Ex Parte Roder et al

Patent Trial and Appeal Board

Apr 13, 2017

12806137 (P.T.A.B. Apr. 13, 2017)

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.
12/806,137 08/06/2010 Heinrich Roder 08-775-Con3 2256
20306 7590 04/14/2017
MrnnNNFT T ROFFTNFN HT TT RFRT Rr RFRGROFF T T P
EXAMINER
300 S. WACKER DRIVE XU, XIAOYUN
3 2ND FLOOR
CHICAGO, IL 60606 ART UNIT PAPER NUMBER
1797
MAIL DATE DELIVERY MODE
04/14/2017 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 HEINRICH RODER, MAXIM TSYPIN, and
JULIA GRIGORIEVA
Appeal 2016-000289
Application 12/806,1371
Technology Center 1700
Before KAREN M. HASTINGS, GEORGE C. BEST, and
WESLEY B. DERRICK, Administrative Patent Judges.
DERRICK, Administrative Patent Judge.
DECISION ON APPEAL
STATEMENT OF THE CASE
Appellants appeal under 35 U.S.C. § 134 from the Examiner’s
maintained 35 U.S.C. § 103(a) rejections of claims 1-11. We have
jurisdiction under 35 U.S.C. § 6.
We AFFIRM-IN-PART.
1 Appellants identify the real party in interest as Biodesix, Inc. Appeal Brief
filed May 24, 2014 (“Appeal Br”), 2.
Appeal 2016-000289
Application 12/806,137
THE INVENTION
The subject matter of the claims on appeal relates to a system for
determining whether a drug will be effective on a patient with a disease.
Spec. Title; Claim 1.
Claim 1—the sole independent claim on appeal—is representative.
1. A laboratory test processing center, comprising:
one or more data storage devices storing (a) class-labeled
matrix-assisted laser desorption/ionization (MALDI) time-of-
flight (TOF)-derived mass spectral data obtained from blood-
based samples of a multitude of cancer patients, the class labels
for the mass spectral data indicating whether or not a patient
associated with the mass spectral data was responsive to
treatment of cancer from administration of a cancer targeting
drug; and (b) a multitude of MALDI-TOF-derived mass spectra
of blood-based samples of a multitude of cancer patients to be
tested;
a processing unit operating in accordance with a set of
instructions to perform the following operations on the
multitude of mass spectra of the blood-based samples of a
multitude of cancer patients to be tested and the class-labeled
mass spectral data:
(a) perform one or more predefined pre-processing
steps on the multitude of MALDI-TOF-derived mass spectra of
the blood-based samples of a multitude of cancer patients to be
tested;
(b) obtain integrated intensity values of features in
the mass spectra of the blood-based samples of the multitude of
cancer patients to be tested at one or more predetermined m/z
ranges in said mass spectra after the performance of said
predefined pre-processing steps;
c) implement a classification algorithm on the
integrated intensity values and the class-labeled mass spectral
data, the classification algorithm assigning a class label for each
of the multitude of mass spectra; and
2
Appeal 2016-000289
Application 12/806,137
d) output the class label assigned by the
classification algorithm to each of the multitude of mass spectra
of the cancer patients to be tested.
Appeal Br. (Claims Appendix) 17.
THE REJECTIONS2
The claims stand rejected under 35 U.S.C. § 103 as follows:
I. Claims 1, 2, 4-6, 10, and 11 over Xiao;3
II. Claim 7 over Xiao in view of Zhao;4
III. Claim 8 over Xiao in view of Zhao and Mazet;5 and
IV. Claims 3 and 9 over Xiao in view of Lynch.6
DISCUSSION
We have reviewed Appellant’s arguments for patentability set forth in
the Appeal Brief and the Reply Brief filed September 30, 2015 (“Reply Br.”)
but, as explained below, are not persuaded that the Examiner erred
reversibly in rejecting the claims except as to claim 6 (subject to Rejection I.
Accordingly, we affirm the rejections of claims 1, 2, 4, 5, 7, 8, 10, and
11, and we reverse the rejections of claim 6.
2 We refer to the Final Office Action mailed October 23, 2014 (“Final Act.”)
and the Examiner’s Answer mailed July 30, 2015 (“Ans.”).
