Ex Parte 7232656 et al

Patent Trial and Appeal Board

Sep 18, 2014

95000528 (P.T.A.B. Sep. 18, 2014)

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.
95/000,528 03/05/2010 7232656 048522-0002 8947
26853 7590 09/19/2014
COVINGTON & BURLING, LLP
ATTN: PATENT DOCKETING
1201 PENNSYLVANIA AVENUE, N.W.
WASHINGTON, DC 20004-2401
EXAMINER
PONNALURI, PADMASHRI
ART UNIT PAPER NUMBER
3991
MAIL DATE DELIVERY MODE
09/19/2014 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
____________

LIFE TECHNOLOGIES CORPORATION
Requester Cross-Appellant and Respondent

v.

ILLUMINA, INC.
Patent Owner, Appellant and Respondent
____________

Appeal 2014-000794
Reexamination Control 95/000,528
Patent 7,232,656 B2
Technology Center 3900
____________

Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN,
1
JEFFREY
B. ROBERTSON, and, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

1
Administrative Patent Judge Rae Lynn P. Guest was on the original panel
which decided this case, but is unavailable at this time. Judge Fredman has
been added to the merits panel. In re Bose Corp., 772 F.2d 866, 869 (Fed.
Cir. 1985).

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Reexamination Control 95/000,528
Patent 7,232,656 B2

