Ex Parte Some et al

Board of Patent Appeals and Interferences

Aug 26, 2009

10184982 (B.P.A.I. Aug. 26, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte MASATO SOME, KATSUAKI MURAISHI,
HITOSHI SHIMIZU, NOBUHIKO OGURA,
TOHRU TSUCHIYA, and HIROHIKO TSUZUKI
__________

Appeal 2009-000089
Application 10/184,982
Technology Center 1600
__________

Decided: August 26, 2009
__________

Before TONI R. SCHEINER, RICHARD M. LEBOVITZ, and
STEPHEN WALSH, Administrative Patent Judges.

SCHEINER, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal under 35 U.S.C. § 134 from the rejection of claims
1, 2, 7-9, and 84-88, directed to a biochemical analysis system. We have
jurisdiction under 35 U.S.C. § 6(b).
We affirm.

Appeal 2009-000089
Application 10/184,982

STATEMENT OF THE CASE
Appellants’ invention “relates to a biochemical analysis system,
wherein a structure or characteristics of an organism-originating substance
are analyzed by use of a biochemical analysis unit” (Spec. 1: 7-10).
According to the Specification, “a first identification information” is
associated with the biochemical analysis unit (a base plate spotted with
specific binding substances); a “second identification information” is
associated with the organism-originating substance (the object of the
analysis); and a “first correspondence relationship specifying means”
acquires the first and second identification information and establishes a
“correspondence relationship between the organism-originating substance
. . . and the biochemical analysis unit” (id. at 7: 8-10; 12: 12-16 and 22-25;
14: 2-6), without “the risk that an error will occur due to a mistake made in
memorization or inputting” (id. at 7: 22-23).
Claim 1 is representative of the subject matter on appeal:
1. A biochemical analysis system, comprising:

i) specific binding means for:
obtaining a biochemical analysis unit, and
subjecting an organism originating substance to selective
specific binding to multiple kinds of specific binding substances,
the biochemical analysis unit further comprising a base plate
and a plurality of spot-shaped regions and a first identification
information that uniquely identifies the biochemical unit,
the plurality of spot-shaped regions being located at different
positions on the base plate,
each of the multiple kinds of specific binding substances being
capable of specifically binding to organism-originating substances and
being fixed to one of the spot-shaped regions,
structures and characteristics of the specific binding substances
being known,
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the organism-originating substance having a second
identification information that uniquely identifies the organism-
originating substance and having been labeled with at least one
labeling substance selected from the group consisting of a radioactive
labeling substance, a fluorescent labeling substance, and a labeling
substance capable of producing chemiluminescence when being
brought into contact with a chemiluminescence substrate,
thereby selectively labeling at least one spot-shaped region
among the plurality of the spot-shaped regions of with the labeling
substance,

ii) label signal forming means for receiving the biochemical analysis
unit, which has been processed by the specific binding means, and forming a
label signal, the label signal corresponding to a position of the at least one
spot-shaped region having been selectively labeled with the labeling
substance,

iii) read-out means for reading the label signal, in order to form data
for a biochemical analysis, and

iv) analysis means for executing a biochemical analysis based on the
data for a biochemical analysis,

wherein the biochemical analysis system further comprises:

a first correspondence relationship specifying means for acquiring the
first identification information of the biochemical analysis unit and the
second identification information of the organism-originating substance, and
feeding the first and the second identification information into the analysis
means to establish a relationship between the first and the second
identification information.

The Examiner relies on the following evidence:
Beattie US 5,843,767 Dec. 1, 1998
Fodor et al. US 5,925,525 Jul. 20, 1999
Cattell US 6,180,351 B1 Jan. 30, 2001
Lockhart et al. WO 97/10365 Mar. 20, 1997
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The Examiner rejected the claims as follows:
(A) Claims 1, 7, and 9 under 35 U.S.C. § 102(b) as anticipated by
Lockhart.

(B) Claims 84, 86, and 88 under 35 U.S.C. § 102(b) as anticipated by
Lockhart.

(C) Claims 1 and 7-9 under 35 U.S.C. § 103(a) as unpatentable over
Cattell and Fodor.

(D) Claims 84 and 86-88 under 35 U.S.C. § 103(a) as unpatentable over
Cattell and Fodor.

(E) Claim 2 under 35 U.S.C. § 103(a) as unpatentable over Cattell, Fodor,
and Beattie.