3 Xiao et al., Serum Proteomic Profiles Suggest Celeocoxib-Modulated
Targets and Response Predictors, 64 Cancer Res. 2904-2909 (2004).
4 Zhao et al., US 2005/0048547 Al, published March 3, 2005.
5 Mazet et al., Background Removal from Spectra by Designing and
Minimising a Non-Quadratic Cost Function, 76 Chemometrics & Intelligent
Lab. Sys. 121-33 (2005).
6 Lynch et al., Activating Mutations in the Epidermal Growth Factor
Receptor Underlying responsiveness of Non-Small-Cell Lung Cancer to
Gefitinib, 350 New Eng. J. Med. 2129-39 (2004).
3
Appeal 2016-000289
Application 12/806,137
Rejection I
Xiao describes aspects of a cancer prevention trial using celecoxib in
familial adenomatous polyposis (FAP) patients. The Examiner relies on
Xiao for its disclosure of a laboratory test processing center comprising:
(1) data storage devices for storing; (a) class-labeled matrix-assisted laser
desorption/ionization (MALDI) time-of-flight (TOF)-derived mass spectra
data from blood-based samples of pre-cancer patients and (b) a mass
spectrum of a blood-based sample of a pre-cancer patient to be tested; and
(2) a processing unit operating in accordance with instructions to (a) perform
one or more pre-processing steps, (b) obtain integrated intensity values of
features in the patient sample mass spectrum, (c) implement a classification
algorithm to provide an indication of whether the patient is likely to benefit
from administration of a cancer targeting drug, and (d) output the class label
(responder or non-responder) assigned by the classification algorithm to the
sample as set forth in claim 1. Ans. 2-3.
As to the laboratory test processing center’s use to store and analyze
cancer patient data, the Examiner also relies on Xiao’s disclosure. The “pre­
cancer patient” and related group of patients for testing as drug responder or
non-responder are individuals with FAP, which—as emphasized by the
Examiner—“have a marked predisposition to colorectal carcinoma and
develop numerous adenomatous polyps, considered to be premalignant
precursors to carcinoma.” Ans. 3 (citing Xiao 2904,11). Celecoxib, the
particular drug for which response was tested in Xiao, targets
cyclooxygenase 2 (COX-2), which—as emphasized by the Examiner—Xiao
teaches is a valid target for cancer prevention and treatment.” Ans. 3 (citing
Xiao, Abstract).
4
Appeal 2016-000289
Application 12/806,137
The Examiner then concludes in essence that it would have been
obvious at the time of the invention to use Xiao’s method for analysis of
colorectal cancer patients because of the related nature of FAP and
colorectal cancer and the action of the drug targeting COX-2 in the treatment
of both FAP and the related cancer. Ans. 3.
Further, the Examiner reasonably finds the disclosed structure of
Xiao’s apparatus meets the limitations of claim 1 because it is capable of
performing the intended use relating to cancer patients. Ans. 3—4. The
Examiner’s determination that Xiao meets the claim includes that:
The data storage device of Xiao’s test data processing center is
capable of storing (a) class-labeled matrix-assisted laser
desorption/ionization (MAFOI) time-of-flight (TOF)-derived
mass spectral data obtained from blood-based samples of a
multitude of cancer patients. The processing unit of Xiao is
capable of operating in accordance with a set of instructions to
perform the following operations on the multitude of mass
spectra of the blood-based samples of a multitude of cancer
patients to be tested and the class-labeled mass spectral data.
Ans. 4, see also 10-11.
Appellants proffer arguments as to the claims subject to Rejection I as
a group—which we discuss in regard to independent claim 1—as well as
additional arguments as to dependent claims 4, 6, 10, and 11.
Appellants contend that there is no basis for one of skill in the art to
have understood that “class labels generated by the laboratory test
processing centers could be used to indicate whether or not the cancer
patients will likely be responsive to treatment of cancer by administration of
a cancer targeting drug.” Appeal Br. 4. Appellants argue that Xiao’s
identification of a marker for FAP patients “in no way teaches or suggests”
markers could be developed for cancer patients and that the Examiner is
5
Appeal 2016-000289
Application 12/806,137
improperly relying on an “obvious to try rationale” for which the requisite
reasonable expectation of success is lacking. Appeal Br. 4-6. The
arguments are grounded on FAP and colorectal cancer being different
diseases and on the unpredictability of response to cancer treatments.
