Ex Parte Lapidus et al

Patent Trial and Appeal Board

Nov 30, 2012

11167046 (P.T.A.B. Nov. 30, 2012)

UNITED STATES PATENT AND TRADEMARKOFFICE
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.
11/167,046 06/23/2005 Stanley N. Lapidus HELI-001/01US
28526/262
5644
21710 7590 12/03/2012
BROWN RUDNICK LLP
ONE FINANCIAL CENTER
BOSTON, MA 02111
EXAMINER
TUNG, JOYCE
ART UNIT PAPER NUMBER
1637
MAIL DATE DELIVERY MODE
12/03/2012 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 STANLEY N. LAPIDUS and PHILIP R. BUZBY
__________

Appeal 2011-007096
Application 11/167,046
Technology Center 1600
__________

Before TONI R. SCHEINER, MELANIE L. McCOLLUM, and
JEFFREY N. FREDMAN, Administrative Patent Judges.

SCHEINER, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 from the rejection of claims
1-3, 5, 7-10, 12, 13, 17-21, and 23-33, directed to a method of determining
the sequence of an anchored circular nucleic acid template. The claims have
been rejected as obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
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STATEMENT OF THE CASE
Claims 1-3, 5, 7-10, 12, 13, 17-21, and 23-33 are pending and on
appeal. Claims 4, 6, 11, 14-16, and 22 have been canceled (App. Br. 4).
Claim 1 is representative of the subject matter on appeal:
1. A method of determining a sequence of a nucleic acid
template, the method comprising:
(a) directly or indirectly anchoring a circular nucleic acid template to
a substrate;
(b) copying the template to produce an amplicon, wherein one or more
detectably labeled nucleotides are incorporated into the amplicon via a
polymerase-mediated reaction;
(c) determining a sequence of the amplicon by optically resolving
individual labeled nucleotides incorporated into the amplicon; and
(d) determining at least a portion of the sequence of the template
based on the sequence of the amplicon.
Claims 1-3, 5, 7-10, 12, 13, 17, 18, 20, 21, and 23-33 stand rejected
under 35 U.S.C. § 103(a) as unpatentable over Rothberg1 and Williams.2
Claim 19 stands rejected under 35 U.S.C. § 103(a) as unpatentable
over Rothberg , Williams, and Mullis.3
PRINCIPLES OF LAW
A reference may be said to teach away when a person of
ordinary skill, upon reading the reference, would be
discouraged from following the path set out in the reference, or
would be led in a direction divergent from the path that was
taken by the applicant. The degree of teaching away will of
course depend on the particular facts; in general, a reference
will teach away if it suggests that the line of development