(F) Claim 85 under 35 U.S.C. § 103(a) as unpatentable over Cattell,
Fodor, and Beattie.

ANTICIPATION
Issues (A) and (B)
The Examiner rejected claims 1, 7, and 9 as anticipated by Lockhart
(Ans. 3-4; rejection (A)), and also rejected claims 84, 86, and 88 as
anticipated by Lockhart in a second, similar rejection (Ans. 5-7; rejection
(B)). Appellants address the two rejections as one, and don’t present
separate arguments for the claims subject to the rejections. We select claim
1 as representative. 37 C.F.R. § 41.37(c)(1)(vii) (2006).
Appellants contend that Lockhart’s biochemical analysis system lacks
a biochemical analysis unit with “a unique first identification information,”
as well as “any explicit or inherent disclosure for a relationship establishing
mean[s] for establishing a correlation between a unique first identification
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information coming from the biochemical analysis unit and a unique second
identification information coming from the organism-originating substance”
(App. Br. 14).
The Examiner finds that the word “MUR-1” on one of Lockhart’s
microarrays uniquely identifies the microarray (Ans. 6-7), and further finds
that Lockhart’s computer system is a means for establishing a relationship
between the uniquely identified microarray and the uniquely identified
sample (i.e., organism-originating substance) hybridized to it (id. at 25).
The issue raised by both rejections is whether Appellants have
established that the Examiner erred in finding that Lockhart describes a
biochemical analysis unit with unique “first identification information,” an
organism-originating substance with unique “second identification
information,” and a relationship specifying means to establish a relationship
between the first and second identification information.
Findings of Fact
The Invention
FF1 Appellants claim a biochemical analysis system with several
components including: a “biochemical analysis unit” comprising “a first
identification information that uniquely identifies the biochemical unit”
(claim 1); a labeled organism-originating substance “having a second
identification information that uniquely identifies the organism-originating
substance” (id.); and “a first correspondence relationship specifying means
for acquiring the first identification information of the biochemical analysis
unit and the second identification information of the organism-originating
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substance . . . to establish a relationship between the first and the second
identification information” (id.).
FF2 The “biochemical analysis unit,” in addition to the “first
identification information,” comprises a base plate and a plurality of spot-
shaped regions (claim 1).
FF3 Multiple kinds of specific binding substances, of known
structure and characteristics, “capable of specifically binding to organism-
originating substances,” are individually fixed to different spot-shaped
regions on the biochemical analysis unit (claim 1).
FF4 The Specification states that examples of specific binding
substances fixed to the biochemical analysis unit include “hormones, tumor
markers, enzymes, antibodies, antigens, abzymes, other proteins, nucleic
acids, cDNA’s, DNA’s, and mRNA’s” (Spec. 2: 7-8).
FF5
[T]he term “identification information of a biochemical analysis
unit” . . . means the information directly or indirectly
representing the information concerning the biochemical
analysis unit . . . . Examples of the identification information of
the biochemical analysis unit include the information
representing the positions of the spot-shaped regions on the
biochemical analysis unit, and the information representing the
kinds of specific binding substances which form the spot-
shaped regions . . . [i.e.] the constitution information of the
biochemical analysis unit.

(Spec. 12: 22 to 13: 12.) “[T]he identification information . . . may be the ID
number, which indirectly represents the constitution information” (id. at 13:
18-20), or “the constitution information itself of the biochemical analysis
unit may be employed as the identification information” (id. at 13: 24-26).
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FF6 The organism-originating substance, i.e., “the object of the
analysis” (Spec. 7: 4-5), “referred to also as the sample” (id. at 14: 5), is
“sampled from an organism through extraction, isolation, or the like . . .
[and] labeled” (Spec. 2: 9-12). Examples are said to include “hormones,
tumor markers, enzymes, antibodies, antigens, abzymes, other proteins,
nucleic acids, cDNA’s, DNA’s, and mRNA’s” (id. at 2: 19-21).
FF7
The term “identification information of an organism-originating
substance” . . . means the information with which the organism-
originating substance . . . is capable of being identified.
Examples of the identification information of the organism-
originating substance include the information, with which the
date of sampling of the sample, the name of the sampling object
(e.g., the patient . . . ), the site of the sampling object, and the
like, are capable of being specified.

