Ex Parte Jung et al

Patent Trial and Appeal Board

Aug 2, 2016

12283128 (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, 128 09/08/2008 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.
17906.21.2 6199
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
Ex parte EDWARD K.Y. JUNG and LOWELL L. WOOD, JR.
Appeal2013-005465
Application 12/283, 128
Technology Center 1600
Before JEFFREYN. FREDMAN, ULRIKE W. JENKS, and
CHRISTOPHER G. PAULRAJ, Administrative Patent Judges.
PAULRAJ, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal 1 under 35 U.S.C. § 134 involving claims to a
computer system for identifying and treating pathogen variants. The
Examiner rejected the claims for 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).
Appeal2013-005465
Application 12/283, 128
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 48-50, 54---61, and 78-84 are under appeal, and are
reproduced in the Claims Appendix of the Appeal Brief. Independent claim
48 is representative and reads as follows:
A system comprising:
at least one processor; and
a computer program product for use with a computer
system and wherein the computer program product includes a
plurality of instructions executable by the at least one
processor, the plurality of instructions including but not limited
to:
a set of instructions for identifying at least one primary
pathogen associated with a disease state;
a set of instructions for predicting at least one pathogenic
variant of the at least one primary pathogen;
a set of instructions for estimating a probability of an
existence of the at least one predicted pathogenic variant in a
given individual; and
a set of instructions for identifying at least one second
treatment targeting the at least one predicted pathogenic variant.
Appeal Br. 82 (Claims App'x).
The Re} ections
The Examiner has rejected the claims as follows:
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I. Claims 48-50, 54---61, and 78-84 under 35 U.S.C. § 103 as
being unpatentable over Smith2 together with Burdette3 and
Chee,4 Armour, 5 or Holland-Staley. 6
II. Claims 48-50, 54---61, and 78-84 under 35 U.S.C. § 103 as
being unpatentable over Modrow7 and Barin,8 together with
Burdette and Chee, Armour, or Holland-Staley.
III. Claims 48-50, 54---61, and 78-84 under 35 U.S.C. § 103 as
being unpatentable over Prior,9 Smith, and Modrow, together
with Burdette and Chee, Armour, or Holland-Staley.
IV. Claims 48-50, 54---61, and 78-84 for non-statutory
obviousness-type double patenting as being unpatentable over
Application No. 11/487,133.
V. Claims 48-50, 54---61, and 78-84 for non-statutory
obviousness-type double patenting as being unpatentable over
Application No. 12/283,158.
VI. Claims 48-50, 54---61, and 78-84 for non-statutory
obviousness-type double patenting as being unpatentable over
Application No. 12/283,184.
June 13, 2012 Non-Final Action ("Non-Final Act."), 6-24. 10
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").
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Application 12/283, 128
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. For the reasons set forth below,
we affirm the obviousness rejection based on the teachings of Modrow,
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).
The Examiner finds that "Modrow teaches prediction of amino acid
sequences of the envelope proteins of seven different HIV strains." Non-
Final Act. 12. The Examiner further finds that Barin "teaches that viral
envelope proteins (gpl60 and gpl20) are the most consistently recognized
by antibodies found in patients with the acquired immune deficiency
syndrome (AIDS)." Id. at 13. The Examiner asserts that:
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 Appellants incorrectly refer to the grounds of rejection from an earlier
Office Action in their Appeal Brief (Appeal Br. 4), but respond to the most
recent grounds of rejection in their Reply Brief (Reply Br. 2-18). We
consider Appellants' arguments only to the extent they are applicable to the
rejections set forth in the June 13, 2012 Non-Final Action and addressed in
the Examiner's Answer.
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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 [sic] a "treatment
targeting pathogen"). Further, as merely using a computer to
automate a known process does not by itself impart
nonobviousness to the invention it would have been prima facie
obvious to computerize the combined teaching of Modrow et al
and Barin and present recommendations as a set of
computerized instructions.
Id. at 13-14.
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 14. 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.