Appeal Br. 4-5; see also Reply Br. 1-2.
On this record, we are not persuaded of reversible error in the
Examiner’s reliance on Xiao. While Appellants argue that FAP and
colorectal cancer are different, they fail to squarely address the Examiner’s
reasoning grounded on the related nature of the two diseases, including that
the drug tested in Xiao—celecoxib—targets COX-2, a known target—for
“cancer prevention and treatment.” Cf. In re Preda, 401 F.2d 825, 826
(CCPA 1968) (“[I]n considering the disclosure of a reference, it is proper to
take into account not only specific teachings of the reference, but also the
inference which one skilled in the art would reasonably be expected to
drawn therefrom.”). Moreover, the “prior art reference must be ‘considered
together with the knowledge of one of ordinary skill in the pertinent art.’” In
re Paulsen, 30 F.3d 1475, 1480 (Fed. Cir. 1994) (quoting In re Samour, 571
F.2d 559, 562 (CCPA 1978)). In this case, the reasonable inferences to be
drawn from Xiao include that markers indicating responsiveness to
celecoxib would be present in both pre-cancer, FAP patients and colorectal
cancer patients as COX-2 is the target in the treatment of both conditions.
See, e.g., Xiao Abstract. As to the unpredictability of response to cancer
treatments, the issue is not that a particular cancer treatment may or may not
work, but rather that there is a correlation between a marker and treatment
efficacy, and Appellants’ arguments fail to address this with any cogent
argument. See generally Appeal Br.; Reply Br.
6
Appeal 2016-000289
Application 12/806,137
Appellants also contend that there is a structural difference between
the laboratory test processing center of the instant claims and that disclosed
in Xiao on the basis that claims requiring data from cancer patients rather
than from FAP patients without cancer. Appeal Br. 6-7. In response to the
cancer patient limitation being merely an intended use, Appellants argue that
the recited storage devices are not capable of performing the intended use
because Xiao does not include data from cancer patients.7 Reply Br. 3—4.
On this record, we are not persuaded that the Examiner erred
reversibly because the requirement that the data be from cancer patients does
not further limit the structure of the claimed apparatus in a manner that
patentably distinguishes it from Xiao’s apparatus. The patentability of an
apparatus “depends on the claimed structure, not on the use or purpose of
that structure.” Catalina Mktg. Inti. Inc. v. Coolsavings.com, Inc., 289 F.3d
801, 809 (Fed. Cir. 2002). Appellants’ argument is in essence that the data
differs, but this fails to apprise us of any difference in the structure,
including in necessary programming, required for Xiao’s apparatus to
perform the intended function of the claimed apparatus. Cf. Typhoon Touch
Techs., Inc. v. Dell, Inc., 659 F.3d 1376, 1380 (Fed. Cir. 2011) (“[T]he
apparatus as provided must be ‘capable’ of performing the recited function,
not that it might be modified to perform the function.”).
7 Appellants further argument as to claim 2 that its recitation that
“‘production and storage of the mass spectrum in the one or data storage
devices’ ... is a structural element” (Reply Br. 4) is not timely as the
Examiner found Xiao’s device meeting the limitation in being “capable of
storing data relating to a cancer patient treated by a cancer targeting drug
(Final Act. 4) and, in the absence of an explanation why Appellants could
not have addressed it in the Appeal Brief, we deem the argument waived (37
C.F.R. § 41.41(b)(2)).
7
Appeal 2016-000289
Application 12/806,137
Claim 4
Claim 4 further recites that “one or more of the predetermined m/z
ranges are selected from” a listing of particular ranges. Claim 4.
