Ex Parte Webb

Board of Patent Appeals and Interferences

Mar 31, 2008

09772723 (B.P.A.I. Mar. 31, 2008)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte PETER G. WEBB
__________

Appeal 2008-0140
Application 09/772,723
Technology Center 1600
__________

Decided: March 31, 2008
__________

Before ERIC GRIMES, RICHARD M. LEBOVITZ, and JEFFREY N.
FREDMAN, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of generating an addressable array of biopolymers. The Examiner has
rejected the claims as obvious and as lacking an adequate written description
in the Specification. We have jurisdiction under 35 U.S.C. § 6(b). We
affirm.
BACKGROUND
“Arrays of biopolymers, such as arrays of peptides or polynucleotides
(such as DNA or RNA), are known and are used, for example, as diagnostic
or screening tools” (Spec. 1). In array fabrication, “it will often be desirable
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to have the arrays fabricated at a fabrication facility and then shipped to the
end user,” thus requiring “a customer to ship the various biopolymers used
to fabricate the array to the fabrication facility” (id.). “One convenient way
of supplying the biopolymers is in multiple 96 well trays,” although “[i]t
may not always be possible or desirable to deposit the biopolymers to form
the array in blocks of 96 due to limitations of the fabricating apparatus. In
such cases, it would be desirable if the customer … [had a] way of
correlating the biopolymers provided to the features of a fabricated array”
(id.).
The Specification discloses “a method of producing an addressable
array of biopolymers … on a substrate. … The method includes obtaining
the biopolymers from individual identified vessels” and depositing them
“onto different regions of the substrate so as to fabricate the array. A map of
the identity of the vessels to the corresponding regions of the substrate … is
saved in a memory in association with a map identifier. The map identifier
may be applied to the substrate or a housing carrying the substrate” (id. at 3).
DISCUSSION
1. CLAIMS
Claims 1-14 and 45-54 are pending and on appeal. Claims 1, 4, 45-
48, 53 and 54 are representative and read as follows:
Claim 1: A method of generating an addressable array of biopolymers
on a substrate, comprising:
(a) providing a plurality of individual vessels each containing a
biopolymer wherein said plurality is provided in a defined format;
(b) assigning a unique format identifier to each member of said
plurality;
(c) obtaining the biopolymers from the plurality of individual
identified vessels;
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(d) depositing the biopolymers onto different regions of the substrate
so as to fabricate the array;
(e) saving in a memory a map of the identity of the vessels to the
corresponding regions of the substrate onto which the biopolymers from
respective vessels are deposited, in association with a map identifier,
wherein said map of the identity of the vessels comprises a unique format
identifier of each vessel of said plurality;
(f) applying the map identifier to the substrate or a housing carrying
the substrate;
(g) shipping the fabricated array with applied map identifier to a
remote location.

Claim 4: A method according to claim 1 wherein the memory is a
database, the method additionally comprising obtaining the identity map
from the memory and communicating the identity map to a remote location
in response to receiving a communication of the map identifier from the
remote location.

Claim 45: The method according to Claim 1, wherein said plurality of
individual identified vessels is in a format of a tray with multiple wells.

Claim 46: The method according to Claim 45, wherein said multiple
wells are arranged in said tray in rows and columns.

Claim 47: The method according to Claim 46, wherein said
individual identity of each vessel is an identifier in the format of: tray
number, column number and row number.

Claim 48: The method according to Claim 46, wherein said
individual identity of each vessel is an identifier assigned to each vessel
relative to a reference mark.

Claim 53: The method according to Claim 1, said method
additionally comprising receiving said array and map identifier and using
said map identifier to identify vessels corresponding to regions of the array.

Claim 54: A method of generating an addressable array of
biopolymers on a substrate, comprising:
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(a) obtaining the biopolymers from a plurality of individual identified
vessels, wherein each of said vessels is marked with a unique identifier that
is not composition information from that vessel;
(b) depositing the biopolymers onto different regions of the substrate
so as to fabricate the array;
(c) saving in a memory a map of the identity of the vessels to the
corresponding regions of the substrate onto which the biopolymers from
respective vessels are deposited, in association with a map identifier,
wherein said map of the identity of the vessels comprises an individual
identity of each vessel of said plurality;
(d) applying the map identifier to the substrate or a housing carrying
the substrate; and
(e) shipping the fabricated array with applied map identifier to a
remote location.