We determine that the Examiner has made a prima facie showing of
obviousness based on the combination of Modrow, Barin, and Chee. We are
not persuaded by Appellants' arguments to the contrary. Appellants focus
their arguments on the limitations of "estimating a probability of an
existence of the at least one predicted pathogenic variant in a given
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individual" (claims 48, 78) and "designating at least one group of the at least
one predicted pathogenic variant" (claim 78). Reply Br. 9-12.
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. 10. The
claims require "estimating a probability of an existence of the at least one
predicted pathogenic variant in a given individual." Cl. 48 (emphasis
added). Under our broadest reasonable interpretation, we determine that the
claim language requires a differential diagnosis that would distinguish the
existence of one variant of the pathogen from another variant of the
pathogen within a given individual/patient.
We nonetheless find that the Examiner has shown that at least the
Chee reference suggests the disputed limitations, and, in combination with
iviodrow 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:
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
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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 claims 48 and 78: a) "identifying at least one primary
pathogen associated with a disease state" (i.e., HIV, associated with AIDS);
b) "predicting at least one pathogenic variant of the at least one primary
pathogen;" (i.e., mutations of HIV); c) "estimating a probability of an
existence of the at least one predicted pathogenic variant in a given
individual; and" (i.e., using DNA chips to monitor mutations of HIV and
diagnosing pathogenic microoganisms associated with HIV infection); and
d) "identifying at least one second treatment targeting the at least one
predicted pathogenic variant" (i.e., switching to a different treatment
regimen as soon as a resistant mutant virus takes hold). Furthermore, Chee
provides a table of the most common mutations of HIV reverse transcriptase,
which satisfies the requirement for "designating at least one group of the at
least one predicted pathogenic variant" set forth in claim 78. Chee, 4:45-
5: 10 (Table 1 ); 15: 8-11. 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
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satisfied by Chee' s teachings regarding the differential diagnosis of patients
infected with HIV.
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, as noted by the Examiner (Non-Final Act.
12), 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 implement a
computer system programmed to identify HIV variants and treatment
options for such variants.
To the extent that the references do not explicitly teach the use of a
computing device to perform any of the recited instructions, we agree with
the Examiner that 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.").
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We therefore affirm the obviousness rejection of independent claims
48 and 78 in view of the teachings of Modrow, Barin, and Chee. Appellants
have not argued the dependent claims separately, and therefore those claims
fall with their respective independent claims. 37 C.F.R. § 41.37(iv).
OBVIOUSNESS-TYPE DOUBLE PATENTING REJECTIONS
The Examiner entered obviousness-type double patenting rejections
over the claims of Application Nos. 11/487, 133, 11/283, 158, and
11/283,184. Application No. 11/487,133 was abandoned on December 16,
2014, and therefore the Examiner's rejection based on that application is
rendered moot.
The other two co-pending applications have not been abandoned and
we address the merits of the rejections. With respect to both Application
Nos. 11/283, 158, and 11/283, 184, 11 Appellants argue that the Examiner
failed to articulate or provide a full and reasoned explanation as to why the
claim recitations in claims 48-50, 54--61, and 78-84 are anticipated by or
rendered obvious by any specific claim of those co-pending applications.
Reply Br. 18. We disagree. The Examiner has pointed out that the claims
recite essentially the same limitations, with the claims of the present
application directed to a "system" with a "computer program product"
containing instructions for performing similar steps to those recited in the
claims of the other co-pending applications. Appellants have not pointed to
any other meaningful difference between the claims. The Examiner has set
11 Application Nos. 11/283,158, and 11/283,184 are available as references
under 35 U.S.C. § 121 because they claim priority as divisionals of a
different application (Application No. 11/525,760, filed Sept. 22, 2006) than
the priority claim (Application No. 11/487, 133, filed July 13, 2006) for the
present application.
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forth a sufficient rationale insofar as it would have been obvious to
implement the same methods on a computer system. We thus affirm the
obviousness-type double patenting rejection over co-pending Application
Nos. 11/283,158, and 11/283,184.
NEW GROUND OF REJECTION
Within our authority under 37 C.F.R. § 41.50(b), we enter the
following new ground of rejection.
