Ex Parte Potts et al

Board of Patent Appeals and Interferences

Jul 17, 2012

11690745 (B.P.A.I. Jul. 17, 2012)

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.
11/690,745 03/23/2007 Steven J. Potts 054769-2802 4373
7590 07/18/2012
Richard J. Warburg
FOLEY & LARDNER LLP
P.O. Box 80278
San Diego, CA 92138-0278
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
MAIL DATE DELIVERY MODE
07/18/2012 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte STEVEN J. POTTS, BERYL CROSSLEY, RONG X. CHEN,
KEVIN Z. QU, and RICHARD A. BENDER
__________

Appeal 2011-004700
Application 11/690,745
Technology Center 1600
__________

Before JAMES T. MOORE, Vice Chief Administrative Patent Judge, and
TONI R. SCHEINER, DONALD E. ADAMS, SALLY G. LANE, and
ERIC GRIMES, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 54-82 (App. Br. 4;
Reply Br. 4). We have jurisdiction under 35 U.S.C. § 6(b).
STATEMENT OF THE CASE
The claims are directed to a method for evaluating the likelihood of a
clinical response for an individual to a treatment for a disease or condition
(claims 54-60); a method for constructing a self-organizing map (SOM)
useful for evaluating the likelihood of a positive clinical response for an
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individual to a treatment for a disease or condition (claims 61-64); and a
method for selecting an individual in need of treatment for a treatment, or
for a clinical trial evaluating a treatment, for a disease or condition (claims
65-82). Claim 54 is representative and is reproduced below:
54. A method for evaluating the likelihood of a clinical response for
an individual to a treatment for a disease or condition, said method
comprising:
a) providing a primary self organizing map (SOM) constructed using a
plurality of data sets of measurements obtained from a plurality of
individuals, said plurality of individuals each having undergone a treatment
for a disease or condition, said individuals each having a clinical response to
said treatment;
b) preparing a secondary SOM using a distinct labeling set, said
distinct labeling set encompassing one or more of said clinical responses of
said plurality of individuals to said treatment, said secondary SOM including
a sample data set obtained from a sample of an individual in need of
evaluation; and
c) visually displaying a result from said secondary SOM that reveals
the extent of similarity between the data sets of measurements of the distinct
labeling set and said sample data set of said individual in need of evaluation;
whereby a medical practitioner can use said result to evaluate the
likelihood of a clinical response for said individual in need of evaluation to
said treatment.

Claims 54-82 stand rejected under 35 U.S.C. § 102(b) as being
anticipated by Golub.
1

Claims 54-82 stand rejected under 35 U.S.C. § 101 as directed to
nonstatutory subject matter.
We reverse the rejection under 35 U.S.C. § 102(b). We affirm the
rejection under 35 U.S.C. § 101. However, because our reasoning differs

1
Golub et al., US 6,647,341 B1, issued November 11, 2003.
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from Examiner‟s, we designate our affirmance a new ground of rejection
under 37 C.F.R. § 41.50(b).

Anticipation:
ISSUE
Does the preponderance of evidence on this record support
Examiner‟s finding that Golub teaches Appellants‟ claimed invention?
FACTUAL FINDINGS
FF 1. The term “„self-organizing map,‟ „SOM,‟ and terms of like import
refer to a clustering technique, and the representation of the result thereof,
which technique groups data such that similar data are generally clustered
closer than are dissimilar data” (Spec. 3, ¶ 0008).
FF 2. Golub‟s method involves (1) the assignment of samples to defined
classes (class prediction) and (2) defining one or more previously
unrecognized biological classes (class discovery) (Golub, col. 9, ll. 24-31;
see also Ans. 10 (“Examiner agrees that Golub teaches two distinct
procedures: class discovery and class prediction”)).
FF 3. While Golub teaches the use of SOMs in the context of class
discovery, Golub does not teach the use of SOMs for class prediction (see
e.g., id. at col. 28, ll. 62-64; see Ans. 10-11 (Examiner “agrees that Golub
teaches SOMs for the purpose of class discovery”); Cf. id. at col. 21, l. 1 –
col. 28, l. 35).
FF 4. Examiner finds that Golub “teaches that class prediction is
subsequent to class discovery” (Ans. 11).
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ANALYSIS
Appellants‟ claimed invention requires, inter alia, the preparation and
comparison of a first and second SOM to evaluate the likelihood that an
individual in need of treatment will exhibit a clinical response to a treatment
(see, e.g., Claim 54). As Appellants explain, “the claimed invention
encompasses class prediction, rather than class discovery, as defined by
Golub” (App. Br. 14 (emphasis added)).
Examiner agrees “that Golub teaches SOMs for the purpose of class
discovery” (FF 3). Examiner fails to identify an evidentiary basis to support
a finding that Golub teaches the use of SOMs for class prediction. We are
not persuaded by Examiner‟s intimation that since a class must first be
discovered before one can predict whether an individual may be a member
of a specific class, Golub teaches Appellants‟ claimed method because
“class prediction is subsequent to class discovery” (FF 4). Simply stated,
Examiner failed to establish an evidentiary basis to support a finding that
Golub teaches the use of SOMs for characterizing an unknown sample with
regard to the likelihood of a clinical response to treatment (e.g. class
prediction).
CONCLUSION OF LAW
The preponderance of evidence on this record fails to support
Examiner‟s finding that Golub teaches Appellants‟ claimed invention. The
rejection of claims 54-82 under 35 U.S.C. § 102(b) as anticipated by Golub
is reversed.

