Ex Parte Jung et al

Patent Trial and Appeal Board

Aug 2, 2016

12283158 (P.T.A.B. Aug. 2, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
12/283, 158 09/09/2008 Edward K.Y. Jung
83722 7590 08/04/2016
Dorsey & Whitney I INVENTION SCIENCE FUND
Intellectual Property Department - SLC
136 S. Main Street
Keams Building, Suite 1000
Salt Lake City, UT 84101-1685
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.
17906.21.4 6206
EXAMINER
BORIN, MICHAEL L
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
08/04/2016 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):
ip.docket.slc@dorsey.com
simon.marcus@dorsey.com
ip.patent.sl@dorsey.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Exparte EDWARD K.Y. JUNG and LOWELL L. WOOD, JR.
Appeal2013-005666
Application 12/283,15 8
Technology Center 1600
Before JEFFREY N. FRED MAN, ULRIKE W. JENKS, and
CHRISTOPHER G. PAULRAJ, Administrative Patent Judges.
P AULRAJ, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal 1 under 35 U.S.C. § 134 involving claims to a
computer-implemented method of identifying and treating pathogen
variants. The Examiner rejected the claims for indefiniteness, non-statutory
subject matter, obviousness, and obviousness-type double patenting. We
have jurisdiction under 35 U.S.C. § 6(b ). We affirm and enter a new ground
of rejection under 35 U.S.C. § 101.
1 Appellants identify the Real Party in Interest as Searate, LLC, an affiliate
of Intellectual Ventures Management, LLC (see Appeal Br. 2).
Appeal2013-005666
Application 12/283,158
STATEMENT OF THE CASE
Background
The Specification relates generally to "[ m ]ethods and systems [that]
involve identifying primary pathogens as well as variants of the pathogens
and treatments." See Spec. 2 (Summary).
The Claims
Claims 1, 2, 11-21, and 78-80 are under appeal, and are reproduced
in the Claims Appendix of the Appeal Brief. Independent claim 1 is
representative and reads as follows:
A computer-implemented-method comprising:
a computing device identifying a primary pathogen;
the computing device estimating a probability of an
existence of the primary pathogen in a given individual;
identifying a primary treatment targeting the primary
pathogen;
the computing device predicting a first pathogenic variant
of the primary pathogen;
identifying a set of first variant treatments targeting the
first pathogenic variant;
the computing device predicting a second pathogenic
variant of the primary pathogen; and
identifying a set of second variant treatments targeting
the second pathogenic variant.
Appeal Br. 74 (Claims App'x).
The Rejections
The Examiner has rejected the claims as follows:
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Application 12/283,158
I. Claims 1, 2, 11-21, and 78-80 under 35 U.S.C. § 112 i-f 2 for
indefiniteness;
II. Claims 1, 2, 11-21, and 78-80 under 35 U.S.C. § 101 as being
directed to non-statutory subject matter;
III. Claims 1, 2, 11-21, and 78-80 under 35 U.S.C. § 103 as being
unpatentable over Smith2 together with Burdette3 and Chee, 4
Armour, 5 or Holland-Staley. 6
IV. Claims 1, 2, 11-21, and 78-80 under 35 U.S.C. § 103 as being
unpatentable over Modrow 7 and Barin, 8 together with Burdette
and Chee, Armour, or Holland-Staley.
V. Claims 1, 2, 11-21, and 78-80 under 35 U.S.C. § 103 as being
unpatentable over Prior, 9 Smith, and Modrow, together with
Burdette and Chee, Armour, or Holland-Staley. 10
VI. Claims 1, 2, 11-21, and 7 8-80 for non-statutory obviousness-
type double patenting as being unpatentable over Application
No. 11/525,760.
VII. Claims 1, 2, 11-21, and 7 8-80 for non-statutory obviousness-
type double patenting as being unpatentable over Application
No. 12/283, 128.
VIII. Claims 1, 2, 11-21, and 78-80 for non-statutory obviousness-
type double patenting as being unpatentable over Application
No. 12/283, 184.
May 8, 2012 Non-Final Action ("Non-Final Act."), 3-32.
