Ex Parte Compton et al

Patent Trial and Appeal Board

Sep 27, 2013

11099891 (P.T.A.B. Sep. 27, 2013)

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.
11/099,891 04/06/2005 Bruce J. Compton AF-308-310 9258
43840 7590 09/30/2013
Waters Technologies Corporation
34 MAPLE STREET - LG
MILFORD, MA 01757
EXAMINER
SODERQUIST, ARLEN
ART UNIT PAPER NUMBER
1777
MAIL DATE DELIVERY MODE
09/30/2013 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 BRUCE J. COMPTON and
ROBERT S. PLUMB
____________

Appeal 2012-002817
Application 11/099,891
Technology Center 1700
____________

Before ADRIENE LEPIANE HANLON, ROMULO H. DELMENDO, and
JAMES C. HOUSEL, Administrative Patent Judges.

HOUSEL, Administrative Patent Judge.

DECISION ON APPEAL

STATEMENT OF THE CASE
Appellants1 appeal under 35 U.S.C. § 134 from the Examiner’s
decision finally rejecting claims 1-22 under 35 U.S.C. § 103(a) as

1 Appellants identify the real party in interest in this appeal as Waters
Technologies Corporation, a wholly owned subsidiary of Waters
Corporation.
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unpatentable over Blanz2 in view of Matson3, and Fiehn4 or Ideker. We
have jurisdiction over the appeal under 35 U.S.C. § 6(b).
We AFFIRM. 5

STATEMENT OF THE CASE
The invention relates to methods and apparatus for identifying one or
more compounds in a sample, wherein the sample is separated by
chromatography into a plurality of aliquots defined by retention time ranges,
each retention time range being associated with the one or more compounds
to produce a retention time value for the compounds in the sample. Spec.
2:3-8. A mass spectroscopy analysis for each of the aliquots is performed,
each mass spectroscopy analysis has one or more mass values associated
with the one or more compounds within the retention time range to produce
a mass value for each compound. Id. at 2:8-11. Further, each aliquot is
subjected to at least one further mode of analysis to produce a further
analytical value for each compound. Id. at 2:11-12. The one or more
compounds are therefore identified by a retention time value, a mass spectra
value and the further analytical value, which can then be used for

2 Blanz, J. et al., “Detection and Identification of Human Urinary
Metabolites of Biantrazole (CI-941)”, Drug Metabolism and Disposition,
1993, Vol. 21, No.5, pp. 955-961.
3 US 4,863,873, issued September 5, 1989.
4 Fiehn, O. et al, “Metabolite profiling for plant functional genomics”,
Nature Biotechnology, 2000, Vol. 18, pp. 1157-1161.
5 Our decision refers to Appellants’ Brief (App. Br.) filed June 21, 2011, the
Examiner’s Answer (Ans.) mailed September 14, 2011, and Appellants’
Reply Brief (Reply Br.) filed November 14, 2011.
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comparisons of sample over time, or between different samples or to normal
values. Id. at 12-15.
Appellants do not separately argue the claims on appeal in the § 103
rejection. See generally, App. Br. 11-17. Accordingly, with regard to our
disposition of the § 103 rejection, all the claims stand or fall with
independent claim 1. 37 C.F.R. § 41.37(c)(1)(vii). Representative claim 1 is
reproduced below:
1. A method of associating two or more components selected from
a group consisting of metabonome, proteome, and genome
components derived from a plurality of samples taken over a period of
time, comprising the steps of:
a) separating each sample of said plurality of samples into a
plurality of aliquots defined by retention time ranges by means of
chromatography, each retention time range associated with one or
more compounds, to produce a retention time value for said
compounds;
b) obtaining a mass spectroscopy analysis for each of said
aliquots, each mass spectroscopy analysis having one or more mass
values associated with said one or more compounds within said
retention time range, to produce a mass value for each compound;
c) subjecting each aliquot to at least one further mode of
analysis, to produce a further analytical value for said each compound,
wherein said one or more compounds in said sample are associated
with said retention time value, said mass value and said further
analytical value, to facilitate comparing all of said values over time
and from different said samples;
d) obtaining said retention time value, said mass value, said
further analytical value and changes in the concentration of said
compounds at different sampling times over said period of time;
e) associating said retention time value, said mass value, said
further analytical value and said changes in the concentration of said
compounds at a sampling time to that of one or more components
selected from a group consisting of metabonome, proteome, and
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genome components linked by said retention time associated with said
sampling time; and,
f) comparing at least two components selected from at least two
of the groups consisting of metabonome, proteome, and genome
components linked by said retention time to determine changes in said
components.6
App. Br. 18-19, Claims App’x.