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Nonstatutory subject matter:
ISSUE
Does the preponderance of evidence on this record support
Examiner‟s conclusion that Appellants‟ claimed invention is directed to
nonstatutory subject matter?
FACTUAL FINDINGS
FF 5. “The use of biochemical assay data . . . is rapidly expanding the
diagnosis and treatment of disease. . . . Thus, techniques have been
developed to present complex data to individuals for evaluation” (Spec. 1:
¶ [0004]).
FF 6. Prior to the date of Appellants‟ claimed invention, it was recognized
in this art that various algorithms could be used to manipulate data sets to
predict whether a particular individual would respond to a particular
treatment regimen (i.e. class prediction) (see Golub, col. 21, l. 1 – col. 28, l.
35; see also Reply Br. 8 (“To the extent that Golub et al. classifies
individuals („class prediction‟), Golub et al. uses a weighted voting scheme,
not SOMs”)).
ANALYSIS
“Phenomena of nature . . ., mental processes, and abstract intellectual
concepts are not patentable.” Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 132 S.Ct. 1289, 1293 (2012). To transform such a
nonpatentable phenomenon, process, or concept into a patent-eligible
application, one must do more than simply state the phenomenon, process,
or concept “while adding the words „apply it.‟” Id. at 1294.
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On this record, Appellants‟ claimed invention involves (1) applying
an algorithm to data relating to the results of patient treatment; (2) visually
displaying the result; and (3) determining, based on the result, whether a
patient in need of treatment will likely respond to treatment (see e.g., Claim
54; see also App. Br. 10). Unlike the claims at issue in Diehr, Appellants‟
claims do not involve the transformation of an article into a different state or
thing. See Diamond v. Diehr, 450 U.S. 175, 184 (1981).
Instead, Appellants‟ claims purport to apply natural laws describing
the relationship between patient-specific data and prior clinical response to
medical treatment to predict the likelihood that another patient will benefit
from a medical treatment. Cf. Mayo, 132 S.Ct. at 1294; see also id. at 1302
(“The laws of nature at issue . . . tell a treating doctor to measure metabolite
levels and to consider the resulting measurements in light of the statistical
relationships they describe”); In re Meyer, 688 F.2d 789, 794 (CCPA 1982)
(“The process recited is an attempt to patent a mathematical algorithm rather
than a process for producing a product as in [Diehr]”); CyberSource Corp. v.
Retail Decisions, Inc., 654 F.3d 1366, 1375 (Fed. Cir. 2011) (“[t]he mere
manipulation or reorganization of data . . . does not satisfy the
transformation prong”). Stated differently, Appellants‟ claims are “more
akin to a manual reorganization of treatment options. This does not satisfy
the transformation prong of the MOT [(machine or transformation)] test.”
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SmartGene, Inc. v. Advanced Biological Laboratories, SA, --- F.Supp.2d ----,
2012 WL 1059611, at *17 (D.D.C., March 30, 2012).
2

Here, as in Mayo, the instructions set forth in Appellants‟ claims “add
nothing specific to the laws of nature other than what is well-understood,
routine, conventional activity, previously engaged in by those in the field.”
Mayo, 132 S.Ct. at 1299. At the time of Appellants‟ claimed invention, the
manipulation of data sets to allow medical practitioners to predict whether
an individual will respond to a particular treatment was known in the art, as

2
The claim, found to be an abstract idea, at issue in SmartGene was directed
to:

1. A method for guiding the selection of a therapeutic treatment
regimen for a patient with a known disease or medical condition,
said method comprising:
(a) providing patient information to a computing device
comprising:
a first knowledge base comprising a plurality of different
therapeutic treatment regimens for said disease or medical
condition;
a second knowledge base comprising a plurality of expert rules
for evaluating and selecting a therapeutic treatment regimen for
said disease or medical condition;
a third knowledge base comprising advisory information useful
for the treatment of a patient with different constituents of said
different therapeutic treatment regimens; and
(b) generating in said computing device a ranked listing of
available therapeutic treatment regimens for said patient; and
(c) generating in said computing device advisory information for
one or more therapeutic treatment regimens in said ranked
listing based on said patient information and said expert rules.

