tissues,” wherein “[njucleic acids
are extracted from embedded clinical samples without the use of
hydrophobic solvents.” Spec. 12.
1 Appellants identify the real party-in-interest as Affymetrix, Incorporated.
App. Br. 1.
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Application 13/068,727
In a general aspect, a method of collecting a nucleic acid
from cells associated with a hydrophobic component can
include suspending the sample, incubating the sample and
separating nucleic- acids from the sample and hydrophobic
component. The sample of cells or tissue with the
hydrophobic component melting at a temperature greater
than 40°C can be suspended in an aqueous solution. The
suspension can be incubated at a temperature higher than
40°C under conditions substantially non-denaturing to double
stranded DNA of the cells, so that the hydrophobic
component melts and the nucleic acid is released from the
cells into the aqueous solution. Finally, the aqueous solution
can be physically separated from the hydrophobic
component, after the incubation, to collect the nucleic acid
released from the cells.
Id. 114.
Claims on Appeal
As claimed, the invention relates to methods of determining a number
of test cells as compared to a reference population based on the quantitation
of ribosomal DNA (rDNA). The test cells may be tumor cells, cells on a
microscope slide, or formalin-fixed paraffin embedded (FFPE) cells.
Claims 20, 22—28, and 48 are on appeal. Claim 20, the sole
independent claim before us recites:
20. A method of determining a number of test cells, the
method comprising:
obtaining a reference nucleic acid sample from a known
number of reference cells;
quantitating an amount of a ribosomal DNA in the
reference sample;
providing a standard function for the reference cell
number versus the reference ribosomal DNA
quantity;
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Application 13/068,727
obtaining test cells selected from the group consisting of:
tumor cells, cells on a microscope slide, and FFPE
cells;
obtaining a test nucleic acid sample from the test cells;
quantitating an amount of the ribosomal DNA in the test
sample; and,
determining a test cell number based on the standard
function and the quantity of test ribosomal DNA.
Grounds of Rejection2,3
I. Claims 20, 22—28, and 48 stand rejected under 35 U.S.C. § 101
as drawn to non-statutory subject matter. Ans. 2.
II. Claims 20, 25—28, and 48 stand rejected under 35 U.S.C.
§ 102(b) as anticipated by Crocetti.2 3 4
III. Claims 20, 25—28, and 48 stand rejected under 35 U.S.C.
§ 103(a) as obvious over Crocetti.
IV. Claims 20, 22—28, and 48 stand rejected under 35 U.S.C.
§ 103(a) as obvious over Crocetti, Mann,5 and statements in the
instant Specification.
2 The Examiner has withdrawn previously entered rejections for lack of
utility, failure to comply with the written description requirement, and for
lack of enablement. Ans. 3.
3 The Examiner raised new grounds of rejection under 35 U.S.C. §§102 and
103 in the Answer. See id. at 3. As Appellants address the substance of
these rejections in the Reply, we consider them here. See Reply Br. 3, 7—10.
4 Crocetti et al., US 2003/0170654 Al, published Sept. 11, 2003.
5 Mann et al., US 6,365,364 Bl, published Apr. 2, 2002.
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Application 13/068,727
I
We have reviewed Appellants’ contentions that the Examiner erred in
rejecting claims 20, 22—28, and 48 as drawn to non-statutory subject matter
under 35 U.S.C. § 101. App. Br. 3—12; Reply 4—6. We disagree with
Appellants’ contentions and agree with the Examiner’s findings and
conclusion. See Ans. 2—15, 19-23. We provide the following comments for
clarity and emphasis.
Section 101 of the Patent Statute broadly provides that, “[wjhoever
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.” Supreme Court precedents, however, provide three specific
exceptions to the broad categories of § 101: laws of nature, natural
phenomena, and abstract ideas. Bilski v. Kappos, 561 U.S. at 625. “The
‘abstract ideas’ category embodies the longstanding rule that ‘[a]n idea of
itself is not patentable.’” Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 134 S. Ct.