INDEFINITENESS REJECTIONS
1. Mixing Method and Apparatus Limitations (Claims 1, 2, 11-21,
and 78---80)
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Application 12/283,158
The Examiner asserts that independent claim 1 recites a "method
comprising ... a computing device," and therefore "it is unclear which of
the four categories of subject matter a claim is directed to -- process,
machine, manufacture, or composition of matter." Non-Final Act. 3--4. The
Examiner relies upon MPEP § 2173.05(p)(II), which states that "[a] single
claim which claims both an apparatus and the method steps of using the
apparatus is indefinite under 35 U.S.C. 112, second paragraph."
We are not persuaded that the claims are indefinite on this basis. The
cases cited in MPEP § 2173 .05(p )(II) address the situation where an
apparatus claim recited method steps to be performed by a user, and not
2 Smith et al., Mapping the Antigenic and Genetic Evolution of the Influenza
Virus, 305 Science 371-76 (2004) ("Smith").
3 Burdette et al., Killing Bugs at the Bedside: A prospective hospital survey
of how frequently personal digital assistants provide expert
recommendations in the treatment of infectious diseases, 3 Annals of Clin.
Microbiology and Antimicrobials 1---6 (2004) ("Burdette").
4 Chee et al., US Patent 5,861,242, issued Jan. 19, 1999 ("Chee").
5 Armour et al., US Patent 6,586,430 Bl, issued July 1, 2003 ("Armour").
6 Holland-Staley, Pub. No. US 2007/0172926 Al, published July 26, 2007
("Holland-Staley").
7 Modrow et al., Computer-Assisted Analysis of Envelope Protein Sequences
of Seven Human Immunodeficiency Virus Isolates: Prediction of Antigenic
Epitopes in Conserved and Variable Regions, 61 J. Virology 570-78 (1987)
("Modrow").
8 Barin et al., Virus Envelope Protein of HTL V-III Represents Major Target
Antigen for Antibodies in AIDS Patients, 228 Science 1094--96 (1985).
9 Prior et al., Publication US 2005/0055188 Al, published Mar. 10, 1985.
10 Although the Examiner's statement of the rejection refers to "Aguiar," the
Examiner does not address any teachings of a reference by the name of
Aguiar, but rather relies upon the teachings of Chee, Armour and Holland-
Staley. Non-Final Act., 20. Therefore, like Appellants, we consider "the
rejection as noted and commented by the Examiner in view of Chee,
Armour, or Holland-Staley, rather than in view of Aguiar, assuming a
typographical error." Appeal Br. 48.
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Application 12/283,158
merely the capability of the apparatus. See In re Katz Interactive Call
Processing Patent Litigation, 639 F.3d 1303, 1318 (Fed. Cir. 2011)
(emphasis added) (claim directed to "[a] system with an 'interface means for
providing automated voice messages ... to certain of said individual callers,
wherein said certain of said individual callers digitally enter data'" was
determined to be indefinite because the italicized claim limitation is not
directed to the system, but rather to actions of the individual callers, which
creates confusion as to when direct infringement occurs); IPXL Holdings v.
Amazon.com, Inc., 430 F.3d 1377, 1384 (Fed. Cir. 2005) (system claim that
recited "an input means" and required a user to use the input means was
found to be indefinite because it was unclear "whether infringement ...
occurs when one creates a system that allows the user [to use the input
means], or whether infringement occurs when the user actually uses the
input means.").
Unlike the situation in Katz and IPXL, the claims here are directed to a
method involving the use of an apparatus (i.e., a computing device). The
Federal Circuit has held that such claims are not indefinite for combining
different classes of statutory subject matter. See Microprocessor
Enhancement Corp. v. Texas Instruments Inc., 520 F.3d 1367, 1374--75
(Fed. Cir. 2008) (claim directed to "method of executing instructions in a
pipelined processor comprising: [structural limitations of the pipelined
processor]" not found indefinite because "[ m ]ethod claim preambles often
recite the physical structures of a system in which the claimed method is
practiced.").
Accordingly, we do not sustain the indefiniteness rejection for mixing
method and apparatus limitations.
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2. "Probability of Association" (Claims 79 and 80)
The Examiner further asserts that the phrase "probability of
association between ... variant of the pathogen in the given individual" in
claim 79 is not clear because it does not state what the association is
"'between"' or to what the probability of association is being compared.
Non-Final Act. 4. Likewise, the Examiner asserts that the phrase
"estimating ... until there is less than a 5% probability of association" in
claim 80 is not clear as to "how the probability for a single individual can
change just because an estimate is being calculated." Id.