ANALYSIS
The Examiner bears the initial burden of establishing a prima facie
case of obviousness. In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992).
“[R]ejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
obviousness.” In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006) quoted with
approval in KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007). After
careful consideration of the respective positions of the Examiner and
Appellants, we find a preponderance of the evidence supports the

6 We note claim 1’s preamble sets forth the objective of the method of
“associating two or more components selected from a group consisting of
metabonome, proteome, and genome components derived from a plurality of
samples taken over a period of time” whereas the final step (f) of the method
requires comparison of at least two components selected from at least two of
the groups consisting of metabonome, proteome, and genome components to
determine changes in said components. Thus, there is an apparent mismatch
between the method’s objective of associating two components that may be
selected from only one of the groups listed over a period of time, versus the
outcome of step (f) of comparing two components selected from at least two
groups listed to broadly determine changes in those components. Should
prosecution continue, the preamble and body of claim 1 should be made to
more directly correspond to one another.
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Examiner’s obviousness conclusion. The Examiner’s findings of fact are
thoroughly discussed in the Answer and we adopt these as our own. We
concur with the conclusions reached by the Examiner. Accordingly, we will
sustain the Examiner’s Section 103(a) rejection for the reasons expressed in
the Answer with the comments below added for emphasis.
The Examiner finds Blanz teaches detection and identification of
metabolites of biantrazole in human urine using a combination of
chromatography and mass spectroscopy. Ans. 4-5. The Examiner further
finds Blanz provides a scanning spectrophotometer to analyze the peaks of
each aliquot defined by a retention time to generate concentration data. Id.
at 6. In addition, the Examiner finds Blanz quantifies biantrazole and its
metabolites in patient urine samples collected during a time period of 100
hours. Id. at 5. Thus, the Examiner finds Blanz provides “a
chromatography system to produce a plurality of aliquots defined by
retention time and a mass spectrometer with two stages of analysis and a
spectrometer for analysis.” Id. These analyses provide data on retention
times, molecular mass spectra, and concentration/quantitation of biantrazole
and its metabolites. Id. Specifically, the Examiner cites to Blanz, Table 2,
in combination with Table 1, and Figures 8-9, showing this data and
comparing the three metabonome compounds linked by their retention times.
Id. at 6. The Examiner concedes Blanz does not teach using this analytical
method and apparatus to associate these metabonomic compounds with
proteomic and/or genomic components. Id.
The Examiner looks to Matson for teaching a method and system for
analyzing body fluid samples from normal and abnormal individuals to
generate analytical patterns for normal and abnormal fluids to facilitate
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comparison. Id. at 7. The Examiner finds that because of the complexity of
the metabolic pathways, Matson’s system provides for resolving and
detecting hundreds of compounds in a single sample to provide a small
molecule inventory or metabolic pathway pattern for a patient. Id. The
Examiner also finds Matson teaches correlation of the patterns covering both
metabonomic and proteomic compounds from a plurality of individuals
provides a rational route to pharmacological development leading to
treatments or cures of disorders, diseases or conditions, wherein either the
presence/absence of compounds is identified and/or differences in
concentration of compounds are assessed. Id. at 7-8. Significantly, the
Examiner finds Matson’s analytical system uses chromatography to provide
aliquots defined by retention times with identification of peaks in each
aliquot to identify compounds therein. Id. at 9.
The Examiner finds Fiehn associates proteomic and genomic
compounds using coupled chromatography and mass spectroscopy as a tool
to study gene function of metabolic phenotypes, identifying and quantifying
