Ex Parte Chang et al

Board of Patent Appeals and Interferences

Sep 1, 2010

11332547 (B.P.A.I. Sep. 1, 2010)

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.
11/332,547 01/12/2006 Howard Yuan-Hao Chang STAN-367 (S03-278) 5704
77974 7590 09/01/2010
Stanford University Office of Technology Licensing
Bozicevic, Field & Francis LLP
1900 University Avenue
Suite 200
East Palo Alto, CA 94303
EXAMINER
AEDER, SEAN E
ART UNIT PAPER NUMBER
1642
MAIL DATE DELIVERY MODE
09/01/2010 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte HOWARD YUAN-HAO CHANG, JULIE SNEDDON,
and PATRICK O. BROWN
__________

Appeal 2010-003626
Application 11/332,547
Technology Center 1600
__________

Before CAROL A. SPIEGEL, FRANCISCO C. PRATS, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of classifying a human carcinoma. The Examiner has rejected the claims as
non-enabled. We have jurisdiction under 35 U.S.C. § 6(b). We reverse.

1 The two-month time period for filing an appeal or commencing a
civil action, as recited in 37 C.F.R. § 1.304, or for filing a request
for rehearing, as recited in 37 C.F.R. § 41.52, begins to run from
the “MAIL DATE” (paper delivery mode) or the
“NOTIFICATION DATE” (electronic delivery mode) shown on
the PTOL-90A cover letter attached to this decision.
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Application 11/332,547

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Statement of the Case
The Claims
Claims 1, 2, 4, 9, 10, and 13-18 are on appeal. The claims are not
argued separately and therefore stand or fall together. 37 C.F.R.
§ 41.37(c)(1)(vii). Claim 1 is representative and can be found in the
evidence appendix.
The issue
The Examiner rejected claims 1, 2, 4, 9, 10, and 13-18 under 35
U.S.C. § 112, first paragraph as based on a disclosure which is not enabling
(Ans. 3-5).
The Examiner finds that the “polynucleotide sequences of the recited
genes, defined by UniGene cluster numbers in the specification, are critical
or essential to the practice of the invention, but not included in the claim(s)
is not enabled by the disclosure” (id. at 3). The Examiner finds that:
one of skill in the art would recognize that UniGene cluster
numbers can be “retired” and changed. Upon retirement of a
UniGene cluster number, the sequence associated with a
UniGene cluster number becomes unavailable and one of
skill would not know how to design primers specific for
mRNA of a gene defined by said retired UniGene cluster
number. Further, if a Unigene cluster number sequence is
changed, new matter would be introduced which would
change the claimed invention.

(Id. at 5.) The Examiner distinguishes Capon v. Eshhar, 418 F.3d 1349
(Fed. Cir. 2005), finding that in “contrast to claims involving broad genera
of sequences encoding polypeptides well-known in the art and defined by
function, the instant claims utilize specific sequences defined by public
databases and are not well-known in the art” (id. at 9).
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Appellants contend that the “genes are identified in the specification
at pages 17 and 61 in tables that provide four different art-recognized
identifiers for each genetic sequence. The identifiers include the Image
Clone ID name (ClonelD), a UniGene Cluster ID number (UG Cluster), a
gene name (Name), and a gene symbol (Symbol)” (App. Br. 8). Appellants
contend that:
one of skill in the art is familiar with public databases and
with identifiers that are used in such public databases,
particularly the databases that are a service of the U.S.
National Library of Medicine and the National Institutes of
Health. Such identifiers are standardized in the art, and are
widely used in the art to reference polynucleotide sequences
of interest, for example by searching any one of many
publicly available databases for a gene symbol, gene name,
clone ID or UG cluster, as provided in the tables in the
specification.

