Ex Parte Rigler

Board of Patent Appeals and Interferences

Aug 20, 2010

11139080 (B.P.A.I. Aug. 20, 2010)

MOD PTOL-90A (Rev.06/08)

APPLICATION NO./
CONTROL NO.
FILING DATE FIRST NAMED INVENTOR /
PATENT IN REEXAMINATION
ATTORNEY DOCKET NO.
11/139,080 05/26/2005 RUDOLF RIGLER

EXAMINER
CALAMITA, HEATHER
ART UNIT PAPER NUMBER
FULBRIGHT & JAWORSKI, LLP
666 FIFTH AVE
NEW YORK, NY 10103-3198

1637
MAIL DATE DELIVERY MODE

08/20/2010 ELECTRONIC

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.

UNITED STATES DEPARTMENT OF COMMERCE
U.S. Patent and Trademark Office
Address : COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
UNITED STATES PATENT AND TRADEMARK OFFICE
_____________________________________________________________________________________

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte RUDOLF RIGLER
____________

Appeal 2010-002568
Application 11/139,080
Technology Center 1600
____________

Before DONALD E. ADAMS, DEMETRA J. MILLS, and
MELANIE L. McCOLLUM, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL1
This appeal under 35 U.S.C. § 134 involves claims 23-33, 35-39, and
45 (App. Br. 5). We have jurisdiction under 35 U.S.C. § 6(b).

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.
Appeal 2010-002568
Application 11/139,080

2
Claims 40-44 were withdrawn from consideration resulting from a
restriction requirement, and claims 1-22 and 34 are canceled (App. Br. 5;
August 11, 2006 Office Action 2).

STATEMENT OF THE CASE
The claims are directed to a method for sequencing a plurality of
single nucleic acid molecules. Claims 23 and 45 are representative and are
reproduced in “APPENDIX A” of Appellant’s Brief (App. Br. 17 and 20).
The rejections presented by the Examiner follow:
1. Claims 23-28, 31-33, 35-39, and 45 stand rejected under 35 U.S.C. §
102(e) as being anticipated by Laugharn.2
2. Claim 45 stands rejected under 35 U.S.C § 103(a) as unpatentable over
the combination of Laugharn and Barbany.3
We reverse.
Anticipation:
ISSUE

Does the preponderance of evidence support the Examiner’s findings?

FINDINGS OF FACT
FF 1. The Examiner finds that Laugharn’s teachings at column 2, lines 15-
19 and 42-49; and column 7, lines 45-50 teach part 23(c) of Appellant’s
claimed invention (Ans. 5).
FF 2. Laugharn teaches an integrated device for sequencing a polymeric
biomolecule, that includes, inter alia, an enzyme that catalyzes the removal

2 Laugharn, Jr. et al., US 6,245,506 B1, June 12, 2001.
3 Gisela Barbany, et al., Molecular genetic applications of streptavidin-
coated manifold supports, 16 BIOMOLECULAR ENGINEERING 105-111 (1999).
Appeal 2010-002568
Application 11/139,080

3
of one monomer unit at a time from one end of the polymeric biomolecule
and a probe for sensing a characteristic (e.g., fluorescence) of the released
monomers (Laugharn, col. 2, ll. 11-18).
FF 3. Laugharn teaches that the device can include multiple probes to
sense characteristics of multiple monomers (Laugharn, col. 2, ll. 47-50).
FF 4. Laugharn teaches that a number of single molecule reactions can be
run simultaneously (Laugharn, col. 7, ll. 45-50).
FF 5. Laugharn teaches that “[a]t least some of the monomers of the
polymeric biomolecule can be labelled with fluorescent tags, and the identity
of the fluorescently labelled monomers can then be determined by
fluorescence resonance energy transfer between the monomers and the
enzyme” (Laugharn, col. 2, ll. 57-62; see also Ans. 8 (Laugharn teaches
“detection of individual cleaved nucleotides”)).
FF 6. Appellant’s Specification teaches that “[d]uring the progressive
removal by cleavage of individual nucleotide building blocks [(e.g.,
monomers)], it is possible to measure a change in fluorescence intensity of
the immobilized nucleic acid strand or/and the nucleotide building block
removed by cleavage, owing to quenching processes or energy transfer
processes” (Spec. 6: 29-32).
ANALYSIS
Appellant’s claim 23 requires the measurement of a time-dependent
change in fluorescence, caused by the removal of nucleotides by cleavage, of
a plurality of single immobilized nucleic acid molecules (Claim 23(c)). As
the Examiner recognizes, Laugharn does not detect the fluorescence of a
plurality of single immobilized nucleic acid molecules, but instead measures
the fluorescence of a nucleotide (e.g., monomer) cleaved from the
Appeal 2010-002568
Application 11/139,080

4
immobilized nucleic acid molecule (FF 5). While Appellant’s Specification
appreciates that the fluorescence of a labeled nucleotide removed from an
immobilized nucleic acid molecule can be measured, it is an alternative to
measuring the fluorescence of the immobilized nucleic acid strand (FF 6).
The Examiner has failed to identify a teaching in Laugharn of the
measurement of a time-dependent change in fluorescence, caused by the
removal of nucleotides by cleavage, of a plurality of single immobilized
nucleic acid molecules as required by Appellant’s claimed invention (see
App. Br. 11 (“Nothing in the[ ] passages [of Laugharn relied upon by the
Examiner] describes determining changes in fluorescence of immobilized
nucleic acid molecules”)).
CONCLUSION OF LAW
The preponderance of evidence fails to support the Examiner’s
findings. The rejection of claims 23-28, 31-33, 35-39, and 45 under 35
U.S.C. § 102(e) as being anticipated by Laugharn is reversed.

Obviousness:
ISSUE
Does the preponderance of evidence on this record support a
conclusion of obviousness?
FINDINGS OF FACT
FF 7. The Examiner relies on Laugharn as discussed above (Ans. 6).
FF 8. The Examiner relies on Barbany to teach “the use of
streptavidin/biotin (a hapten binding complex) to immobilize DNA to a
substrate for sequencing” (id.).

Appeal 2010-002568
Application 11/139,080

5
ANALYSIS
Appellant’s claim 45 requires the measurement of a time-dependent
change in fluorescence, caused by the removal of nucleotides by cleavage, of
a plurality of single immobilized nucleic acid molecules (Claim 45(c)).
Appellant contends that Barbany fails to make up for the deficiencies in
Laugharn (see App. Br. 12). We agree.
CONCLUSION OF LAW
The preponderance of evidence on this record fails to support a
conclusion of obviousness. The rejection of claim 45 under 35 U.S.C
§ 103(a) as unpatentable over the combination of Laugharn and Barbany is
reversed.
REVERSED

cdc

FULBRIGHT & JAWORSKI, LLP
666 FIFTH AVE
NEW YORK, NY 10103-3198