Ex Parte Fu et al

Patent Trial and Appeal Board

Jun 19, 2018

13793461 (P.T.A.B. Jun. 19, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/793,461 03/11/2013
34791 7590 06/19/2018
Quine Intellectual Property Law Group P.C.
P.O. Box458
Alameda, CA 94501
FIRST NAMED INVENTOR
Glenn K. Fu
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
70-006800US (3885.lA) 5763
EXAMINER
FORMAN, BETTY J
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
06/19/2018 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 PATENT TRIAL AND APPEAL BOARD
Ex parte GLENN K. FU, ROBERT G. KUIMELIS and
RONALD J. SAPOLSKY
Appeal2017-005845
Application 13/793 ,461 1
Technology Center 1600
Before DEMETRA J. MILLS, ULRIKE W. JENKS, and
RICHARD J. SMITH, and 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 ).
We affirm.
1 According to Appellants, the real party in interest is Affymetrix,
Incorporated. App. Br. 1.
Appeal2017-005845
Application 13/793 ,461
STATEMENT OF CASE
"The present invention relates to the field of molecular biology, and
more specifically to methods for nucleic acid amplification and analysis."
Spec. ,r 2. The
described invention is a method to enable solid-phase locus
specific amplification of limiting amounts of target molecules
hybridized to arrayed probes. The hybridized target molecules are
amplified while they remain specifically hybridized to the arrayed
probes. Post solid-phase amplification, the amplified DNAs can then
be assayed by methods similar to any of those used by the above
mentioned technologies. This invention makes possible locus specific,
low redundancy sequencing of genomic regions of interest or whole
genomes.
Spec. ,r 87.
The following claim is representative.
21. A method for sequencing a target nucleic acid, the method
compnsmg:
hybridizing the target nucleic acid to a support bound probe, wherein
the support bound probe is attached to a solid support, wherein the support
bound probe comprises a first probe region and a second probe region,
wherein the first probe region comprises a 5' end and the second probe
region comprises a 3' end, and wherein both the first and second probe
regions hybridize to the target nucleic acid;
extending the 3' end of the second probe region using the hybridized
target nucleic acid as a template;
circularizing the support bound probe to create a circularized probe,
wherein circularizing comprises ligating the 5' end of the first probe region
with the extended 3' end of the second probe region;
2
Appeal2017-005845
Application 13/793 ,461
amplifying the support bound circularized probe using the circularized
probe as template to create an amplification product; and
sequencing the amplification product.
Cited References
Knott US 2005/0147973 Al July 7, 2005
DrManac et al. US 2008/0318796 Al Dec. 25, 2008
Chee et al., us 6,355,431 Mar. 12, 2002
Spies us 5,736,334 Apr. 7, 1998
Grounds of Rejection
1. Claims 21-23, 27-29, 32-40 are rejected under pre-AIA 35
U.S.C. § 103(a) as being unpatentable over Knott in view of
Drmanac.
2. Claims 21-40 are rejected underpre-AIA 35 U.S.C. §I03(a) as
being unpatentable over Knott in view ofDrmanac, Spies, and
Chee.
FINDINGS OF FACT
The Examiner's findings of fact are set forth in the Final Action at
pages 2-9. The following facts are highlighted.
1. One embodiment of the method of the invention as depicted in
Figures 1- 3B of the Specification is reproduced below.
3
Appeal2017-005845
Application 13/793 ,461
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Appeal2017-005845
Application 13/793 ,461
FIG. 1 shows a structure having synthesis points at the 5' and 3' end
of a detection oligonucleotide for the synthesis of target specific pre
circle probes on a solid support.
FIG. 2 shows a schematic of a detection pre circle probe on a solid
support.
FIG. 3A shows a method for gap filling and ligation to close a pre
circle probe on a solid support.
FIG. 3B shows a gap fill and ligate method performed in parallel with
each of the four different nucleotides in a single reaction. A closed
circle is formed in one of the four reactions and the other three are
unligated and the unligated probes are digested. The ligated probe is
detected by hybridization with a labeled detection oligonucleotide.
Spec. 5.
2. The figure on page 3 of Knott is reproduced below.
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