Ex Parte McLaughlin et al

Patent Trial and Appeal Board

Dec 21, 2018

12985237 (P.T.A.B. Dec. 21, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/985,237 01/05/2011
83092 7590 12/26/2018
Rigel Pharmaceuticals, Inc.
Bozicevic, Field & Francis LLP
201 REDWOOD SHORES PARKWAY
SUITE 200
REDWOOD CITY, CA 94065
FIRST NAMED INVENTOR
John McLaughlin
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www .uspto.gov
ATTORNEY DOCKET NO. CONFIRMATION NO.
RIGL-067 3909
EXAMINER
MORAN, MARJORIE A
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
12/26/2018 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
docket@bozpat.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JOHN McLAUGHLIN, ZACHARY PINCUS, and
JIM BERNSTEIN1
Appeal2017-001478
Application 12/985,237
Technology Center 1600
Before ERIC B. GRIMES, JOHN G. NEW, and RICHARD J. SMITH,
Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims relating to a
screening method, which have been rejected as directed to ineligible subject
matter, anticipated, and obvious. We have jurisdiction under 35 U.S.C.
§ 6(b ).
We reverse.
1 Appellants identify the Real Party in Interest as Rigel Pharmaceuticals, Inc.
Appeal Br. 3.
Appeal2017-001478
Application 12/985,237
STATEMENT OF THE CASE
Claims 1, 2, and 4--21 are on appeal. Claims 1 and 16 are illustrative
and read as follows:
1. A screening method comprising:
a) contacting a population of test cells with a test compound to
provide contacted test cells;
b) obtaining values for a plurality of cytological attributes of said
contacted test cells;
c) determining whether the phenotype of the test cells matches the
phenotype of cells that have been treated with a compound having known
mode of action, wherein the determining is done by:
(i) obtaining a set of classifiers for a plurality of compounds of
known mode of action, wherein the classifiers are defined using values
for said cytological attributes obtained from cells that have been
contacted with compounds of known mode of action; and
(ii) calculating a likelihood score indicating the likelihood that
the values obtained for the contacted cells match a classifier of the set
of classifiers,
wherein an increased likelihood score increases the confidence that the
phenotype of the test cells matches the phenotype of cells that have been
treated with a compound having known mode of action, and
d) identifying the test compound as having a desired mode of action,
wherein said test compound has a profile of likelihood scores that is similar
to that of a compound of known mode of action.
16. A method for providing a phenotypic classifier, comprising:
a) contacting a first population of cells with a first compound having a
first known mode of action to provide a first population of contacted cells;
and
b) contacting a second population of cells with a second compound
having a second known mode of action to provide a second population of
contacted cells;
c) obtaining values for a plurality of cytological attributes of:
i. said first population of contacted cells,
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Application 12/985,237
ii. said second population of contacted cells, and
iii. an untreated population of cells, and
d) identifying ranges of values for each of said cytological attributes
that, together, distinguish said first population of contacted cells from said
second population of contacted cells and said untreated population of cells.
The claims stand rejected as follows:
Claims 1, 2, and 4--21 under 35 U.S.C. § 101 as directed to patent-
ineligible subject matter (Ans. 4);
Claims 16, 17, and 19--21 under 35 U.S.C. § I02(b) as anticipated by
Adams 2 (Ans. 7);
Claims 1, 2, and 4--11 under 35 U.S.C. § I03(a) as obvious based on
Adams, Callahan, 3 Gama, 4 and Jones5 (Ans. 11 ); and
Claim 18 under 35 U.S.C. § I03(a) as obvious based on Adams.
I
The Examiner has rejected claims 1, 2, and 4--21 as directed to patent-
ineligible subject matter. The Examiner finds that
elements of claim 1 are directed to a JE Uudicial exception], for
example, the abstract ideas of "obtaining values ... ,"
"determining whether the phenotype ... matches ... ,"
"obtaining a set of classifiers ... ," "calculating a likelihood
score ... " and "identifying ... , " which are claimed as a
combination of mathematical steps operating entirely on data
2 Adams, 2007/0082327 Al, published Apr. 12, 2007.
3 Callahan, US 2009/0285469 Al, published Nov. 19, 2009.
4 Gama, Combining Classifiers by Constructive Induction, 1398 Machine
Leaming 178-189 (1998).
5 Jones, Predicting Gene Function from Images of Cells, Dissertation,
MASSACHUSETTS INSTITUTE OF TECHNOLOGY, 1-118 (2007).
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Application 12/985,237
( e.g. mathematical operations and logical comparisons). Each of
these elements represents an abstract idea.
Ans. 4 ( emphasis omitted).
The Examiner finds that "the additional elements in claim 1, other
than the JE, amount to no more than: conventional experimental and data
gathering steps routinely practiced in the art." Id.
Appellants argue that the "claims are directed to methods that
endeavor to solve problems during drug discovery. In particular, the present
claims help determine how drug candidates act in a biological system. The
ability to determine how drug candidates act is paramount to high-
throughput identification of candidates which may further be developed into
therapeutics." Appeal Br. 7. Specifically, Appellants argue that the claimed
methods "represent functional and palpable applications in the field of high-
throughput drug discovery with specific improvements to technologies in the
same." Id. at 8.
We agree with Appellants that the Examiner has not shown that the
claims are directed to patent-ineligible subject matter. "[T]he examiner bears
the initial burden, on review of the prior art or on any other ground, of
