Ex Parte Webb et al

Patent Trial and Appeal Board

Sep 18, 2012

11001700 (P.T.A.B. Sep. 18, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte PETER G. WEBB, CHARLES F. NELSON,
AMITABH SHUKLA, and MARYLINN MUNSON
__________

Appeal 2011-005635
Application 11/001,700
Technology Center 1600
__________

Before DONALD E. ADAMS, LORA M. GREEN, and
FRANCISCO C. PRATS, Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims to a system and
method for producing polynucleotide array layouts. The Examiner entered
rejections for obviousness.
We have jurisdiction under 35 U.S.C. § 6(b). We reverse.

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STATEMENT OF THE CASE
Claims 1-5, 7-12, 15-18, 20, 28-30, and 41-43 stand rejected and
appealed (App. Br. 3).
1
Claims 1 and 41, the independent claims, illustrate
the appealed subject matter and read as follows:
1. A system for producing an array layout, said system
comprising:
(a) an input manager for receiving array request information
from one or more users;
(b) a processing module comprising:
(i) an array layout developer having a memory
comprising a plurality of rules relating to array
layout design, wherein said array layout developer
is configured to develop one or more array layout
versions based on the application of one or more of
the rules to information that includes the array
request information received from the one or more
users;
(ii) an array customizing manager configured to allow
said array layout developer to develop an array
layout that includes a first set of probe sequences
provided by a first user and a second set of probe
sequences provided by an additional party,
wherein said second set of probe sequences is
approved by the first user; and
(iii) a differencing engine for comparing a first of said
one or more array layout versions to one or more
second array layouts; and
(c) an output manager for providing said first array layout
version and differences between said first array layout version and
said one or more second array layouts to the one or more users in a
user-readable format.

41. A computer program product comprising a computer
readable storage medium having a computer program stored thereon,

1
Appeal Brief entered August 20, 2010.
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wherein said computer program, when loaded onto a computer,
controls said computer to:
(a) receive chemical array request information from one or
more users;
(b) develop an array layout based on said received
information by applying one or more array layout design rules to said
received information;
(c) include in the array layout a first set of probe sequences
provided by a first user and a second set of probe sequences provided
by an additional party, wherein said second set of probe sequences is
approved by the first user;
(d) compare said array layout to one or more second array
layouts; and
(e) provide said array layout and differences between said
array layout and said one or more second array layouts to the one or
more users in a user-readable format.

The following rejections are before us for review:
(1) Claims 1, 2, 4, 5, 7-12, 15-18, 28, 29, and 41-43, under 35 U.S.C.
§ 103(a) as obvious over Schena
2
and Markowitz
3
(Ans. 4-9);
(2) Claim 20, under 35 U.S.C. § 103(a) as obvious over Schena,
Markowitz, and Zhou
4
(Ans. 9-10); and
(3) Claims 3 and 30, under 35 U.S.C. § 103(a) as obvious over
Schena, Markowitz, and Cuticchia
5
(Ans. 10-12).

2
Mark Schena et al., Parallel human genome analysis: Microarray-based
expression monitoring of 1000 genes, 93 PROC. NATL. ACAD. SCI. USA
10614-10619 (1996).
3
U.S. Patent App. Pub. No. 2003/0009295 A1 (published January 9, 2003).
4
U.S. Patent App. Pub. No. 2003/0120432 A1 (published June 26, 2003).
5
A.J. Cuticchia et al., CMAP: contig mapping and analysis package, a
relational database for chromosome reconstruction, 8 CABIOS 467-474
(1992).
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DISCUSSION
The Examiner found that, as to claim 1, Schena‟s “Figures 1A, 1 B,
and 2A represent the first array layout, the second array layout, and
differences between the first and second array layouts, respectively, in user
readable formats” (Ans. 5). The Examiner thus found that Schena differed
from claim 1 in that Schena did not “teach the computer limitations of the
instant claim (i.e. input manager and output manager)” and also did not
“teach user(s) or that the second probe set is provided by an additional party
and is approved by a user” (id.).
To address those deficiencies, the Examiner cited Markowitz as
describing “a system and method for retrieving and using gene expression
data from multiple sources” (id. at 6). Specifically, the Examiner found that
Markowitz discussed “the management of input data for the microarray
technologies,” the “management of output information,” the “different type
of users and each of their roles,” and the fact that “some users (i.e. the
„administrator‟ users of paragraph 24) can give other users permission
(approval) to write and/or modify data” (id.).
The Examiner further noted, as to independent claim 41, “which
represent[s] the systems of claims 1 and 18 in „computer program product‟
form,” that Markowitz taught “their systems in computer program product
form” (id. at 8). Based on the references‟ teachings, the Examiner reasoned:
It would have been obvious to someone of ordinary skill
in the art at the time of the instant invention to modify the
plurality of array layouts and their comparisons in Schena et al.
by use of the multi-user, Internet accessible Interface of
Markowitz et al. wherein the motivation would have been that
the computerized limitations of Markowitz et al. facilitate the
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ability to acquire the appropriate data pertaining to array layout
with multiple users remotely [see cover figure and paragraph
176 of Markowitz et al.] Additionally, it would have been
obvious to add and modify the roles of the pluralities of users
and managers as taught in Markowitz et al. wherein the
motivation would have been to increase accessibility and
“hierarchical” control of the microarray data (see for example
paragraph 414 wherein it is possible to regulate the authorities
of users at various levels including users and administrators
with the rights to accept or refuse entries from the users).

