Ex Parte Brenner

Patent Trial and Appeal Board

Oct 29, 2012

11377462 (P.T.A.B. Oct. 29, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte SYDNEY BRENNER
__________

Appeal 2011-012114
Application 11/377,462
Technology Center 1600
__________

Before DEMETRA J. MILLS, JEFFREY N. FREDMAN, and STEPHEN
WALSH, Administrative Patent Judges.

MILLS, Administrative Patent Judge.

DECISION ON APPEAL

This is an appeal under 35 U.S.C. § 134. The Examiner has rejected
the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b).
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STATEMENT OF THE CASE
“The invention provides methods and compositions for labeling
polynucleotides and for providing multiplex readouts from assays on
polynucleotides. In one aspect, the invention provides compositions of
oligonucleotide tags that have properties favorable for labeling
polynucleotides and for permitting readouts on various analytical platforms,
such as microarrays and DNA separation instruments, such as
electrophoresis devices.” (Spec. 2.) “Preferably, sizes of fragments in
fragment sets are selected so that distinguishable bands or peaks are formed
for each metric tag in a separation profile after separation” (Spec. 14),
including separation by electrophoresis.
The following claim is representative and reads as follows:
13. A method of determining the number of copies of a polynucleotide in a
sample, the method comprising the steps of:
attaching to each copy of the polynucleotide in the sample a different
nucleotide tag to form tag-polynucleotide conjugates, wherein each different
nucleotide tag has a unique nucleotide sequence;
attaching to each of said tag-polynucleotide conjugates a different
metric tag to form metric tag-polynucleotide conjugates, wherein each
different metric tag has a unique nucleotide length and each metric tag has a
one-to-one correspondence with a different nucleotide tag;
cleaving the attached metric tags from said metric tag-polynucleotide
conjugates to generate cleaved metric tags;
separating and detecting said cleaved metric tags by
electrophoretically driven size separation; and
counting the number of different cleaved metric tags to determine the
number of copies of said polynucleotide in said sample.

Cited References

The Examiner relies on the following prior art references:

Matray et al. US 2003/0207300 A1 Nov. 6, 2003
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Mao et al. WO 02/097113 A2 Dec. 5, 2002
Sorge US 2003/0050453 A1 Mar. 13, 2003

Moore et al., Isolation and Purification of Large DNA Restriction
Fragments from Agarose Gels, Current Protocols in Molecular Biology,
2.6.1-2.6.12 (2002).

Grounds of Rejection
 Claims 7, 9-10, 13 and 22-23 are rejected under 35 U.S.C. §103(a) as
being unpatentable over Matray in view of Mao and Sorge.

 Claims 24 and 25 are rejected under 35 U.S.C. §103(a) as being
unpatentable over Matray in view of Mao, Sorge and Moore.

FINDINGS OF FACT
The Examiner’s findings of fact are set forth in the Answer at pages 5-
10.

Discussion
 Claims 7, 9-10, 13 and 22-23 are rejected under 35 U.S.C. §103(a) as
being unpatentable over Matray in view of Mao and Sorge.

Appellants provide separate argument for claim 13 (Br. 5.), which we select
as representative claim.

ISSUE
The Examiner concludes that
it would have been prima facie obvious to one of ordinary skill in the
art at the time the invention was made to improve the method of
Matray for detecting the abundance of a polynucleotide to include the
use of cleavable tags with unique nucleic acid sequence tags of Mao
and the unique length segments of Sorge that encode the sequence of
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the nucleic acid tag of Mao. The combined teachings of Matray, Mao
and Sorge demonstrate all the elements of the known invention were
known and used in the detection of nucleic acids in a population by
use of a tag. The artisan would merely be providing the specific
unique tagging method of Mao and encoding the unique tag of Mao
by the methods of encoding polynucleotide sequences by length
taught by Sorge for the general teaching of Matray to result in a
method for quantitating the number of nucleic acids in the sample.
The artisan would be motivated so as to be able to detect the amount
of a nucleic acid as suggested by Matray. The artisan would have a
reasonable expectation of success as the artisan is substituting the
specific unique nucleic acid tags of Mao into the nucleic acids being
labeled with length based codes as taught by Sorge in the method of
detecting nucleic acid abundance by the use of cleavable tags taught
by Matray.

(Ans. 8-9.)
Appellant principally argues, among other things, that
1) “Mao et al. teaches that each differently sized fragment in a size
ladder has the same tag attached.” (App. Br. 7.) “Appellants submit
that Mao et al. does not teach that fragments of a different size have a
different tag attached (i.e., a tag of a different sequence).” (Id. at 8.)
2) The teachings of Mao et al., when considered in full,
fail to teach “attaching to each of said tag-polynucleotide conjugates a
different metric tag to form metric tag-polynucleotide conjugates,
wherein each different metric tag has a unique nucleotide length and
each metric tag has a one-to-one correspondence with a different
nucleotide tag” as claimed. (Id. at 9.)
3) “Sorge et al. teaches that the same tag is attached to
polynucleotides having the same sequence (similar to the size ladders
in Mao et al.), which is in direct contrast to the claimed invention in
which a different tag is attached to each copy of a polynucleotide in a
sample.” (Id. at 10.)

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The issue is: Has the Examiner established with evidence and
reasoning that the pending claims are obvious in view of the cited
references?

PRINCIPLES OF LAW
“In rejecting claims under 35 U.S.C. § 103, the examiner bears the
initial burden of presenting a prima facie case of obviousness. Only if that
burden is met, does the burden of coming forward with evidence or
argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed.
Cir. 1993) (citations omitted). In order to determine whether a prima facie
case of obviousness has been established, we consider the factors set forth in
Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content
of the prior art; (2) the differences between the prior art and the claims at
issue; (3) the level of ordinary skill in the relevant art; and (4) objective
evidence of nonobviousness, if present.
“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).

ANALYSIS
We agree with the Examiner’s fact finding, statement of the rejection
and responses to Appellant’s arguments as set forth in the Answer. We find
that the Examiner has provided evidence to support a prima facie case of
obviousness. We provide the following additional comment.
The Examiner provided a thorough response to Appellant’s arguments
in the Answer at pages 10-22, which we adopt as our own. More
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specifically, the Examiner addresses Appellant’s argument 1) on page 11 of
the Answer, the Examiner addresses Appellant’s argument 2) on page 12-13
of the Answer, and the Examiner addresses Appellant’s argument 3) on page
11 of the Answer pages 14-15.
Appellant presents similar arguments for the rejection of claims 24-25
as presented in the original obviousness rejection. The rejection of these
claims is also affirmed for the reasons given by the Examiner in the Answer.
We note that while Appellant’s Specification and figures provide a
detailed method of determining the number of copies of a polynucleotide in
a sample which are not claimed and which may include novel features not
found in the prior art, the pending claim scope is broad and remains obvious
in view of the cited prior art.

CONCLUSION OF LAW
The cited references support the Examiner’s obviousness rejection.

TIME PERIOD
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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