2. WRITTEN DESCRIPTION
Claim 54 stands rejected under 35 U.S.C. § 112, first paragraph, on
the basis that it lacks adequate written description in the Specification. The
Examiner finds that, “[b]ecause there is a lack of written basis for the phrase
‘wherein each of said vessels is marked with a unique identifier that is not
composition information from that vessel’ as stated in claim 54, this
amended limitation is considered to be NEW MATTER” (Ans. 4).
Appellant argues that throughout the Specification, the unique
identifier is described “as specifically marking an individual vessel from the
plurality of vessels provided” (Appeal Br. 11). Appellant further argues that
the Specification (citing p. 10, ll. 17-22) and the exemplary embodiment
shown in Table 1 of the Specification (p. 11) make “clear that the unique
identifier is an identifying mark with respect to the specific location of a
specific vessel, e.g., ‘tray number, column number, row number,’” and “that
the unique identifier does not include compositional information from the
vessel itself” (Appeal Br. 11-12).
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The purpose of the written description requirement is to “ensure that
the scope of the right to exclude, as set forth in the claims does not
overreach the scope of the inventor’s contribution to the field as far as
described in the patent specification.” Reiffin v. Microsoft Corp., 214 F.3d
1342, 1345 (Fed. Cir. 2000). To that end, to satisfy the written description
requirement, the inventor “must convey with reasonable clarity to those
skilled in the art that, as of the filing date sought, he or she was in possession
of the invention.” Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed.
Cir. 1991). “One shows that one is ‘in possession’ of the invention by
describing the invention, with all its claimed limitations.” Lockwood v.
American Airlines, 107 F.3d 1565, 1572 (Fed. Cir. 1997).
We agree with Appellant that the Specification provides adequate
descriptive support for the disputed limitation. The Specification discloses
in the embodiment shown in Table 1 (Spec. 11) that the vessel identifiers are
the tray, column, and row number of the microtitre plate in which the
samples were provided and do not contain composition information (see also
Spec. 10: 20-24). Given this description of the vessel identifiers, we
conclude that the written description of the invention, as originally filed,
conveys to those of skill in the art that the inventor was in possession of the
claimed invention at the time the application was filed.
The rejection of claim 54 under 35 U.S.C. § 112, first paragraph, on
the basis of lack a written description in the specification is reversed.
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3. OBVIOUSNESS
Claims 1-14 and 45-54 stand rejected under 35 U.S.C. § 103(a) as
obvious in view of Hunkapiller1, Zeleny2, Brown3, Anderson4, Shakib5, and
Balaban6.
Appellant has argued the claims in eight groups as follows: (i) claims
1-3 and 8-10; (ii) claims 4-7 and 11-14; (iii) claims 45 and 49; (iv) claims 46
and 50; (v) claims 47 and 51; (vi) claims 48 and 52; (vii) claim 53; and (viii)
claim 54. The claims in each group stand or fall together (37 C.F.R.
§ 41.37(c)(1)(vii)).
The Examiner relies on Hunkapiller as disclosing the creation of
“arrays with addressable locations where multiple biopolymer samples can
be fixed or mounted in fixed locations” and that liquid reagents are
“delivered from vessels to solid supports … which include addressable
arrays … which represents obtaining and providing a plurality of individual
vessels” (Ans. 5). The Examiner also finds that Hunkapiller discloses
“placing vessels in cooling/heating zones, such as heating blocks … which
represents providing a plurality of vessels in a defined format” (id.).
The Examiner finds that Hunkapiller does not describe “saving in a
memory a map of the identity of the vessels corresponding to substrate
regions where the biopolymers are deposited, applying the map identifier to
the substrate or housing carrying the substrate, or shipping the fabricated