Claims 48-50, 54---61, and 78-84 are rejected under 35 U.S.C. § 101
as being drawn to a patent-ineligible abstract idea as set forth by the
Supreme Court in Mayo Collaborative Servs. v. Prometheus Labs., 132 S.
Ct. 1289, 1297 (2012) ("Mayo") and Alice Corp. v. CLS Bank Int 'l, 134 S.
Ct. 2347, 2358-59 (2014) ("Alice").
In accordance with the Mayo/Alice framework for determining patent
eligibility, we must determine whether a claim that is drawn to a statutory
class of subject matter (process, machine, manufacture, or composition of
matter) is a) otherwise "directed to" a judicially recognized exception (i.e.,
law of nature, natural phenomena, or abstract idea) and, if so, b) whether the
claim recites additional elements that amount to "significantly more" than
the judicial exception. See 2014 Interim Guidance on Patent Subject Matter
Eligibility, 79 Fed. Reg. 74618, 74621 (Dec. 16, 2014).
Here, although the claims are drawn to a statutory class (machine), we
determine that each of the claims are directed to a patent-ineligible abstract
idea insofar as they are directed generally to the identification of medical
treatment options for pathogen variants. See, e.g., Cl. 48 (reciting
instructions for a) "identifying at least one primary pathogen associated with
a disease state"; b) "predicting at least one pathogenic variant of the at least
one primary pathogen;" c) "estimating a probability of an existence of the at
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Application 12/283, 128
least one predicted pathogenic variant in a given individual; and" d)
"identifying at least one second treatment targeting the at least one predicted
pathogenic variant."). The claims do "no more than call on a 'computing
device,' with basic functionality for computing stored and input data and
rules, to do what doctors routinely do." Cf SmartGene, Inc. v. Advanced
Biological Labs., SA, 555 F. App'x 950, 954--55 (Fed. Cir. 2014)
("Whatever the boundaries of the 'abstract ideas' category, the claim at issue
here involves a mental process excluded from section 101: the mental steps
of comparing new and stored information and using rules to identify medical
options."). The claims at issue here are not meaningfully distinguishable
from those found to be ineligible for patent protection in SmartGene.
As recognized in SmartGene, the fact that a computer is used to
perform the recited steps does not add "significantly more" to the abstract
idea embodied in the claims. Furthermore, the fact that the claims are drawn
to a computer system rather than to a method also makes no difference in the
analysis. The use of a generic computer to identify information and estimate
a probability simply takes advantage of some of the "most basic functions a
computer." Cf Alice, 134 S. Ct. at 2359---60 ("Because petitioner's system
and media claims add nothing of substance to the underlying abstract idea,
we hold that they too are patent ineligible under § 101. ").
SUMMARY
We affirm the rejection of claims 48-50, 54---61, and 78-84 under
35 U.S.C. § 103 as being unpatentable over the combination ofModrow,
Barin, and Chee.
We dismiss as moot the rejection of claims 48-50, 54---61, and 78-84
for non-statutory obviousness-type double patenting as being unpatentable
over Application No. 11/487,133.
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We affirm the rejections of claims 48-50, 54---61, and 78-84 for non-
statutory obviousness-type double patenting as being unpatentable over
Application Nos. 11/283,158, and 11/283,184.
We enter a new ground of rejection of claims 48-50, 54---61, and 78-
84 under 35 U.S.C. § 101 as being drawn to a patent-ineligible abstract idea.
This decision contains a new ground of rejection pursuant to
37 C.F.R. § 41.50(b) (Sept. 13, 2004; revised, 76 FR 72270, Nov. 22, 2011,
effective Jan. 23, 2012). 37 C.F.R. § 41.50(b) provides "[a] new ground of
rejection pursuant to this paragraph shall not be considered final for judicial
review."
37 C.F.R. § 41.50(b) also provides that the Appellants, 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). See 37 C.F.R.
§ 1.136(a)(l )(iv).
AFFIRMED; 37 C.F.R. § 41.50(b)
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