Norman C. Nelson et al.

Patent Trials and Appeals Board

Jul 31, 2019

14342764 - (D) (P.T.A.B. Jul. 31, 2019)

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.
14/342,764 07/21/2014 Norman C. Nelson 057516-443110 1094
13837 7590 07/31/2019
Alston & Bird LLP/ Gen-Probe Incorporated
Bank of America Plaza
101 South Tryon Street, Suite 4000
Charlotte, NC 28280-4000
EXAMINER
CHUNDURU, SURYAPRABHA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
07/31/2019 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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
patentdept@hologic.com
usptomail@alston.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte NORMAN C. NELSON, JIJUMON CHELLISERRY,
STEVEN T. BRENTANO, DMITRY LYAKHOV,
MATTHEW C. FRIEDENBERG, and ANNE-LAURE SHAPIRO1
____________

Appeal 2018-004190
Application 14/342,764
Technology Center 1600
____________

Before RYAN H. FLAX, RACHEL H. TOWNSEND, and
CYNTHIA M. HARDMAN, Administrative Patent Judges.

FLAX, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision under 35 U.S.C. § 134(a) involving claims directed
to a method of forming a closed nucleic acid structure comprising a segment
of a target nucleic acid. Claims 66–82 and 85–87 are on appeal as rejected
under 35 U.S.C. § 102(b). We have jurisdiction under 35 U.S.C. § 6(b).
We reverse.

1 Appellants identify the Real Party in Interest as “Gen-Probe Incorporated,
a wholly owned subsidiary of Hologic, Inc.” Appeal Br. 2.
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STATEMENT OF THE CASE
Independent claims 66 is representative and is reproduced below:
66. A method of forming a closed nucleic acid structure
comprising a segment of a target nucleic acid, the method
comprising:
(a) contacting the target nucleic acid with a primer pair
under amplification conditions, each of the primers of the pair
including a 5' phosphate group and a 3' segment, the 3' segments
of the primers being target-binding segments; thereby forming
an amplified nucleic acid comprising duplex target nucleic acid
flanked by the primers of the pair duplexed with their
complementary segments, wherein each strand of the amplified
nucleic acid includes a 5' phosphate group and a 3' hydroxyl
group;
(b) denaturing the amplified nucleic acid and contacting
a strand of the denatured amplified nucleic acid with a stem-
loop adaptor having a 5' phosphate group, a 5' segment, a 3'
segment having a stem-loop structure, and a 3' hydroxyl group,
wherein the 5' segment is complementary to a segment at the 5'
end of the amplified nucleic acid strand;
(c) annealing the 5' segment of the stem-loop adaptor to
the 5' end segment of the amplified nucleic acid strand, thereby
forming a partially duplex, two-stranded intermediate structure
wherein the 5' phosphate group of the amplified nucleic acid
strand is separated by a nick from the 3' hydroxyl group of the
stem-loop adaptor; and
(d) providing a ligase that seals the nick between the 5'
phosphate group of the amplified nucleic acid strand and the
3' hydroxyl group of the stem-loop adaptor and additionally
links the 5' phosphate group of the stem-loop adaptor to the 3'
hydroxyl group of the amplified nucleic acid strand, thereby
forming a closed nucleic acid structure.
Supplemental Appeal Br. 2 (Claims Appendix, emphasis added––see infra
Discussion).
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The following rejection is appealed:
Claims 66–82 and 85–87 stand rejected under 35 U.S.C. § 102(b) as
anticipated by Patel.2 Final Action 3.
DISCUSSION
“[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting a prima facie case of unpatentability.
[Only once] that burden is met, [does] the burden of coming forward with
evidence or argument shift[] to the applicant.” In re Oetiker, 977 F.2d 1443,
1445 (Fed. Cir. 1992).
Regarding anticipation, our reviewing court has held:
a patent is invalid [or unpatentable] as anticipated if “the
[claimed] invention was described in” a patent or published
application “before the invention by” the patentee. 35 U.S.C.
§ 102(e). In order to anticipate the claimed invention, a prior art
reference must “disclose all elements of the claim within the four
corners of the document,” and it must “disclose those elements
‘arranged as in the claim.’” Net MoneyIN, Inc. v. VeriSign, Inc.,
545 F.3d 1359, 1369 (Fed. Cir. 2008) (quoting Connell v. Sears,
Roebuck & Co., 722 F.2d 1542, 1548 (Fed. Cir. 1983)).
Microsoft Corp. v. Biscotti, Inc., 878 F.3d 1052, 1068 (Fed. Cir. 2017). Put
another way, an anticipating reference must clearly and unequivocally
disclose the claimed subject matter or direct those skilled in the art to the
claimed subject matter without any need for picking, choosing, and
combining various disclosures of the reference not directly related to each
other by its teachings. In re Arkley, 455 F.2d 586, 587–88 (CCPA 1972)
(“[P]icking and choosing may be entirely proper in the making of a 103,