2347, 2355 (2014) (citing Gottschalk v. Benson, 409 U.S. 63, 67 (1972)).
In Alice, the Supreme Court referred to the two-step analysis set forth
in Mayo Collaborative Servs. v. Prometheus Labs., Inc., 132 S. Ct. 1289
(2012), as providing “a framework for distinguishing patents that claim laws
of nature, natural phenomena, and abstract ideas from those that claim
patent-eligible applications of those concepts.” Alice, 134 S. Ct. at 2355
(citing Mayo, 132 S. Ct. at 1289). Under Mayo, “[w]e must first determine
whether the claims at issue are directed to a patent-ineligible concept.” Id.
Next, “we consider the elements of each claim both individually and ‘as an
ordered combination’ to determine whether the additional elements
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‘transform the nature of the claim’ into a patent-eligible application.” Id.
(citing Mayo, 132 S. Ct. at 1297—98).
To be patentable under Mayo, a claim must do more than simply state
the law of nature or abstract idea and add the words “‘apply it.’” Mayo, 132
S. Ct. at 1294; Benson, 409 U.S. at 67. Likewise, “[sjimply appending
conventional steps, specified at a high level of generality,” is not “ewowg/z”
for patent eligibility. Alice, 134 S. Ct. at 2357 (quoting Mayo, 132 S. Ct. at
1300).
With respect to step one of the Mayo/Alice analysis, we agree with the
Examiner that the claims on appeal are drawn to a natural phenomenon or
law of nature, in particular, that a “natural correlation exists between the
amount of rDNA and the number of cells from which rDNA has been
obtained.” See Ans. 9—10.
In accord with step 2 of the Mayo/Alice framework, we are satisfied
that the Examiner correctly considered the elements of each claim both
individually and as an ordered combination to determine whether the
additional elements transform the nature of the claim into a patent-eligible
application. See id. at 10—11. Accordingly, we agree with the Examiner that
the recited claim steps “amount to instructions that are well-understood,
routine, conventional activity, previously engaged in by those in the field[,
that] add nothing specific to the natural principle that would render it patent-
eligible.”6 Id. at 10, 22-23; see also 132 S. Ct. 1289, 1298 (“[T]he claims
inform a relevant audience about certain laws of nature; any additional steps
6 Our determination includes the mental steps of “normalizing a result” and
“determining and efficiency” limitations of dependent claims 27 and 28,
which Appellants briefly address. See App. Br. 9; Reply Br. 5—6; Ans. 8.
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consist of well-understood, routine, conventional activity already engaged in
by the scientific community; and those steps, when viewed as a whole, add
nothing significant beyond the sum of their parts taken separately.’). In sum,
the claims before us merely inform the relevant audience of certain laws of
nature: specifically, the relationship between the amount of rDNA and the
number of cells from which rDNA has been obtained. See Genetic Techs.
Ltd. v. Merial L.L.C., 818 F.3d 1369, 1379—80 (Fed. Cir. 2016), cert, denied,
(U.S. Oct. 3, 2016) (finding claims unpatentable under § 101 where, “the
novelty of looking to non-coding DNA to detect a coding region allele of
interest resides in the novelty of the newly discovered natural law of linkage
disequilibrium between coding and non-coding regions and adds little more
than a restatement of the natural law itself’).
Appellants argue that the claimed “method[s] do[] not monopolize
methods of counting cells or use of rDNA.” App. Br. 3. Appellants
similarly argue that the invention as claimed “do[es] not provide a monopoly
over a correlation between nucleic acids or rDNA and a number of cells.”
Id. at 11. We do not find these arguments persuasive. “While preemption
may signal patent ineligible subject matter, the absence of complete
preemption does not demonstrate patent eligibility. . . . Where a patent’s
claims are deemed only to disclose patent ineligible subject matter under
the Mayo framework, as they are in this case, preemption concerns are fully
addressed and made moot.” Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788
F.3d 1371, 1379 (Fed. Cir. 2015), cert, denied, No. 15-1182, 2016 WL
1117246 (U.S. June 27, 2016); see also Vehicle Intelligence & Safety LLC v.