The Examiner finds, inter alia, that the limitation to the predetermined
m/z ranges “merely describes the intended use of the processing unit and
does not further limit the structure of the processing unit.” Ans. 5. The
Examiner further finds Xiao’s processing unit is capable of processing data
with the predetermined m/z ranges selected from the group recited in claim
4. Ans. 5; see also Xiao Tables 1-3.
Appellants contend the Examiner is relying on an obvious to try
rationale and argue that that there is no proper basis for the recited m/z
ranges, particularly where there is no teaching that different cancers have
different m/z ranges and Xiao does not disclose a marker within a claimed
range or for cancer. Appeal Br. 7-9; Reply Br. 5-6.
Appellants’ arguments are not persuasive of reversible error because
they fail to address the Examiner’s rationale for the rejection of claim 4
grounded on the recited predetermined m/z ranges not constituting a
structural limitation that distinguishes the claimed apparatus from Xiao’s
apparatus which relates to processing data that includes similar m/z values.
Claim 6
Appellants contend that the Examiner’s “assertion] that a
‘ [probabilistic k-nearest neighbor classification algorithm with improved
performance is well-known in the art’” is an improper use of judicial or
administrative notice. Appeal Br. 9-10.
On this record, the Examiner’s assertion of fact (Final Act. 5), which
is not later supported by citation to evidence (see generally Ans.), is
8
Appeal 2016-000289
Application 12/806,137
improper for the reasons highlighted by Appellants’ argument, including that
it relates to an area of specific knowledge of the prior art. Accordingly, we
are unable to sustain the rejection of claim 6.
Claims 10 & 11
Citing the Examiner’s statements regarding what Xiao teaches that
include reference to “cancer patients” (Appeal Br. 10; Final Act. 5),
Appellants contend the Examiner erred in the rejection of both claims 10 and
11 because “Xiao teaches absolutely nothing about cancer patients and
therefore cannot support an obviousness rejection” (Appeal Br. 10).
Appellants’ argument is not persuasive of harmful error because, as
explained above, Xiao’s explicit teaching as to pre-cancer, FAP reasonably
teaches the skilled artisan the like methods for analysis of cancer patients.
In reFritch, 972 F.2d 1260, 126^65 (Fed. Cir. 1992); Preda, 401 F.2d at
826. Appellants’ argument here, accordingly, establishes no error in the
Examiner’s determination that one of ordinary skill in the art, armed with
knowledge of Xiao, at the time of the invention, would have been led to the
subject matter of claims 10 and 11.
Rejection II
In rejecting claim 7, the Examiner further relies on Xiao for its
disclosure of predefined pre-processing steps, including subtracting
background contained in the mass spectrum of the blood-based sample of the
patient to produce a background subtracted spectrum, normalizing the
background subtracted spectrum, and aligning the normalized, background
subtracted spectrum to a predefined mass scale. Ans. 6 (citing Xiao 2905,
13).
9
Appeal 2016-000289
Application 12/806,137
The Examiner relies on Zhao for its teaching that the subtracting step
comprises estimating non-constant levels of background and subtracting the
estimated background from the mass spectral data, particularly with the use
of a moving window (sliding window) using locally weighted background
levels in the calculations. Ans. 6 (citing Zhao Tflf 50, 73).
The Examiner concludes that one of ordinary skill in the art, armed
with the teachings of Xiao and Zhao, at the time of the invention, would
have found it obvious to estimate non-constant levels of background and
subtracting the estimated background from the mass spectral data for the
benefit of more accurately estimating the background. Ans. 6; see also Ans.
11-12.
Appellants argue that Zhao does not correct the deficiencies of Xiao,
but do not otherwise address the relied on teachings of Xiao. Appeal Br.
10-12. Appellants’ arguments as to Zhao are directed wholly to portions
other than || 53 & 70 and do not, accordingly, address the rejection set forth
by the Examiner. Compare Appeal Br. 11-12 with Ans. 6.
Appellants’ arguments are wholly unpersuasive of reversible error
because they fail to address the rejection as set forth by the Examiner.
Further, the arguments are also unpersuasive of error because—as
highlighted by the Examiner (Ans. 11-12)—the arguments attack the
references individually rather than the combination. When a claim is
rejected as obvious over a combination of references, the question is not
what the references teach individually, but whether the differences between
the claimed invention and the prior art would have been obvious over the
combined teachings of the references and what these teachings would have
suggested to a person of ordinary skill in the art. In re Mouttet, 686 F.3d
10
Appeal 2016-000289
Application 12/806,137
1322, 1332-33 (Fed. Cir. 2012); In re Keller, 642 F.2d 413, 425 (CCPA
1981).