(Spec. 14: 2-11.) “[T]he identification information of the organism-
originating substance may be the ID number of the sample, or the like,
which indirectly represents the sample specifying information of the
organism-originating substance” (id. at 14: 20-23).
Lockhart
FF8 Lockhart describes a system and method for monitoring the
expression levels of multiple target genes simultaneously “in a wide variety
of circumstances, including detection of disease, identification of differential
gene expression between two samples . . . and so forth” (Lockhart 24: 11-
20).
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FF9 Different oligonucleotide probes are bound to a planar substrate
to form a high density array (Lockhart 4: 13 to 5: 21), using a “spotting”
technique (id. at 49: 20).
FF10 The location and sequence of each different probe on the array
is known (Lockhart 23: 21-22).
FF11 A pool of labeled target nucleic acids, e.g., “mRNA isolated
from a biological sample, or cDNA made by reverse transcription of the
RNA” (Lockhart 7: 10-11), is hybridized to the array (id. at 4: 13 to 5: 21).
“The hybridization intensities indicate hybridization affinity between the
nucleic acid probes and the target nucleic acid (which corresponds to a
gene)” (id. at 57: 28-30).
FF12 Lockhart describes one particular array “that contains over
65,000 different oligonucleotide probes . . . for 118 [mostly murine] genes”
(Lockhart 78: 19-24). The array, clearly labeled “MUR-1,” is shown in
Lockhart’s Figure 5 after hybridization with a sample comprising RNA from
a murine B cell.
FF13 Lockhart teaches that gene expression monitoring “may be
performed utilizing a computer . . . [that] typically runs a software program
that includes computer code . . . for analyzing hybridization intensities
measured from a substrate or chip and thus, monitoring the expression of
one or more genes” (Lockhart 55: 24-28). The computer system includes a
CD-ROM drive, a system memory, and a hard drive “which may be utilized
to store and retrieve software programs incorporating computer code that
implements the invention, data for use with the invention, and the like” (id.
at 56: 6-8).
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FF14 Lockhart also teaches that the computer system “should have
available other details of the experiment including possibly the gene name,
gene sequence, probe sequences, probe locations on the substrate, and the
like” (Lockhart 57: 22-25).
FF15 The Examiner finds that Lockhart’s high density array is a
“biochemical analysis unit” (Ans. 3), and that the label “MUR-1” is “a first
identification information that uniquely identifies the biochemical unit” (id.
at 6, 22-23).
FF16 The Examiner further finds that Lockhart’s computer system
inherently establishes a “relationship between the first unique identification
means (the MUR-1) of the chip and the second unique identification means
(the identity of the mRNA)” (Ans. 23, 25).
Principles of Law
“To anticipate a claim, a prior art reference must disclose every
limitation of the claimed invention, either explicitly or inherently.” In re
Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997).
During examination, the PTO must interpret terms in a claim using
“the broadest reasonable meaning of the words in their ordinary usage as
they would be understood by one of ordinary skill in the art, taking into
account whatever enlightenment by way of definitions or otherwise that may
be afforded by the written description contained in the applicant’s
specification.” In re Morris, 127 F.3d 1048, 1054 (Fed. Cir. 1997).
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Analysis
Appellants contend that the claims “require[ ] the identification of
the unique information corresponding to the biological analysis unit (for
example, the identification number stored in the barcode in exemplary
embodiment of Figure 4) so that it can be fed to the analysis means by the
relationship specifying means” (App. Br. 12). Appellants contend that the
label “MUR-1” on Lockhart’s array “identifies a type of chip and not the
specific chip” (id.), and “falls far short of uniquely identifying a specific
biochemical unit” (id. at 13).
This argument is not persuasive. A barcode may be one example of
“a first identification information,” but it’s not the only one. The
Specification indicates that identification information may also comprise
“information representing the positions of the spot-shaped regions on the
biochemical analysis unit, and the information representing the kinds of
specific binding substances which form the spot shaped regions . . . [i.e.] the
constitution information of the biochemical analysis unit” (Spec. 12: 22 to
13: 12), and “the identification information of the biochemical analysis unit
may . . . indirectly represent[ ] the constitution information” (id. at 13: 18-
20), or “the constitution information itself of the biochemical analysis unit
may be employed as the identification information” (id. at 13: 24-26) (FF5).
Thus, the Specification teaches that the first identification information
may be “constitution information” representing the kinds of specific binding
substances on the array. “MUR-1” is a designation reflecting the constitution
of one of Lockhart’s arrays containing probes for certain, mostly murine
genes (FF12). Moreover, Appellants have not established that the MUR-1
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designation is not unique to the array described in Lockhart’s Example 3,
and depicted in Figure 5.
Appellants also contend that Lockhart lacks “any explicit or inherent
disclosure for a relationship establishing mean[s] for establishing a
correlation between a unique first identification information coming from
the biochemical analysis unit and a unique second identification information
coming from the organism-originating substance” (App. Br. 14).
This argument is not persuasive. Lockhart’s computer has available
the details of experiments including “the gene name, [and] gene sequence,”
i.e., identification information for the organism-originating substance, as
well as “probe sequences, probe locations on the substrate, and the like,” i.e.,
identification information for the biochemical analysis unit (FF14). The
results of the experiments (“The hybridization intensities indicat[ing]
hybridization affinity between the nucleic acid probes and the target nucleic
acid (which corresponds to a gene)” (FF11)) would be meaningless unless
the “details” stored in the computer included the identifying information for
both the array and the sample, and the computer could associate a particular
sample with a particular array.
We agree with the Examiner that Lockhart’s computer system is a
“correspondence relationship specifying means” which establishes a
relationship between the first identification information of the array (i.e., the
biochemical analysis unit) and the second identifying information of the
sample (the organism-originating substance).
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Conclusions of Law
Appellants have not established that the Examiner erred in finding that
Lockhart describes a biochemical analysis unit with unique “first
identification information,” an organism-originating substance with unique
“second identification information,” and a relationship specifying means to
establish a relationship between the first and second identification
information.