Mercedes-Benz USA, LLC, 635 F. App’x 914, 918 (Fed. Cir. 2015), cert,
denied, No. 15-1201, 2016 WL 1171121 (U.S. May 31,2016) (“And while
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Application 13/068,727
assessing the preemptive effect of a claim helps to inform the Mayo/Alice
two-step analysis, the mere existence of a non-preempted use of an abstract
idea does not prove that a claim is drawn to patent-eligible subject matter.”).
Appellants further appear to argue that the claims satisfy the
“machine-or-transformation” test and/or comprise more than mere mental
steps because claim steps involving “obtaining” a nucleic acid sample and
“quantitating” an amount of ribosomal DNA expressly or inherently involve
physical transformation. See App. Br. 4—5; Reply Br. 4—5. We do not find
Appellant’s argument persuasive.
The Supreme Court in Bilski held that the “machine-or-transformation
test” is not determinative of unpatentability under § 101. Bilski v. Kappos,
561 U.S. at 604. Moreover, the steps Appellants rely on are no more
transformative than the claim steps of “administering a drug” or
“determining the level of 6-thioguanine” at issue in Mayo (132 S. Ct. at
1295). Nor are the steps of the instant claims any more transformative than
the claim steps “obtaining a non-cellular fraction of [a] blood sample,”
“amplifying a . . . nucleic acid” from that fraction, and “performing nucleic
acid analysis on the amplified nucleic acid,” in Ariosa. See 788 F.3d 1371 at
1373—1374. In each case, the courts determined that the claims as a whole
were unpatentable and the recited steps merely provided general instructions
to apply routine, conventional techniques, where the only new and useful
subject matter is the underlying unpatentable natural phenomenon itself. See
id. at 1377. As noted in Mayo, such “[pjurely conventional or obvious [pre]-
solution activity is normally not sufficient to transform an unpatentable law
of nature into a patent-eligible application of such a law.” 132 S. Ct. 1289 at
1298 (internal quotations and citations omitted).
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For the above reasons, we sustain the rejection.
II-IV
The Examiner rejects claims 20, 25—28, and 48 as anticipated and/or
obvious over Crocetti; and further rejects claims 20, 22—28, and 48 as
obvious over Crocetti in combination with Mann and statements in the
instant Specification regarding the scope and content of the prior art. Ans.
12—18. Appellants oppose. Reply Br. 7—10.
Findings of Fact
FF1. Crocetti teaches methods for the identifying and quantifying
polyphosphate-accumulating organisms (PAOs) in wastewater by
identifying 16S rDNA sequences unique to those organisms using
oligonucleotide probes or primers. Crocetti, Abstract, || 1, 10, 41. In
one embodiment, these 16S rDNA sequences are used to quantitate PAOs
in a sample by hybridization.
[Tjhis is done by comparing the signal obtained from the
probe-nucleic acid hybrid with a reference standard or a
number of standards. That is, a standard is constructed
comprising a known number of cells or a known amount of
PAO DNA and the signal from the standard used to give a
quantitative measure of the cells or DNA in the test sample.
Id. | 56. In one embodiment, fluorescence in situ hybridization (FISH)
using PAO-specific probes is preferred. Id. 36, 51,
FF2. Crocetti Example 1 describes the development and use of PAO-
specific FISH probes to analyze the bacteria in wastewater reactor
sludges. See id. ]Hf 64—125. The Example includes microscopic analysis,
in which bacteria were “collected, fixed and probed.” Id. 1 82. “FISH
probed samples were viewed on both a Zeiss LSM510 and on a Zeiss
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Axiophot” microscope. Id. “Generally all three designed PAO-probes,
PA0462, PA065 1 and PA0846 . . . were applied to any one individual
sample spotted on the slide.” Id. 1 85. “Counts of a, P (including pi and
P2), and y-Proteobacteria, Actinobacteria, and Cytophaga-
Flavobacterium were determined as proportions of all Bacteria
(according to probe EUB338; Bond et al., 1999a-see below for details of
probes).” Id. 1 82; see 1 85, Table 4. “The micrographs shown in FIGS
2D and 2E . . . . clearly show that the PAO probes are specific for
polyphosphate accumulating organisms.” Id. 114—115.