presenting aprimafacie case ofunpatentability. In re Oetiker, 977 F.2d
1443, 1445 (Fed. Cir. 1992).
Here, the Examiner has pointed to "elements of claim 1 [that] are
directed to a[n] .... abstract idea[]." Ans. 4. However, the analysis under
§ 101 begins with the issue of "whether the claims at issue are directed to
one of those patent-ineligible concepts." Alice Corp. Pty. Ltd. v. CLS Bank
Int'!, 134 S. Ct. 2347, 2355 (2014) (emphasis added). The fact that the
claims include elements that, by themselves, would not be eligible for
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Application 12/985,237
patenting does not make the claims as a whole patent-ineligible. See id. at
2358 ("[W]e held that a computer-implemented process for curing rubber
was patent eligible .... The claim employed a 'well-known' mathematical
equation, but it used that equation in a process designed to solve a
technological problem in 'conventional industry practice."' ( citing Diamond
v. Diehr, 450 U.S. 175 (1981)).
For example, claim 1 requires: (1) contacting a first and second
population of cells with, respectively, a first and second compound; (2)
obtaining values for a plurality of cytological attributes of the contacted test
cells; (3) determining whether the phenotype of the test cells matches the
phenotype of cells that have been treated with a compound having a known
mode of action; and (4) evaluating the degree of confidence that the
phenotype of the test cells matches the phenotype of cells that have been
treated with a compound having known mode of action. Steps 1-3 require
the performance of physical tests to determine the responses of two groups
of test cells to determine whether the test compounds emulate the known
mode of action of other, known, test compounds. Although step ( 4) may
involve a mental process of evaluation (i.e., an abstract idea), we are not
persuaded that the Examiner's conclusory finding that all of the remaining
steps are directed to no more than "abstract ideas" are persuasive, because
the Examiner's findings have not persuaded us that these are steps that, as
abstract ideas, could be performed mentally, or that they do not add
significantly more to the claim than the mere abstract idea itself. See
Gottschalkv. Benson, 409 U.S. 63, 67 (1972) (holding that: "Phenomena of
nature, though just discovered, mental processes, and abstract intellectual
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Application 12/985,237
concepts are not patentable, as they are the basic tools of scientific and
technological work"); but see also Mayo Collaborative Servs. v. Prometheus
Labs, Inc., 566 U.S. 66 (2012) (recognizing that: "For all inventions at some
level embody, use, reflect, rest upon, or apply laws of nature, natural
phenomena, or abstract ideas").
We therefore conclude that the Examiner has not made a prima facie
case that the claims as a whole are directed to patent-ineligible subject
matter, and we reverse the rejection based on 35 U.S.C. § 101.
II
The Examiner has rejected claims 16, 1 7, and 19--21 as anticipated by
Adams. The Examiner finds that Adams discloses all of the limitations of
claim 16, including contacting cells with "compounds having known modes
of action." Ans. 7.
Appellants argue that "[a]s defined in the instant specification, page 5
lines 21-22, the term 'mode of action' refers to 'a specific biochemical
interaction through which a bioactive agent produces a pharmacological
effect.[']". Appeal Br. 12. Appellants argue that
Adams teaches the use of, e.g. "mp2 stimulus compounds" or
"rice compounds" which are compounds that induce the mp2 or
rice phenotype in contacted cells, respectively .... Adams is
only interested in identifying a particular class of novel
compounds that induce the mp2 phenotype (Adams, i138).
Hence, Adams' mp2 and rice compounds are of unknown mode
of action and are defined purely in terms of the mp2 and rice
phenotypes they induce.
Id. at 13.
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Application 12/985,237
We agree with Appellants that the Examiner has not shown that
Adams discloses all of the limitations of claim 16 under the broadest
reasonable interpretation of the claim language. Adams discloses its
"invention relates to specific phenotypes and the cells that exhibit these
phenotypes." Adams ,r 6. "The phenotype is referred to as the mp2
phenotype." Id. ,r 7. "Typically, the mp2 phenotype will be produced by
applying a stimulus to the cell or cell population that does not initially
exhibit the mp2 phenotype." Id. ,r 9.
Adams discloses experiments in which "cell populations [were]
treated with two different mp2 stimulus compounds at various
concentrations, as well as on DMSO-treated ( control) cells, cells treated with
0.5 µM Taxol, and cells treated with compounds that produce a rice
phenotype. (Rice compounds are another class of mitotic inhibitors.[)]" Id.
,r 71. Adams does not, however, identify the mp2 stimulus compounds that
were used, nor does it identify the biochemical interaction through which it
produces its effect. Thus, reading claim 16 in light of the express definition
of "mode of action" in the Specification, we conclude that Adams does not
disclose contacting cells with "compounds having known modes of action."
We therefore reverse the rejection under 35 U.S.C. § 102(b).
III
The Examiner has rejected claims 1, 2, and 4--11 as obvious based on
Adams, Callahan, Gama, and Jones. The Examiner has rejected claim 18 as
obvious based on Adams. Each of these rejections relies on the Examiner's
finding that Adams discloses compounds having a "known mode of action"
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Application 12/985,237
(Ans. 14), which, for the reasons discussed above, we disagree with. We
therefore reverse the rejections under 35 U.S.C. § 103(a).
SUMMARY
We reverse all of the rejections on appeal.
REVERSED
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