Appellants argue that "dependent claims 79 and 80 are definite on
their face" because "[t]he claims provide what is performing the act- the
computing device- as well as that the act is 'estimating a probability of
association"' and "[t]he claims further specify that the 'estimating' is carried
out 'until there is less than a 5 percent probability of association between the
at least one variant of the pathogen and the given individual."' Appeal Br.
14--15.
We agree with the Examiner that claims 79 and 80 are indefinite as to
the "probability of association" limitations. Appellants' response to the
Examiner's rejection merely repeats the claim language and similar language
in the Specification without explaining the methodology by which a
"probability of association" is calculated. Without any such explanation
identified in the claims or the Specification, a skilled artisan would not be
reasonably apprised of how to estimate the probability and/or determine
whether the less than 5% probability of association requirement is satisfied.
We therefore affirm the§ 112 indefiniteness rejection as to claims 79
and 80. See In re Packard, 751F.3d1307, 1311 (Fed. Cir. 2014) (A§ 112
indefiniteness rejection is proper "when the USPTO has initially issued a
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well-grounded rejection that identifies ways in which language in a claim is
ambiguous, vague, incoherent, opaque, or otherwise unclear in describing
and defining the claimed invention").
NON-STATUTORY SUBJECT MATTER REJECTION
The Examiner rejected claims 1, 2, 11-21, and 78-80 under 35 U.S.C.
§ 101 as being drawn to non-statutory subject matter because claims are
directed to a "method comprising ... a computing device." The Examiner's
rationale for this rejection is similar to the Examiner's rationale for the
indefiniteness rejection based on mixing method and apparatus limitations.
Non-Final Act. 5.
For the reasons stated above, we find that the claims are drawn to a
statutory class of subject matter (i.e., a process). For the reasons set forth in
the new ground of rejection under 35 U.S.C. § 101 below, however, we
determine that the claims are nonetheless patent-ineligible because they are
directed to an abstract idea.
OBVIOUSNESS REJECTIONS
The Examiner has set forth three separate obviousness rejections, each
of which rely upon Burdette, Chee, Armour, or Holland-Staley, together
with Smith, Modrow, Barin, and/or Prior. Non-Final Act. 8-29. For the
reasons set forth below, we affirm the obviousness rejection as to claims 1,
2, 11-21, and 78 based on the teachings ofModrow, Barin, and Chee. We
do not rely upon the other references as the basis for our affirmance. See In
re Kronig, 539 F.2d 1300, 1303 (CCPA 1976) (Board may rely upon less
than all the references cited by Examiner in affirming a rejection without
designating a new ground). We reverse the obviousness rejections as to
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claims 79 and 80, which we find indefinite as to the "probability of
association" limitations for the reasons stated above.
The Examiner finds that "Modrow teaches prediction of amino acid
sequences of the envelope proteins of seven different HIV strains." Non-
Final Act. 16. The Examiner further finds that Barin "teaches that viral
envelope proteins (gp160 and gp120) are the most consistently recognized
by antibodies found in patients with acquired immune deficiency syndrome
(AIDS)." Id. at 17. The Examiner asserts that:
Id.
It would have been prima facie obvious to one skilled in
the art to be motivated to identify HIV pathogenic variants of
envelope glycoproteins as taught in Modrow because
knowledge of such variant structures will enable detection of
antibodies in patients with AIDS, as taught by Barin. Thus,
identifying HIV pathogenic variants of envelope glycoproteins
will allow identifying presence of the acquired humoral
response (which is viewed as viewed as a "treatment targeting
pathogen").
The Examiner acknowledges that "[a] combination of Modrow and
Barin does not teach estimating probability of an existence of a pathogen
using a computing device," but asserts that "[i]nasmuch as the step of
estimating probability of existence of a virus in an individual is interpreted
to encompass detecting/diagnosing the presence of a variant in an individual,
such detecting/diagnosing is a routine step in determining effective antiviral
therapy as exemplified by," inter alia, Chee. Id. at 17-18. The Examiner
finds that Chee teaches "a DNA chip (and method of use) for
diagnosing/detecting (i.e. estimating the probability of) HIV variants in
patients," and "that this is important so that therapy can be changed as drug-
resistant variants are detected." Id.
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We determine that the Examiner has made a prima facie showing of
obviousness of claim 1 based on the combination of Modrow, Barin, and
Chee. We are not persuaded by Appellants' arguments to the contrary,
which focus on the limitation of "estimating a probability of an existence of
the primary pathogen in a given individual." Appeal Br. 34-47.