326 distinct compounds from different samples. Id. Finally, the Examiner
finds Ideker demonstrates an integrated approach to building, testing and
refining a cellular pathway model, whereby a large number of proteomic and
genomic compounds are identified and quantified from different samples to
detect patterns therein. Id. at 9-10.
The Examiner then concludes it would have been obvious to one of
ordinary skill in the art to practice the Blanz methods using larger sets of
sample components including metabonomic and proteomic compounds as
taught by Matson “because of [Matson’s] recognition that many different
compounds are involved in metabolic pathways and ability to identify
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several metabolic pathways from a large number of compounds in a single
sample leads to the ability to diagnose or provide a treatment protocol.” Id.
at 10. The Examiner further concludes it would have been obvious to have
practiced Blanz’s methods in an integrated profiling approach as taught by
Fiehn and Ideker thereby providing associations between metabonomic,
proteomic and genomic compounds, reflecting the underlying cellular
pathways and the genome that produces them. Id.
Appellants contend the above combination of prior art fails to disclose
certain features of the claimed invention. See generally, App. Br. 11-17.
Appellants argue the proposed combination fails to teach or suggest linking
metabonomic, proteomic and genomic components by retention times
associated with a sampling time, and comparing the components associated
with different sampling times to determine changes in the components over
time. App. Br. 12. In support of this argument, Appellants discuss each of
Blanz, Matson, Fiehn and Ideker, individually. Id. at 13-14; Reply Br. 5-8.
In particular, Appellants note that Blanz does not teach linking
metabonomic, proteomic and genomic components by a retention time; that
Matson does not compare metabolic profiles to proteomic or genomic
components; that Fiehn’s comparative studies exclude proteomic
components; and that Ideker fails to teach or suggest comparing at least two
components selected from at least two of metabonomics, proteomic and
genomic components to determine changes over time. App. Br. 13-14;
Reply Br. 5-8.
The Appellants’ arguments are not persuasive of reversible error. We
note one cannot show nonobviousness by attacking references individually
when the rejection is based on a combination of references. In re Keller,
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642 F.2d 413, 425 (CCPA 1981). Each reference cited by the Examiner
must be read, not in isolation, but for what it fairly teaches in combination
with the prior art as a whole. See In re Merck & Co., Inc., 800 F.2d 1091,
1097 (Fed. Cir. 1986). In this regard, we are satisfied that the prior art
findings of the Examiner support the Examiner’s obviousness conclusions.
The Examiner articulates reasoning with “some rational underpinning to
support the legal conclusion of obviousness.” Kahn, 441 F.3d at 988. That
Matson does not individually teach or suggest linking at least two
compounds from at least two groups of metabonomic, proteomic and
genomic compounds is immaterial, as Matson teaches a system for
generating metabonomic data for a large set of compounds, wherein the data
reflect underlying proteomic activity and provide an operational measure of
genomic activity, while both Fiehn and Ideker suggest such identification of
associations amongst the compounds from metabonomic, proteomic and
genomic groups. The utilization of Blanz’s methods which provide
associating components by retention times with a sampling time, and
comparing the components associated with different sampling times to
determine changes in the components over time, to perform the linking
between metabonomic, proteomic and genomic compounds is further
strengthened by the fact that Fiehn also utilizes a coupled chromatographic
and mass spectrometric process.
CONCLUSION
In sum, for the reasons expressed in the Answer and above, we find a
preponderance of the evidence favors the Examiner’s conclusion of
obviousness as to appealed claims 1-22. The Section 103 rejection over
claims 1-22 is affirmed.
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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)(1)(iv).

AFFIRMED

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