1 Hunkapiller et al., US 5,942,609, Aug. 24, 1999
2 Zeleny et al., US 6,215,894 B1, Apr. 10, 2001
3 Brown et al., US 5,807,522, Sep. 15, 1998
4 Anderson, US 6,456,942 B1, Sep. 24, 2002
5 Shakib et al., US 5,812,793, Sep. 22, 1998
6 Balaban et al., US 6,229,911 B1, May 8, 2001
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array with applied map identifier to a remote location” (id.) as recited in
claim 1.
The Examiner relies on Zeleny for disclosing “an identifier
corresponding to each experiment imprinted on [a] biochip” (Answer 5) and
“a computer-stored record corresponding to each identifier” (id. at 6). The
Examiner also finds that Zeleny discloses that the computer-stored record
may contain “various parameters of the experimental array including a map
of the reagents deposited in the array” (id.).
The Examiner relies on Brown as disclosing the “mass fabrication of
microarrays . . . and shipment of DNA reagents via microarrays to
researchers” (id.).
The Examiner relies on Anderson for disclosing “a server that designs
a set of probes to capture target sequences requested by a user, a synthesizer
(fabrication station) that builds the probes on the surface of an array, and a
chip that is shipped to a user” (id.). The Examiner relies on Balaban and
Shakib for disclosing limitations of dependent claims (id. at 6-8).
The Examiner concludes that it “would have been obvious to one of
ordinary skill in the art at the time of the invention to add automated
techniques, beginning with the automated delivery of liquid reagents from
vessels to the array, as stated by Hunkapiller … using barcode identifiers
and mapping reagent location as stated by Zeleny” (id. at 8). The Examiner
finds that the skilled artisan would have been motivated to do so in order to
avoid unnecessary error and to speed efficiency because Zeleny discloses
that the “analysis of raw data from a biochip array collected by a scanner
was previously performed manually which involved significant operator
time as well as errors in the scanning and analysis procedure” (id.).
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Finally, the Examiner concludes that it “would have been further
obvious to the person of ordinary skill in the art to mass fabricate and ship
the completed microarrays” as disclosed by Brown because one would be
motivated by the desire of researchers to perform numerous genetic
applications including genome mapping and medical diagnosis, as disclosed
by Brown (id.).
We conclude that the Examiner has set forth a prima facie case that
claim 1 would have been obvious to the ordinary artisan. Hunkapiller
teaches methods of making addressable arrays of biopolymers (Hunkapiller,
col. 3, ll. 35-47; col. 18, ll. 11-18). We agree with the Examiner that
Hunkapiller’s description of automated assembly, including placing reaction
vessels in “cooling/heating zones, e.g. heating blocks, ovens, chillers” (id. at
col. 17, ll. 52-66) describes a plurality of vessels in defined format, as
recited in claim 1.
Zeleny discloses that “[m]icroarray biochips are available in a variety
of form[s]” and that the “reagents involved in the chemical reactions in the
array dots are typically biological samples such as DNA, RNA, peptides,
proteins or other organic molecules” (Zeleny, col. 1, ll. 47-52). Zeleny also
discloses that an “experiment identifier is imprinted on the chip prior to the
deposition of the array experiment. A file folder (i.e., ‘directory’) is opened
in a computer system and is logically linked to the array identifier. An
operator may enter into that folder the various parameters of the experiment
array, e.g., a map of the reagents deposited in the array.” (Id. at col. 2, ll. 18-
24.)
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Brown discloses that an efficient prior art technique “for making
ordered arrays of genomic fragments uses an array of pins dipped into the
wells, e.g., the 96 wells of a microtitre plate, for transferring an array of
samples to a substrate” (Brown, col. 1, l. 64 to col. 2, l. 1). Brown also
discloses an automated “method and apparatus for forming microarrays of
biological samples on a support . . . involv[ing] dispensing a known volume
of a reagent at each selected array position, by tapping a capillary dispenser
on the support under conditions effective to draw a defined volume of liquid
onto the support” (id., abstract).
Anderson discloses “methods for interfacing computer technology
with biological and chemical processing and synthesis equipment”
preferably in a remote manner (Anderson, abstract). Anderson also
discloses that, in one embodiment, “a user submits a list of target sequences
of interest through a network server; the server designs a set of probes to
capture the target sequences and submit that list of probes to the synthesizer;
the synthesizer builds the probes on the surface of an array; [and] the chip is
shipped to the user” for performance of a hybridization experiment (id. at
col. 2, ll. 57-63).
We agree with the Examiner that it would have been prima facie
obvious to one of skill in the art to combine the teachings of Hunkapiller,
Zeleny, Brown, and Anderson and thereby arrive at the invention of claim 1.
Hunkapiller discloses method of making an addressable array of
biopolymers using vessels in a defined format. Zeleny discloses imprinting
an identifier on the biochip, and creating a computer record corresponding to
the identifier (e.g., a map of the reagents deposited in the array). Brown
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discloses that microtitre plates are known for use in the fabrication of arrays,
where the contents of each well in a microtitre plate corresponds to a single
spot on an array.
In view of the teaching in Brown of the one-to-one correspondence
between wells of a microtitre plate and spots on an array and the teachings
of Zelany, one of skill in the art would have considered it obvious to store in
a computer record a map of reagents deposited on an array that refers to the
microtitre wells (i.e., tray number and column and row number) from which
the reagents in each spot were obtained. The cited references show that the
other steps recited in claim 1 – fabricating an array (e.g., Hunkapiller,
Brown), applying a map identifier to a substrate (Zelany), and shipping a
fabricated array (e.g., Brown) – are conventional in the art.
Appellant argues that there is no teaching or suggestion in the
combination of cited references of the element of assigning unique format
identifiers to a plurality of source vessels and saving in a memory a map of
the unique format identifiers and corresponding substrate regions (Appeal
Br. 17). Appellant further argues that the instantly claimed “unique format