OBVIOUSNESS
Issues (C)-(F)
The Examiner rejected claims 1, 7, 9, 84, and 86-88 as unpatentable
over Cattell and Fodor (Ans. 7-10, 13-16; rejections (C) and (D)), and claims
2 and 85 as unpatentable over Cattell, Fodor, and Beattie (Ans. 10-13, 16-
19; rejections (E) and (F)). Appellants do not present separate arguments for
the claims subject to these rejections and we select claim 1 as representative.
37 C.F.R. § 41.37(c)(1)(vii) (2006).
Appellants contend that Cattell lacks the “second identification
information that uniquely identifies the organism-originating substance”
(i.e., the sample) as well as the “correspondence relationship specifying
means . . . to establish a relationship between the first and second
identification information” required by the claims.
The Examiner finds that Cattell discloses unique identifiers for an
array and a sample hybridized to it, and a means to establish a relationship
between the identifiers on the array and the sample, “in order to allow
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matching of the array layout information so as to ‘meaningfully interpret the
information obtained from . . . the array’” (Ans. 26).
The issue raised by all four of these rejections is whether Appellants
have established that the Examiner erred in concluding that a biochemical
analysis unit with unique “first identification information,” an organism-
originating substance with unique “second identification information,” and a
means for establishing a relationship between the first and second
identification information would have been obvious over the teachings of the
prior art.
Additional Findings of Fact
Cattell
FF17 Cattell describes a method and apparatus for generating a
custom made addressable array of biopolymers, e.g., DNA or RNA, “useful
in diagnostic, screening, gene expression analysis, and other applications”
(Cattell, col. 1, ll. 5-9).
FF18 Arrays are produced at a central fabrication station according to
layout information received from a remote user station, and then shipped to
the remote user station for testing (Cattell, col. 3, ll. 6-18).
FF19 Each array has a “unique identifier” (Cattell, col. 3, l. 10),
“often referred to as ‘Globally Unique Identifiers’ or ‘GUIDs’ or
‘Universally Unique Identifiers’ or ‘UUIDs’” (id. at col. 2, ll. 28-30), and a
“local identifier . . . which corresponds to the unique identifier and
associated array, the local identifier being shorter in length than the
corresponding unique identifier” to take up less space on the array (id. at col.
3, ll. 10-12). The unique identifier, the local identifier, and the layout
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information for the array “are stored in memory . . . in association with one
another” (id. at col. 11: 67 to col. 12, l. 17).
FF20 The remote user station comprises an apparatus that includes a
processor, computer memory, a bar code reader, a data writer/reader, a
scanner, and a communication module (Cattell, col. 10, ll. 5-29). Once the
remote user station receives an addressable array, the reader reads the local
identifier carried on the array, the processor retrieves the corresponding
unique identifier from memory (together with the associated layout
information), the array is exposed to a test sample, and the exposed array is
inserted into the scanner for interrogation (id. at col. 11, l. 62 to col. 12, l.
17).
FF21 “Following array interrogation, the test sample can be evaluated
for the presence of a target based on the results of the interrogation” (Cattell,
col. 12, ll. 27-29). “The results of the evaluation, or alternatively the
interrogation results (processed or raw data), could be forwarded to a remote
location for further evaluation and/or processing using [the] communication
[module] . . . or [the] reader/writer” (id. at col. 12, ll. 30-34).
Principles of Law
“The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results.”
KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007).
When there is a design need or market pressure to solve a
problem and there are a finite number of identified, predictable
solutions, a person of ordinary skill has good reason to pursue
the known options within his or her technical grasp. If this
leads to the anticipated success, it is likely the product not of
innovation but of ordinary skill and common sense. In that
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instance the fact that a combination was obvious to try might
show that it was obvious under § 103.