FF3. Mann is directed to methods of making and using angiogenesis
inhibitors. Mann, Abstract. According to Mann, suitable assays for
measuring the activity of such inhibitors “include those that are capable
of. . . quantifying the proliferation of specific cells such as endothelial
cells and tumor cells.” Id. at 12:55—65.
FF4. The instant Specification states: “Each ribosomal gene is part of a
43 kb repeat unit that can be divided into two regions: a 13.3 kb
transcribed region which contains the highly conserved genes for 18S,
5.85 and 28S rRNA subunits of the ribosome, and a 30 kb non-
transcribed spacer (NTS) (Gonzalez, F. I., Wu, S., Fi, W., Kuo, A. B. and
Sylvester, E. J. (1992) Nucleic Acids Res., 20, 5846-5847.).” Spec. 21—
22.
Analysis
The Examiner finds that Crocetti discloses “1) preparing and using
one or more standards, which can be based on a known number of cells,
2) the normalization of such results by comparing, as well as 3) knowing
how much rDNA was known standard/control cells, and then using this to
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compare with test rDNA, (determination of efficiency of test nucleic acid
extraction).” Ans. 14. With respect to claim step “obtaining test cells
selected from the group consisting of: tumor cells, cells on a microscope
slide, and FFPE cells,” the Examiner points to paragraph 82 of Crocetti as
“teaching] performing microscopy of the cells.” The Examiner construes
such cells “as being on a microscope slide . . . from which cells are used in
the analysis of rDNA.” Id. at 13—14. In the context of the § 101 discussion,
the Examiner construes the steps of “‘obtaining’ sample and reference rDNA
... as not requiring the actual isolation of any rDNA from any cell,” and
thus reading on in situ hybridization. Id. at 6—7 (referencing Spec. 1126).
Appellants contend that the Examiner fails to demonstrate that
Crocetti teaches or suggests the subsequent claim steps of “obtaining a test
nucleic acid sample from the test cells” and “quantitating an amount of the
ribosomal DNA in the test sample,” because the mere presence of cells on a
slide “does not actually or inherently disclose obtaining cells from a slide, or
quantitating nucleic acid obtained from such cells.” Reply 7; see also id. at
8 (“It is not even alleged that Crocetti obtains nucleic acids from cells on a
slide, or that Crocetti quantitates rDNA from a test sample of cells from a
microscope slide.”).
We agree with Appellants. The Specification focuses on the analysis
of nucleic acids extracted from embedded clinical samples. See Spec. 112,
14. The Examiner’s citation to an isolated passage in the Specification
suggesting that a particular DNA detection methodology is applicable to in
situ hybridization studies does not convince us that the step of “obtaining a
test nucleic acid sample from the test cells” is reasonably construed to
encompass in situ techniques. Because the Examiner does not allege that
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this element is satisfied by Mann or any admission of prior art in the
Specification, we reverse.
SUMMARY
I. We affirm the rejection of claims 20, 22—28, and 48 as drawn to non-
statutory subject matter under 35U.S.C. § 101.
II. We reverse the rejection of claims 20, 25—28, and 48 under 35 U.S.C.
§ 102(b) as anticipated by Crocetti.
III. We reverse the rejection of claims 20, 25—28, and 48 under 35 U.S.C.
§ 103(a) as obvious over Crocetti.
IV. We reverse the rejection of claims 20, 22—28, and 48 under 35 U.S.C.
§ 103(a) as obvious over Crocetti, Mann, and statements in the
Specification.
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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