Although we agree with the Examiner's observation that the
Specification teaches that "[ e ]stimating the probability of existence includes,
but is not limited to, clinical differential diagnosis techniques" (Spec. 8, 11.
7-9), we do not agree with the Examiner's conclusion that the recited step is
no different than simply "identifying a pathogen." Non-Final Act. 12. The
claims require "estimating a probability of an existence of the primary
pathogen in a given individual." Cl. 1 (emphasis added). Under our
broadest reasonable interpretation consistent with the Specification, we
determine that the claim language requires the differential diagnosis of the
primary pathogen within a given individual/patient.
We nonetheless find that the Examiner has shown that at least the
Chee reference suggests the disputed limitation, and, in combination with
Modrow and Barin, renders the claims as a whole obvious. Chee teaches the
use of an array of nucleic acid probes on biological chips for diagnosis of
HIV. Chee, Title. More specifically, Chee teaches:
[a]fter [the HIV] virus acquires drug resistance via a mutation,
the patient suffers dramatically increased viral load, worsening
symptoms (typically more frequent and difficult-to-treat
infections), and ultimately death. Switching to a different
treatment regimen as soon as a resistant mutant virus takes hold
may be an important step in patient management which
prolongs patient life and reduces morbidity during life.
Chee, 4:37--44. Chee further teaches:
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When the immune system in AIDS patients fails, these
normally latent pathogens can grow and generate rampant
infection. In treating such patients, it would be desirable
simultaneously to diagnose the presence or absence of a variety
of the most lethal common infections, determine the most
effective therapeutic regime against the HIV virus, and monitor
the overall status of the patient's infection.
The present invention provides DNA chips for detecting
the multiple mutations in HIV genes associated with resistance
to different therapeutics. These DNA chips allow physicians to
monitor mutations over time and to change therapeutics if
resistance develops. Some chips also provide probes for
diagnosis of pathogenic microorganisms that typically occur in
AIDS patients.
Id. at 5:21-35.
The foregoing teachings of Chee suggest the following limitations
recited in independent claim 1: a) "identifying a primary pathogen" (i.e.,
HIV); b) "estimating a probability of an existence of the primary pathogen in
a given individual" (i.e., diagnosing a patient with HIV I AIDS); c)
"identifying a primary treatment targeting the primary pathogen" (i.e.,
determining an effective therapeutic regiment against the HIV virus); d)
"predicting a [first/second] pathogenic variant of the primary pathogen" (i.e.,
using DNA chips to monitor different mutations of HIV); and e)
"identifying a set of [first/second] variant treatments targeting the
[first/second] pathogenic variant" (i.e., switching to a different treatment
regimen as soon as a resistant mutant virus takes hold). Contrary to
Appellants' arguments, neither the claims nor the Specification require
determining a numerical value (e.g., in terms of percentage) in order satisfy
the "estimating a probability" requirement. We find under our claim
construction that the requirement is satisfied by Chee' s teachings regarding
the differential diagnosis of patients infected with HIV.
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A skilled artisan would have recognized that the diagnosis of HIV
variants using DNA chips as taught by Chee would involve the use of a
computing device. Moreover, Modrow further teaches the prediction of
antigenic epitopes for the envelope proteins of seven different HIV strains
using a computer, which may be used to identify vaccine/antibody
candidates as potential treatment options for those HIV strains. See
Modrow, 572 ("we predicted antigenic determinants in the amino acid
sequences [of envelope protein gp120] with a computer program which
predicted the secondary structure and calculated the values for
hydrophilicity"); Barin, 228 (teaching that gp120 represents a major target
antigen for antibodies in AIDS patients). In view of these teachings, a
skilled artisan would have found it obvious to practice the claimed methods
to predict HIV variants and identify treatment options for such variants.
Furthermore, to the extent that the references do not explicitly teach the use
of a computing device to perform any of the claimed steps, the skilled
artisan would have found it obvious to implement those steps using a
computer. The use of a computer to automate the steps of a known process
is generally obvious. Cf Leapfrog Enterprises, Inc. v. Fisher-Price, Inc.,
485 F.3d 1157, 1161 (Fed. Cir. 2007) ("Accommodating a prior art
mechanical device that accomplishes [the goal of teaching a child to read
phonetically] to modem electronics would have been reasonably obvious to
one of ordinary skill in designing children's learning devices.").