(Id.)
The issues with respect to this rejection are: Does the evidence of
record support the Examiner’s conclusion that the claims are not enabled
because the polynucleotide sequences of the listed genes are defined by
UniGene cluster numbers in the Specification rather than by their complete
nucleotide sequence?
Findings of Fact
1. The Specification teaches a list of “significantly upregulated
genes” with a gene name, a gene ID, and scores in the assay (see, e.g., Spec.
17).
2. The Examiner finds that UniGene clusters can be retired, but
that “[u]sing a retired cluster number (Hs.######) in UniGene’s search tool
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will generate a page with links to the current clusters for the sequences”
(Ans. 5).
Principles of Law
Falko-Gunter teaches that “we hold that where, as in this case,
accessible literature sources clearly provided, as of the relevant date, genes
and their nucleotide sequences (here ‘essential genes’), satisfaction of the
written description requirement does not require either the recitation or
incorporation by reference (where permitted) of such genes and sequences.”
Falko-Gunter Falkner v. Inglis, 448 F.3d 1357, 1368 (Fed. Cir. 2006).
Analysis
We recognize the Examiner’s concern regarding the potential
uncertainty in determining what sequences are encompassed by the
disclosure of UniGene clusters in the Specification.
However, in Falko-Gunter, the Federal Circuit addressed a claim to a
poxvirus vaccine and commented that “[w]e note, in addition, that Inglis did
not attempt to incorporate by reference any literature that described the DNA
sequence of the poxvirus genome and the locations of the ‘essential
regions.’” Id. at 1367. Falko-Gunter continued that “[h]owever, it is the
binding precedent of this court that Eli Lilly does not set forth a per se rule
that whenever a claim limitation is directed to a macromolecular sequence,
the specification must always recite the gene or sequence, regardless of
whether it is known in the prior art.” Id.
Falko-Gunter concluded that “we hold that where, as in this case,
accessible literature sources clearly provided, as of the relevant date, genes
and their nucleotide sequences (here ‘essential genes’), satisfaction of the
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written description requirement does not require either the recitation or
incorporation by reference (where permitted) of such genes and sequences.”
Id. at 1368.
Thus, applying the logic of Falko-Gunter to the instant situation, there
is no dispute that accessible literature sources, specifically Genbank, provide
the nucleotide sequence of the genes at issue (FF 1). It is also clear that
entry of a “retired” cluster number will still function to obtain the sequence,
but that an additional step of linking to the new cluster number will be
required (FF 2). We conclude that Falko-Gunter supports the position of
Appellants that incorporation of the specific nucleic acid sequences is not
required.
The Examiner acknowledges that the “state of the art with respect to
human genetic sequence information with respect to public databases is very
high” (Ans. 9) but then contends that after “retirement of a UniGene cluster
number, one of skill would not know how to design primers specific for
mRNA of a gene defined by said retired UniGene cluster number” (id.).
We are not persuaded. We agree with the Appellants that “such effort
on the part of one of ordinary skill in the art is routine in the art” (App. Br.
9). Entry of a UniGene number into Genbank is routine, and recognition
that if the UniGene number is changed, a single link will identify the new
UniGene number for the gene. For example, the very first UniGene name on
page 17, Hs.77152 (identified as the MCM 7 gene) is identified as retired at
the NCBI website.2 However, clicking on that link brings up the current
entry as Hs.438720 which is also identified as the MCM7 gene and which

2 http://www.ncbi.nlm.nih.gov/unigene?term=hs.77152
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provides links to protein and nucleic acid sequences for the MCM7 gene.3
This amount of effort is much closer to “routine” than to “undue
experimentation.”
We appreciate the Examiner’s concern regarding new matter, but
whether or not an application adequately describes a claimed invention is
determined as of the application’s filing date. See Hyatt v. Boone, 146 F.3d
1348, 1354 (Fed. Cir. 1998) (“[T]he purpose of the description requirement
is ‘to ensure that the inventor had possession, as of the filing date of the
application relied on, of the specific subject matter later claimed by him.”’)
Therefore, consistent with Falko-Gunter, sequences not present in a
public domain database at the time of filing would not be available to satisfy
the written description inquiry. However, this is a fact based analysis and no
evidence that any specific genes lack such support is before us.
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that the claims are not enabled because the polynucleotide sequences of the
listed genes are defined by UniGene cluster numbers in the Specification
rather than by their complete nucleotide sequence.
SUMMARY
In summary, we reverse the rejection of claims 1, 2, 4, 9, 10, and 13-
18 under 35 U.S.C. § 112, first paragraph as based on a disclosure which is
not enabling.

3http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=Hs&CID=
438720
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Application 11/332,547

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REVERSED

cdc

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