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DECISION ON REHEARING
This is a Request for Rehearing under 37 C.F.R. § 41.79(a)(4) of the
February 3, 2014 Decision under 37 C.F.R. § 41.77(f) (“41.77 Dec.”) in
which the Board affirmed the anticipation and obviousness rejections of
claim 9 of US 7,232,656 (“the ’656 patent”), but reversed the written
description rejection of the claim. 41.77 Dec. 12. The full text of claim 9,
and claim 8, from which it depends, is reproduced in the 41.77 Decision.
Claim 9 recites “a polynucleotide duplex forming a hairpin loop
structure.” The hairpin has a target polynucleotide at one end and a primer
at the other end. Requester contends that claim 9 is broader than the
supporting disclosure in the '656 patent because the disputed language
covers a hairpin structure in which the primer for the template strand is not
covalently linked to primer. Requester Comments 10-11, dated May 20,
2013. The Examiner agreed with Requester and rejected claim 9 as lacking
a written description as required by 35 U.S.C. § 112, first paragraph.
Examiner's Determination 4, dated March 19, 2013.
In the Decision, the hairpin structure was interpreted to cover only
those structures in which the primer and template are covalently linked.
Requester contends that this interpretation was an error and requests
rehearing under 37 C.F.R. § 41.79(a)(4). Request for Rehearing (“Req.
Reh’g”), dated March 3, 2014. Patent Owner has filed on comments on the
Request for Rehearing. Patent Owner Comments, April 2, 2014.
The Decision arrived at the clam interpretation by examining the plain
language of the claim.
As indicated in claim 8, upon which claim 9 depends, the target
polynucleotide is sequenced. The target polynucleotide is
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recited in step ii) of claim 8 to be contacted with a nucleotide
primer used for DNA sequencing. The primer is therefore used
to sequence the polynucleotide in the array. Claim 9 refers to
the same polynucleotide ("target polynucleotide molecule") and
expressly requires a) the target polynucleotide which is
sequenced, and b) the primer for sequencing the target
polynucleotide, to be on the same "polynucleotide duplex
forming a hairpin loop structure" because the claim states a)
and b) are on either end of the molecule.
41.77 Dec. 12.
Requester contends that we erred because there is no requirement that
the polynucleotide be a single polynucleotide. Requester’s argument, which
is unbuttressed by objective evidence, is that “a ‘molecule’ can be made of
other smaller molecules that are associated together only by non-covalent
interactions such as hydrogen bonding.” Req. Reh’g 3. As an example,
Requester states that DNA is referred to as a single molecule although it
contains “two different DNA strands held together only by hydrogen
bonding - the two.” Id. The Requester points to the definition of “hairpin
loop structure” in the specification which defines the term “as a structure in
which the hairpin and the target sequence are on the same single strand.” Id.
at 5. However, Requester contends that claim 9 is broader and that the
polynucleotide molecule in claim 9 can comprise two separate molecules
with the target polynucleotide at one end (first molecule) and the unlinked
primer at the other end (second molecule), just as a DNA molecule is
comprised of two separate single-stranded molecules hybridized together.
Id.
We agree with Requester that our analysis was flawed, but not for the
reasons given by Requester. Specifically, we did not reference the
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specification of the ‘656 patent in construing claim 9. However, as
explained below, this defect does not change the interpretation of the claim
as set forth in the § 41.77(f) Decision.
During reexamination of an unexpired patent, claims are given their
broadest reasonable interpretation consistent with the patent specification.
In re Suitco Surface, Inc., 603 F.3d 1255, 1259 (Fed. Cir. 2010); In re
Abbott Diabetes Care Inc., 696 F.3d 1142 (Fed. Cir. 2012). The “PTO
applies to verbiage of the proposed claims the broadest reasonable meaning
of the words in their ordinary usage as they would be understood by one of
ordinary skill in the art, taking into account whatever enlightenment by way
of definitions or otherwise that may be afforded by the written description
contained in applicant’s specification.” In re Morris, 127 F.3d 1048, 1054
(Fed. Cir. 1997). “Though understanding the claim language may be aided
by explanations contained in the written description, it is important not to
import into a claim limitations that are not part of the claim. For example, a
particular embodiment appearing in the written description may not be read
into a claim when the claim language is broader than the embodiment.”
Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875 (Fed. Cir.
2004).
We shall first turn to the patent specification to determine the usage of
the phrase “hairpin loop structure.” The patent describes the embodiment of
claim 9 as follows. Underlining has been added to indicate where the
verbiage of the specification and the claim are the same; brackets have been
added to show where the claim language diverges from the specification:
In one aspect of the present invention, the devices comprise
arrayed polynucleotides, each polynucleotide [of the array]
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comprising [comprises a polynucleotide duplex forming] a
hairpin loop structure, one end of which comprises a [the] target
polynucleotide, the other end comprising a relatively short
polynucleotide capable of acting as a primer in the polymerase
reaction.
Col. 7, ll. 1-6.
As indicated by both Requester and Patent Owner, the ’656 expressly
describes what is meant by “hairpin loop structure.” Following the
paragraph reproduced above, the following passage appears:
The term “hairpin loop structure” refers to a molecular stem and
loop structure formed from the hybridisation of complementary
polynucleotides that are covalently linked. The stem comprises
the hybridised polynucleotides and the loop is the region that
covalently links the two complementary polynucleotides.
Anything from a 10 to 20 (or more) base pair double-stranded
(duplex) region may be used to form the stem. In one
embodiment, the structure may be formed from a single-
stranded polynucleotide having complementary regions. The
loop in this embodiment may be anything from 2 or more non-
hybridised nucleotides. In a second embodiment, the structure
is formed from two separate polynucleotides with
complementary regions, the two polynucleotides being linked
(and the loop being at least partially formed) by a linker moiety.
The linker moiety forms a covalent attachment between the
ends of the two polynucleotides. Linker moieties suitable for
use in this embodiment will be apparent to the skilled person.
For example, the linker moiety may be polyethylene glycol
(PEG).
Col. 7, ll. 11-30.
The ‘656 Patent refers to the hairpin loop structures as “a molecular
stem and loop structure formed from the hybridisation of complementary
polynucleotides that are covalently linked,” indicating that the latter phrase
is a denotation for a hairpin loop structure. Col. 7, ll. 11-13. Each of the
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two examples that follow is of hybridized complementary polynucleotides
covalently linked on a single molecule. In the first example, the two
complementary polynucleotides are the same single-strand. Col. 7, ll. 18-20
(“the structure may be formed from a single-stranded polynucleotide having
complementary regions”). The second embodiment is of the two
polynucleotides covalently attached by a linker. Col. 7, ll. 21-25.
From these disclosures in the ’656 Patent, which use substantially the
same language that appears in claim 9 (col. 7, ll. 1-6), it is apparent that
“hairpin loop structure,” as recited in the claim, is defined to mean a
structure formed by two hybridized polynucleotides which are covalently
linked (col. 7, ll. 11-13). Requester specifically acknowledged this
definition. Req. Reh’g 5. Despite this express definition, Requester takes a
broader view that a hairpin loop structure also encompasses a primer which
is not covalently linked to the template to which it is hybridized.
Requester’s interpretation is inconsistent with the definition of a hairpin loop
as formed by “hybridisation of complementary polynucleotides that are
covalently linked,” where the template and primer constitute the hybridized
complementary polynucleotides.
Under Requester’s interpretation, the primer is not necessarily
covalently joined to the target because “molecule” can mean two separate
single-stranded molecules together. While this is a possible interpretation
left open in the Decision by our sole reliance on the claim language, when
the written description of the ’656 patent is consulted, the definition of
“hairpin loop structure” which appears in the patent excludes Requester’s
interpretation. This is not a case of importing a limitation from the
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specification into the claims, because there is an express description of what
is meant by “hairpin loop structure.” Superguide, 358 F.3d at 875.

REHEARING DENIED

CC

Patent Owner:

COVINGTON & BURLING, LLP
ATTN: PATENT DOCKETING
1201 PENNSYLVANIA AVENUE, N.W.
WASHINGTON, DC 20004-2401

Third Party Requester:

LIFE TECHNOLOGIES CORPORATION
ATTN: IP DEPARTMENT
5791 VAN ALLEN WAY
CARLSBAD, CA 92008