1 US Patent No. 6,274,320 B1, issued August 14, 2001 to Rothberg et al.
2 US Patent Application US 2002/0137062 A1 of Williams et al, published
September 26, 2002.
3 US Patent No. 4,965,188, issued October 23, 1990 to Mullis et al.
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flowing from the reference’s disclosure is unlikely to be
productive of the result sought by the applicant.
In re Gurley, 27 F.3d 551, 553 (Fed. Cir. 1994).
OBVIOUSNESS
The Examiner rejected claims 1-3, 5, 7-10, 12, 13, 17, 18, 20, 21, and
23-33 as unpatentable over Rothberg and Williams.
Fact Findings
The Examiner’s fact findings, set forth on pages 3-5 and 11 of the
Answer, are not in dispute, and we adopt them as our own. We reiterate the
following facts for emphasis:
1. Rothberg uses a method termed “Pyrosequencing™” to
determine the sequence of an amplicon as follows:
Incorporation of the dNTP is determined by assaying for
the presence of a sequencing byproduct. In a preferred
embodiment, the nucleotide sequence of the sequencing product
is determined by measuring inorganic pyrophosphate (PPi)
liberated from a nucleotide triphosphate (dNTP) as the NTP is
incorporated into an extended sequence primer. This method of
sequencing, termed PyrosequencingTM technology
(PyroSequencing AB, Stockholm, Sweden) can be performed in
solution (liquid phase) or as a solid phase technique. PPi-based
sequencing methods are described generally in e.g.,
WO9813523A1, Ronaghi, et al., 1996. Anal. Biochem. 242-:
84-89, and Ronaghi, et al., 1998. Science 281: 363-365 (1998).
These disclosures of PPi sequencing are incorporated herein in
their entirety, by reference.
Pyrophosphate released under these conditions can be
detected enzymatically (e.g., by generation of light in the
luciferase-luciferin reaction).
(Rothberg, col. 14, ll. 35-52.)
2. Williams discusses Pyrosequencing™ and its shortcomings in
the “Background of the Invention” section:
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A variety of methods may be used to detect the
polymerase-catalyzed incorporation of deoxynucleoside
monophosphates (dNMPs) into a primer at each template site.
For example, the pyrophosphate released whenever DNA
polymerase adds one of the four dNTPs onto a primer 3' end
may be detected using a chemiluminescent based detection of
the pyrophosphate . . . This approach has been utilized most
recently in a sequencing approach referred to as “sequencing by
incorporation” as described in Ronaghi (1996, Analytical
Biochem. 242:84) and Ronaghi (1998, Science 281:363-365).
However, there exist two key problems associated with this
approach, destruction of unincorporated nucleotides and
detection of pyrophosphate. The solution to the first problem is
to destroy the added, unincorporated nucleotides using a dNTP-
digesting enzyme such as apyrase. The solution to the second is
the detection of the pyrophosphate using ATP sulfurylase to
reconvert the pyrophosphate to ATP which can be detected by a
luciferase chemiluminescent reaction as described in U.S. Pat.
No. 4,971,903 and Ronaghi (1998, Science 281:363-365).
Deoxyadenosine a-thiotriphosphate is used instead of dATP to
minimize direct interaction of injected dATP with the
luciferase.
Unfortunately, the requirement for multiple enzyme
reactions to be completed in each cycle imposes restrictions on
the speed of this approach while the read length is limited by
the impossibility of completely destroying unincorporated, non-
complementary, nucleotides. If some residual amount of one
nucleotide remains in the reaction system at the time when a
fresh aliquot of a different nucleotide is added for the next
extension reaction, there exists a possibility that some fraction
of the primer strands will be extended by two or more
nucleotides, the added nucleotide type and the residual impurity
type, if these match the template sequence, and so this fraction
of the primer strands will then be out of phase with the
remainder. This out of phase component produces an erroneous
incorporation signal which grows larger with each cycle and
ultimately makes the sequence unreadable.
(Williams ¶¶ 8-9.)
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3. Williams discloses an alternative sequencing method termed
“reactive sequencing,” comprising real-time detection of DNA polymerase-
catalyzed incorporation of each of four chemiluminescently- or
fluorescently-labeled nucleotide bases into a template system (i.e., a DNA
fragment of unknown sequence and an oligonucleotide primer) (Williams ¶¶
11-13, 18).
Discussion
We agree with the Examiner’s conclusion that the invention of claim
1 would have been obvious over the combined teachings of Rothberg and
Williams for the reasons set forth in the Examiner’s Answer, and adopt the
Examiner’s rationale as our own. We make the following comments for
emphasis:
The Examiner finds, and Appellants do not dispute, that Rothberg
discloses producing an amplicon according to steps (a) and (b) of the
claimed method (Ans. 3-4; App. Br. 5-6), and differs from the claimed
invention only in step (c) - the method of detecting the sequence of the
amplicon (Ans. 4; App. Br. 6). That is, Rothberg determines the sequence of
the amplicon in step (c) by the so called “pyrosequencing” method (Ans. 4,
11; App. Br. 6, 16), rather than determining the sequence by optically
resolving individual labeled nucleotides incorporated into the amplicon.
The Examiner further finds that Williams discusses pyrosequencing,
particularly “the disadvantage[s] of using pyrosequencing” (Ans. 11), and
discloses an alternative sequencing method comprising “analyzing nucleic
acid sequences based on real-time [optical] detection of DNA polymerase-
catalyzed incorporation of each of the four [fluorescently-tagged] nucleotide
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bases” (id. at 5), thereby “eliminating the problems associated with”
pyrosequencing (id.).
Appellants agree that Williams “is replete with statements about the
shortcomings of pyrosequencing, the detection method used in Rothberg”
(App. Br. 16). However, Appellants contend that “the ordinarily skilled user
would have been strongly motivated against combining Williams and
Rothberg, let alone even referring to Rothberg, a reference that relies on
pyrosequencing to detect incorporation of a nucleotide into an extended
sequence primer” (id. at 16-17), because of “these repeated statements in
Williams that are teaching away from use of pyrosequencing” (id. at 16).
Appellants’ argument is not persuasive. Again, there is no dispute
that Rothberg discloses making an amplicon according to steps (a) and (b) of
claim 1, and differs from claim 1 only in using pyrosequencing to determine
the sequence of the amplicon, rather than optically resolving individual
labeled nucleotides incorporated into the amplicon. We agree with the
Examiner that Williams’ disparagement of pyrosequencing, far from
teaching away from the claimed invention, is precisely what would have led
one of ordinary skill in the art to replace the pyrosequencing step in
Rothberg’s method with Williams’ alternative sequencing method, in order
to avoid the problems known to be associated with pyrosequencing. As
discussed above, a reference may be said to teach away if it “suggests that
the line of development flowing from the reference’s disclosure is unlikely
to be productive of the result sought by the applicant.” In re Gurley, 27 F.3d
at 553. In this case, Appellants have identified nothing in Williams that
suggests that Rothberg’s circular nucleic acid templates (made according to
steps (a) and (b) of claim 1) could not be sequenced using Williams’ method
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and would not have been a desirable nucleic acid preparation method for
sequencing using the William’s method.
To the extent Appellants argue that combining Rothberg and Williams
“would have rendered Rothberg’s intended method unsatisfactory for its
intended purpose” (App. Br. 9), we disagree. At least one of Rothberg’s
objectives is to determine the sequence of an amplified circular nucleic acid
template. We agree with the Examiner that Appellants have not established
that replacing Rothberg’s sequencing method with Williams’ would have
impeded the objective of “obtaining the desired sequence information” from
the amplified circular template (Ans. 12).
Claim 19
The Examiner also rejected claim 19 as unpatentable over Rothberg,
Williams, and Mullis.
Appellants briefly reiterate their arguments regarding the examiner’s
proposed combination of Rothberg and Williams, and contend that Mullis
“provides no teaching or suggestion for reconciling the different methods
used by Rothberg and Williams” (App. Br. 18).
We are not persuaded by this argument for the reasons discussed
above in connection with Rothberg and Williams.
SUMMARY
The rejection of claim 1 as unpatentable over Rothberg and Williams
is affirmed. Claims 2, 3, 5, 7-10, 12, 13, 17, 18, 20, 21, and 23-33 were not
separately argued and therefore fall with claim 1 and the rejection is
affirmed with respect to these claims as well. See 37 C.F.R. §
41.37(c)(1)(vii).
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In addition, the rejection of claim 19 as unpatentable over Rothberg,
Williams, and Mullis is affirmed.
TIME PERIOD FOR RESPONSE
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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