We therefore affirm the obviousness rejection of independent claim 1
in view of the teachings ofModrow, Barin, and Chee. Appellants do not
provide any meaningful substantive argument regarding dependent claims 2,
11-21, and 78; rather, only asserting that those claims "are patentable by
virtue of their own separate recitations as well as by virtue of being
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dependent from independent claim 1." Appeal Br. 46. We accordingly
determine that claims 2, 11-21, and 78 fall with claim 1. See 37 C.F.R.
§ 41.37(iv); In re Lovin, 652 F.3d 1349, 1357 (Fed. Cir. 2011) ("[T]he Board
[has] reasonably interpreted Rule 41.3 7 to require more substantive
arguments in an appeal brief than a mere recitation of the claim elements and
a naked assertion that the corresponding elements were not found in the
prior art.").
With respect to dependent claims 79 and 80, Appellants separately
argue that "the Examiner failed to demonstrate that the cited references
recognized the parameter of 'probability of association' as a result-effective
variable." Appeal Br. 47. As discussed above, we find that the term
"probability of association" is indefinite and thus we are unable to ascertain
the proper scope of claims 79 and 80. In view of our inability to ascertain
the proper claim scope, we cannot determine whether the prior art teaches or
suggests those limitations and thus we do not reach the merits of the
Examiner's rejection because these claims cannot be properly interpreted.
See In re Steele, 305 F.2d 859, 862 (CCPA 1962) (holding that the Examiner
and the Board were wrong in relying on what, at best, were speculative
assumptions as to the meaning of the claims and in basing a prior-art
rejection thereon) ..
OBVIOUSNESS-TYPE DOUBLE PATENTING REJECTIONS
The Examiner entered obviousness-type double patenting rejections
over the claims of Application Nos. 11/525,760, 12/283,128, and
12/283,184. Application No. 11/525,760 was abandoned on December 30,
2011, and therefore the Examiner's rejection based on that application is
rendered moot.
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Application 12/283,158
The other two co-pending applications have not been abandoned and
we address the merits of the rejections.
We note that Application No. 12/283,184 and the present application
both claim priority as divisionals of Application No. 11/525,760 (filed Sept.
22, 2006). In view of the original restriction requirement in Application No.
11/525,760 that led to the filing of both divisional applications, the
Examiner has not shown why Application No. 12/283, 184 is available as a
reference over the present application. An obviousness-type double
patenting rejection as between the two applications is improper under
35 U.S.C. § 121, which states that:
[a] patent issuing on an application with respect to which a
requirement for restriction under this section has been made, or
on an application filed as a result of such a requirement, shall
not be used as a reference either in the Patent and Trademark
Office or in the courts against a divisional application or against
the original application or any patent issued on either of them,
if the divisional application is filed before the issuance of the
patent on the other application.
There has been no showing that Applicants failed to maintain consonance
with the original restriction requirement. See Gerber Garment Technology
Inc. v. Lectra Systems Inc., 916 F.2d 683, 688 (Fed. Cir. 1990). We
accordingly reverse the obviousness-type double patenting rejection over co-
pending Application No. 12/283,184.
With respect to co-pending Application No. 12/283,128, which claims
priority as a divisional to a different application (Application No.
11/487,133, filed July 13, 2006) and is thus available as a reference under
35 U.S.C. § 121, the Examiner asserts that "[a]lthough the conflicting claims
are not identical, they are not patentably distinct from each other because the
claims of 12/283128 are directed to a system comprising a processor and
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Application 12/283,158
computer readable medium with instructions for executing the same method
steps as the instant method." Non-Final Act. 31. We agree. Contrary to
Appellants' arguments (Appeal Br. 71), we find that the Examiner
articulated a sufficient rationale as to why the claims of the two applications
would have been obvious insofar as it would have been obvious to
implement the methods recited in the instant claims on a computer system.
Appellants have not pointed to any other meaningful difference between the
claims. We thus affirm the obviousness-type double patenting rejection over
co-pending Application No. 12/283,128.
NEW GROUND OF REJECTION
Within our authority under 37 C.F.R. § 41.50(b), we enter the
following new ground of rejection.
Claims 1, 2, 11-21, and 78-80 are rejected under 35 U.S.C. § 101 as
being drawn to a patent-ineligible abstract idea as set forth by the Supreme
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