Rejection III
In rejecting claim 8, the Examiner relies on Xiao and Zhao as set forth
in Rejection II (Ans. 6) but, conceding Zhao’s method of background
correction may not be asymmetric, finds “asymmetric estimation, non­
constant level of background is well known in the art” and relies on Mazet
for its relevant teaching of “asymmetric estimation, non-constant levels of
background” (Ans. 7 (citing Mazet 126, Figs. 2a, 2b)). The Examiner
further relies on Mazet for its teaching that “when there are only positive
peaks in the spectrum, asymmetric estimation of background gives [the] best
result” and concludes one of ordinary skill in the art at the time of the
invention would have found it obvious “to use asymmetric estimation of
background for mass spectrum, because mass spectrum only has positive
peaks.” Ans. 7.
Appellants contend that the combination relied on by the Examiner
does not teach or suggest all elements of claim 8. Appeal Br. 12-13.
Appellants argue that the background estimation method according to the
claim is asymmetric in contrast to that of Zhao’s symmetric method. Appeal
Br. 12. Appellants argue that Mazet differs from that according to the claim
because it does not disclose performing an asymmetric estimate of
background in a moving window, but rather treats the spectrum as a whole,
and does not consider mass spectra. Appeal Br. 13. Appellants further
contend that they “considered the references in combination.” Reply Br. 6.
Appellants’ argument is not persuasive of reversible error because it
fails to address the combination as set forth by the Examiner. The
11
Appeal 2016-000289
Application 12/806,137
arguments are grounded on deficiencies in the individual references or on
modification of Xiao and Zhao to include features from Mazet not relied on
by the Examiner in the rejection. Arguments against references individually
can not overcome rejections grounded on combinations of references.
Mouttet, 686 F.3d at 1332—33; Keller, 642 F.2d at 425. Arguments as to the
additional features from Mazet contrary to what is set forth in the claim are
likewise without merit. Cf. In re Sneed, 710 F.2d 1544, 1550 (Fed. Cir.
1983) (“[I]t is not necessary that the inventions of the references be
physically combinable to render obvious the invention under review.”); In re
Nievelt, 482 F.2d 965, 968 (CCPA 1973) (“Combining the teachings of
references does not involve an ability to combine their specific structures.”).
Thus in neither case are the arguments persuasive of error.
Rejection IV
The Examiner relies on Fynch for its teachings relating to non-small
cell lung cancer patients and a drug targeting that cancer that comprises an
epidermal growth factor receptor inhibitor. Final Act. 6-7; Ans. 7, 12-13.
The Examiner further determines, however, that the recitations as to “a
multitude of non-small cell lung cancer patients administered a cancer
targeting drug” (claim 3) and as to “the cancer targeting drug compris[ing]
an epidermal growth factor receptor inhibitor” (claim 9) merely describe
intended uses of the storage device and thus do not further limit the
structure. Final Act. 6-7; Ans. 8-9.
Appellants proffer various arguments directed to Fynch and the
Examiner’s reasoning related to its teachings. Appeal Br. 13-15; Reply Br.
6-9.
12
Appeal 2016-000289
Application 12/806,137
We need not reach the proffered arguments. Appellants fail to address
the Examiner’s findings and conclusions grounded on claims 3 and 9
describing intended uses rather than structural limitations. Appeal Br. 13-
15; 6-9. Appellants fail to apprise us, accordingly, of any error in the
Examiner’s determination that there is no difference in the structure required
for Xiao’s apparatus to perform the intended function of the claimed
apparatus according to claims 3 and 9. Finding the Examiner’s
determination well-founded that Xiao’s device is capable of performing the
recited use, for the reasons set forth above in respect to Rejection I, we
sustain the Examiner’s rejection of claims 3 and 9 on this ground.
DECISION
The Examiner’s decision rejecting claims 1, 2-\, 5, 7, and 8-11 is
AFFIRMED.
The Examiner’s decision rejecting claim 6 is REVERSED.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l)(iv).
AFFIRMED-IN-PART
13