SmartGene, 2012 WL 1059611, at *2.
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was manipulation of data using SOMs (see, e.g. FF 2-6). The difference, as
Appellants point out, is that while the prior art recognized that patient data
can be manipulated using an SOM (App. Br. 13), the prior art methods
utilize a different algorithm to manipulate the data in a manner that would
allow a medical practitioner to predict whether an individual will respond to
treatment (FF 6). Cf. Parker v. Flook, 437 U.S. 584, 585 (1978) (“[t]he only
novel feature of the method is a mathematical formula”).
Thus, the notion that patient data relating to a clinical response to
treatment can be manipulated to allow a medical practitioner to predict
whether another patient, i.e., one in need of treatment, will respond to a
particular treatment was “„well known,‟ to the point where, putting the
formula to the side, there was no „inventive concept‟ in the claimed
application of the formula.” Mayo, 132 S.Ct. at 1299, citing Parker v.
Flook, 95 U.S. 594. Accordingly, we are not persuaded by Appellants‟
contention that “[t]he claimed methods rely on mathematical manipulations
and presentations of data but do not seek to patent the mathematical
formulae underlying those manipulations and presentations” (Reply Br. 6).
A “basic mathematical equation, like a law of nature, . . . [is] not
patentable.” Mayo, 132 S.Ct. at 1299. The “prohibition against patenting
abstract ideas „cannot be circumvented by attempting to limit the use of the
formula to a particular technological environment.‟” Id. at 1297, citing
Bilski v. Kappos, 130 S.Ct. 3218, 3230 (2010); see also Parker v. Flook, 95
U.S. at 595 n. 18 (“a claim for an improved method of calculation, even
when tied to a specific end use, is unpatentable subject matter under § 101”).
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We are also not persuaded by Appellants‟ reliance on In re Abele, 684
F.2d 902 (CCPA 1982) (see App. Br. 10). Here, as in SmartGene,
Appellants‟
[R]eliance on Abele is misplaced. In Abele, the patent
application sought to patent a process for improving the
accuracy and reliability of CAT scan imaging techniques, while
simultaneously reducing the X-ray exposure of the patient. . . .
This process of improving imaging is very different than the
data manipulation at issue here. Unlike in Abele, the patents
here do not manifest any sort of physical transformation, and
therefore do not satisfy the transformation prong of the MOT.

SmartGene, 2012 WL 1059611, at *18.
In sum, we find that Appellants‟ claims are directed to nonstatutory
subject matter. For the foregoing reasons, we are not persuaded by
Appellants‟ contentions to the contrary, which rely on “the patent-eligibility
requirements articulated in Bilski I, Bilski II, and Abele” (App. Br. 9-13; see
also Reply Br. 4-6).
CONCLUSION OF LAW
The preponderance of evidence on this record supports a conclusion
that Appellants‟ claims are directed to nonstatutory subject matter. The
rejection of claims 54-82 under 35 U.S.C. § 101 is affirmed. However,
because our reasoning differs from that of the Examiner, we designate our
affirmance a new ground of rejection under 37 C.F.R. § 41.50(b).
TIME PERIOD FOR RESPONSE
This decision contains a new ground of rejection pursuant to 37 CFR
§ 41.50(b) (effective September 13, 2004, 69 Fed. Reg. 49960 (August 12,
2004), 1286 Off. Gaz. Pat. Office 21 (September 7, 2004)). 37 CFR §
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41.50(b) provides “[a] new ground of rejection pursuant to this paragraph
shall not be considered final for judicial review.
37 CFR § 41.50(b) also provides that the appellant, WITHIN TWO
MONTHS FROM THE DATE OF THE DECISION, must exercise one of
the following two options with respect to the new ground of rejection to
avoid termination of the appeal as to the rejected claims:
(1) Reopen prosecution. Submit an appropriate amendment of
the claims so rejected or new evidence relating to the claims so
rejected, or both, and have the matter reconsidered by the examiner, in
which event the proceeding will be remanded to the examiner . . . .

(2) Request rehearing. Request that the proceeding be reheard
under § 41.52 by the Board upon the same record . . . .

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, 37 C.F.R. § 41.50(b)

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