Id. at 421. It is proper to “take account of the inferences and creative steps
that a person of ordinary skill in the art would employ.” Id. at 418. See also
id. at 421 (“A person of ordinary skill is also a person of ordinary creativity,
not an automaton.”).
Analysis
Appellants concede that Cattell “suggests having a unique identifier
for a biochemical analysis unit which may be scanned both prior to and after
being subjected to a sample” (App. Br. 15), but contends “there is no
teaching or suggestion related to the second identification information
dealing with the organism-originating substance” or “a relationship
establishing means that establishes a correspondence between the second
identification information . . . and the first identification information related
to the biochemical analysis unit” (id.). Appellants contend that having “a
uniqueness to the identity of the samples does not mean that the information
equivalent to the first and the second identification is fed to a relationship
specifying means and a relationship thereby established” (Reply Br. 9).
Appellants contend that Fodor does not overcome these deficiencies (App.
Br. 16).
These arguments are not persuasive. The Specification teaches that
the identification information related to the organism-originating substance
can include “the date of sampling of the sample, the name of the sampling
object (e.g., the patient . . . ), the site of the sampling object, and the like”
(FF7). These are nothing more than conventional labeling practices. It
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would have been obvious for one skilled in the art to assign such a label to a
sample, especially a diagnostic sample, prior to analysis, even in the absence
of explicit instructions to do so. Moreover, Cattell teaches that “[t]he results
of the evaluation, or alternatively the interrogation results (processed or raw
data), could be forwarded to a remote location for further evaluation and/or
processing using [the] communication [module] . . . or [the] reader/writer”
(FF21). Clearly, the forwarded results would be meaningless unless the
information stored in the computer included the identifying information for
the array and for the sample, and the computer could associate a particular
sample with a particular array.
We agree with the Examiner that the apparatus at Cattell’s remote
user station includes a “correspondence relationship specifying means”
which establishes a relationship between the first identification information
of the array (i.e., the biochemical analysis unit) and the second identifying
information of the sample (the organism-originating substance).
Conclusions of Law
Appellants have not established that the Examiner erred in concluding
that a biochemical analysis unit with unique “first identification
information,” an organism-originating substance with unique “second
identification information,” and a means for establishing a correlation
between the first and second identification information would have been
obvious over the teachings of the prior art.
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SUMMARY
(A) The rejection of claims 1, 7, and 9 under 35 U.S.C. § 102(b) as
anticipated by Lockhart is affirmed.

(B) The rejection of claims 84, 86, and 88 under 35 U.S.C. § 102(b) as
anticipated by Lockhart is affirmed.

(C) The rejection of claims 1 and 7-9 under 35 U.S.C. § 103(a) as
unpatentable over Cattell and Fodor is affirmed.

(D) The rejection of claims 84 and 86-88 under 35 U.S.C. § 103(a) as
unpatentable over Cattell and Fodor is affirmed.

(E) The rejection of claim 2 under 35 U.S.C. § 103(a) as unpatentable over
Cattell, Fodor, and Beattie is affirmed.

(F) The rejection of claim 85 under 35 U.S.C. § 103(a) as unpatentable
over Cattell, Fodor, and Beattie is affirmed.

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with this
appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv)(2006).

AFFIRMED

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