identifier” is distinguishable from Zeleny's “experiment identifier” because
the vessel identifier is the unique format identifier assigned to the original
vessel prior to fabrication of the array (id. at 19).
We are not persuaded by this argument. It is true that none of the
cited references expressly suggest that the map of the reagents deposited on
the array is a map of the source vessel unique format identifiers and
corresponding substrate regions, but the prior art need not expressly suggest
an invention in order to have made it obvious. “[T]he ‘motivation-
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suggestion-teaching’ test asks not merely what the references disclose, but
whether a person of ordinary skill in the art, possessed with the
understandings and knowledge reflected in the prior art, and motivated by
the general problem facing the inventor, would have been led to make the
combination recited in the claims.” In re Kahn, 441 F. 3d 977, 988 (Fed.
Cir. 2006). See also KSR Int’l Co. v. Teleflex Inc., 127 S.Ct. 1727, 1741
(2007) (The obviousness analysis “can take account of the inferences and
creative steps that a person of ordinary skill in the art would employ.”).
Zeleny teaches a computer-stored map of the reagents on an array and
Brown teaches a one-to-one correspondence between material transferred
from microtitre wells to spots on an array. In addition, it is well known in
the art that microtitre plates typically contain unique identifiers for each well
of a particular tray such as column and row number. Based on these
teachings and the knowledge of those skilled in the art, the claimed feature
of assigning unique format identifiers to a plurality of source vessels and
saving in a memory a map of the source vessel identifiers for each
corresponding substrate region would have been obvious to a person skilled
in the art for the reasons stated by the Examiner (Ans. 8).
With respect to claim 4, Appellant argues that the claim further
specifies “additional features relating to saving the identity map in a memory
and communicating the identity map to a remote location” (Appeal Br. 20).
Appellant argues that “because the cited references fail to teach or suggest
saving in a memory a map of the unique format identifiers assigned to each
original source vessel as is claimed, (discussed above), they likewise fail to
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teach or suggest the additional features relating to saving the identity-map in
a memory and communicating the identity map to a remote location” (id.).
We are not persuaded by this argument. As discussed above, we find
that the references suggest saving in a memory a map of the unique format
identifiers assigned to each original source vessel. Further, in view of the
Anderson’s disclosure of methods for remotely interfacing computer
technology with biological and chemical processing and synthesis, and
communicating via a network server, one of skill in the art would have
considered the claimed feature of “obtaining the identity map from the
memory and communicating the identity map to a remote location in
response to receiving a communication of the map identifier from the remote
location” to be obvious because of the advantages described by Anderson
(see Ans. 10).
With respect to claims 45-47, Appellant argues that “the references
neither teach nor suggest a method wherein the plurality of individual
identified vessels is in a format of a tray with multiple wells” (Appeal Br.
21) (claim 45), or that the “multiple wells are arranged in said tray in rows
and columns” (id.) (claim 46), or that the “individual identity of each vessel
is an identifier in the format of: tray number, column number and row
number” (id., emphasis deleted) (claim 47).
We are not persuaded by this argument. As discussed above, Brown
specifically discloses that reagent samples for array formation may be
transferred from microtitre wells to a substrate to form the array. Microtitre
plates are well known in the art to contain markings to identify each well,
such as by column and row letters and numbers. Thus, one of skill in the art
would have considered the additional features recited in claims 45-47 to be
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obvious in view of the cited references because multiple wells with rows and
columns were conventional formats from which reagents are dispensed.
With respect to claim 48, Appellant further argues that the references
do not teach or “suggest a method wherein the individual identity of each
vessel is an identifier assigned to each vessel relative to a reference mark”
(Appeal Br. 22).
We are not persuaded by this argument. For any given microtitre
plate, the identity for each well (i.e. vessel) would be assigned relative to
reference marks of the column number and row number assigned to the first
well, i.e. the well at column 1, row 1. Thus, one of skill in the art would
have considered the claimed feature that the “individual identity of each
vessel is an identifier assigned to each vessel relative to a reference mark” to
be obvious in view of the cited references.
With respect to claim 53, Appellant further argues that cited
references do not teach or suggest the claimed limitation of “additionally
comprising receiving said array and map identifier and using said map
identifier to identify vessels corresponding to regions of the array” (Appeal
Br. 23).
We do not find this argument to be persuasive. Anderson specifically
teaches that an array formed at a fabrication site is shipped to the user for
hybridization experiments, and thus Anderson clearly teaches the claimed
limitation.
With respect to claim 54, Appellant further argues that the claim
requires “that each of the individual identified vessels is marked with a
unique identifier that is not composition information from that vessel” and
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that the cited references neither teach nor suggest this limitation (Appeal Br.
23-24).
This argument is also not persuasive. As discussed above, Brown
teaches that it is known in the art to transfer array reagents from microtitre
wells to array substrates, and it is well known in the art that microtitre plates
are typically marked with row and column numbers to indicate a specific
identity for each well. Thus, the claimed limitation is clearly suggested by
the cited references.
SUMMARY
The Examiner’s obviousness rejection is supported by the
preponderance of the evidence of record. We therefore affirm the rejection
of claims 1-14 and 45-54 under 35 U.S.C. § 103. However, we reverse the
rejection of claim 54 under 35 U.S.C. § 112, first paragraph.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED

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