2 US 2009/0280538 A1 (published Nov. 12, 2009) (“Patel”).
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obviousness rejection, . . . but it has no place in the making of a 102,
anticipation rejection.”).
The Examiner determined that the appealed claims are anticipated by
Patel. Final Action 3–7 and Answer 3–9 (citing Patel generally, but
specifically ¶¶ 10–19, 34, 35, 58, 60, 61, 71–75, 90–93, 102, 126–128,
claims 1, 6, 7, 62). In response, Appellants argue, inter alia,
Our appeal brief points out that each of the independent claims
requires the respective ends of a stem loop adaptor are linked to
the opposing ends of the same strand of a target nucleic acid (as
shown in present Fig. 15A). See appeal brief at p. 6, last
paragraph to p. 7 first paragraph. By contrast, in Patel, the
respective ends of the stem loop adaptor are linked to adjacent
ends of opposing strands of the target nucleic acid (as shown in
Fig. 6 of Patel).
Reply Br. 2; see also Appeal Br. 5–7. Further to this same argument,
Appellants present a comparison between Figure 15A of their Specification,
which they argue is an embodiment covered by the appealed claims, and
Figure 6 of Patel, which they argue embodies Patel’s teachings with respect
to the use of hairpin/stem loop structures (Appeal Br. 6); we reproduce this
comparison below:
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Appellants’ Specification’s Figure 15A is shown above-top and Patel’s
Figure 6 is shown above-bottom.
Appellants’ Specification’s Figure 15A illustrates the claim elements
emphasized above (see supra Statement of the Case), for example, the
recited step of forming a duplexed target nucleic acid having the recited 5'
phosphate and 3' hydroxyl groups, the recited denaturing of this structure
and contacting it with a stem-loop adaptor with similar 5' and 3' ends, the
recited annealing step where the stem-loop adaptor joins with the nucleic
acid strand to form a partial duplex, two-strand structure, and finally the
recited ligase sealing a nick at the 5' end of the stem-loop adaptor and the 3'
end of the nucleic acid to form a closed loop structure. See also Spec.
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¶¶ 245–269 (describing “Method 16: generating a closed nucleic acid
structure following amplification/primer extension followed by ligation to a
stem-loop primer” and discussing Figures 15A–15H). Patel’s Figure 6, on
the other hand, shows the annealing of two hairpin oligonucleotides
segments to a double-stranded nucleic acid structure, where each hairpin
pairs with both nucleic acid strands, to thereby “generate the set of closed
single-stranded nucleic acid loops that comprise regions of internal
complementarity.” See, e.g., Patel ¶¶ 34, 35, 90–93. Patel’s closed loop
structure includes two complementary nucleotide strands separated by two
hairpin structures, not a single nucleotide strand and a single stem-loop
structure.
Considering the evidence before us, we conclude Appellants have the
better position. Although Patel may teach various claimed elements across
the expanse of its disclosure, it does not disclose the entirety of the claimed
method where a single stem-loop structure is joined to a single nucleotide
strand and then this structure is reconfigured to be a closed loop by joining
the two free ends of these two formerly separate components. The
differences between the claimed method and Patel’s disclosed process are
well illustrated by the figures reproduced above. For these reasons, we
conclude the Examiner has not made a sufficient case for anticipation.
SUMMARY
The rejection under 35 U.S.C. § 102 is reversed.

REVERSED