(Id. at 9.)
It is well settled that, “[i]n proceedings before the Patent and
Trademark Office, the Examiner bears the burden of establishing a prima
facie case of obviousness based upon the prior art.” In re Fritch, 972 F.2d
1260, 1265 (Fed. Cir. 1992).
It is also well settled that, 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).
Here, we agree with Appellants that the Examiner has not made out a
prima facie case of obviousness as to independent claims 1 and 41. In
particular, we are not persuaded, as the Examiner argues (Ans. 12-13), that
an ordinary artisan would have reasonably interpreted the development of
array layouts as specified in claims 1 and 41 as being encompassed by the
experiments disclosed in Schena. Rather, we agree with Appellants that the
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Examiner‟s prima facie case is not based on a claim interpretation that an
ordinary artisan would consider reasonable in light of the Specification.
An ordinary artisan viewing claims 1 and 41 in light of the
Specification would have understood that Appellants‟ invention is directed
to the fabrication of polynucleotide arrays (see Spec. 3 (“As the use of
specialized array fabricators grows, there is continued interest in the
development of improved methods performing one or more aspects of the
interaction between a customer and array fabricator.”)).
Therefore, when claim 1 recites that its system includes an array
layout developer configured to develop one or more array layout versions
based on a set of rules, as well as array request information from one or
more users, an ordinary artisan would have interpreted the claim as requiring
the system to include a component that designates the ultimate position on
the array grid of each probe that will be attached to the array substrate:
By “array layout” is meant a collection of information,
e.g., in the form of a file, which represents the location of
probes that have been assigned to specific features of an array
format.
The phrase “array format” refers to a format that defines
an array by feature number, feature size, cartesian coordinates
of each feature, and distance that exists between features within
a given array.

(Spec. 8.) Claim 41 similarly requires its computer program product to
direct a computer to “develop an array layout based on said received
information by applying one or more array layout design rules to said
received information” (App. Br. 19).
As the Specification further explains, the rules to be used for
producing the array layouts are directed to parameters for determining which
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probe sequences are to be placed on which specific positions on the array
grid (see Spec. 4:7-27).
In contrast to producing two or more different array layouts which are
compared to each other, as specified in both claim 1 and 41, Figures 1A and
2A of Schena show the same array which has been hybridized to mRNA
from cells cultured under different conditions, heat shock and non-heat
shock (Schena 10615). As Schena explains, this comparison allows
identification of sequences that are differentially expressed in heat shock
conditions, as compared to normal culture conditions (see id. (“Comparative
expression analysis of heat shocked versus control cells in the two
experiments revealed 17 array elements that displayed altered fluorescence
ratios of ≥2.0-fold (Figs. 1 and 2A).”)).
Similarly, rather than being directed to generating array multiple
layouts and analyzing their differences, Markowitz is directed to systems for
analyzing the large amount of gene expression data generated by array
hybridization experiments:
Microarray technologies enable the generation of vast
amounts of gene expression data. Effective use of these
technologies requires mechanisms to manage and explore large
volumes of primary and derived (analyzed) gene expression
data. . . . The present invention uses data warehousing
methodology to manage and explore gene expression and
related data.

(Markowitz [0013].) Thus, we agree with Appellants that when Markowitz
discloses that its system can include “access permissions indicating which
users can read (view) the object, and access permission indicating which
users can write to (modify) the object” (id. at [0414]), an ordinary artisan
would not have understood Markowitz as teaching production of an array
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layout from a set of probe sequences provided by first and second users of
the system, with the sequences provided by the second user being approved
by the first user, as claims 1 and 41 require.
Therefore, as we agree with Appellants that an ordinary artisan
reasonably interpreting claims 1 and 41 in light of the Specification would
not have viewed Schena‟s hybridization experiments as being directed to
producing the array layouts required in the claims, and as Markowitz does
not remedy that shortcoming, we also agree with Appellants that the
Examiner has not made out a prima facie case of obviousness as to those
claims. Accordingly, we reverse the Examiner‟s obviousness rejection of
claims 1 and 41, and their dependents over Schena and Markowitz.
Moreover, as the Examiner does not point to any specific teachings in
either Zhou or Cuticchia that remedy the deficiencies discussed above as to
the combination of Schena and Markowitz, we also reverse the Examiner‟s
rejection of claim 20 over Schena, Markowitz, and Zhou, as well as the
Examiner‟s rejection of claims 3 and 30 over Schena, Markowitz, and
Cuticchia.

REVERSED

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