Ex Parte Sood et al

Board of Patent Appeals and Interferences

Apr 14, 2010

10773000 (B.P.A.I. Apr. 14, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte ANUP SOOD, SHIV KUMAR, JOHN NELSON, and
CARL FULLER
____________

Appeal 2009-003262
Application 10/773,000
Technology Center 1600
____________

Decided: April 14, 2010
____________

Before ERIC GRIMES, DONALD E. ADAMS, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 1-56, the only
claims pending in this application. We have jurisdiction under 35 U.S.C.
§ 6(b).

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STATEMENT OF THE CASE
The claims are directed to a method of sequencing a target region of a
nucleic acid template. Claims 1 and 32 are illustrative:
1. A method of sequencing a target region of a nucleic acid template,
comprising:
a) conducting a nucleic acid polymerization reaction on a solid support,
by forming a reaction mixture, said reaction mixture including a
nucleic acid template, a primer, a nucleic acid polymerizing enzyme,
and one terminal-phosphate-labeled nucleoside polyphosphate which
is substantially non-reactive to phosphatase, said nucleoside
polyphosphate is selected from a nucleoside with a natural base or a
base analog
wherein a component of said reaction mixture or complex of
two or more of said components, is immobilized on said solid
support, and said component or components are selected from
the group consisting of said nucleic acid template, said primer,
and said nucleic acid polymerizing enzyme,
and
said reaction results in production of labeled polyphosphate if
said terminal-phosphate-labeled nucleoside polyphosphate
contains a base complementary to the template base at the site
of polymerization;
b) subjecting said reaction mixture to a phosphatase treatment to produce
a detectable species if said labeled polyphosphate is produced in step
a);
c) detecting said detectable species without first separating by charge of
said detectable species from the reaction mixture;
d) continuing said polymerization reaction by adding a different
terminal-phosphate-labeled nucleoside polyphosphate selected from
the remaining natural bases or base analogs to said reaction mixture
and repeating steps b and c; and
e) identifying said target region sequence from the identity and order of
addition of terminal-phosphate labeled nucleoside polyphosphates
resulting in production of said detectable species.

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32. A method of sequencing a target region of a nucleic acid template,
comprising:
a) conducting a nucleic acid polymerization reaction on a solid
support, by forming a reaction mixture, said reaction mixture including a
nucleic acid template, a primer, a nucleic acid polymerizing enzyme, and
one terminal-phosphate-labeled nucleoside polyphosphate with 4 or more
phosphates which nucleoside polyphosphate is substantially non-reactive to
phosphatase, and said nucleoside polyphosphate is selected from a
nucleoside with a natural base or a base analog and
wherein a component of said reaction mixture or a complex of two or
more of said components, is immobilized on said solid support, and
said component or components are selected from the group consisting
of said nucleic acid template, said primer, and said nucleic acid
polymerizing enzyme,
and
said reaction results in production of labeled polyphosphate if said
terminal-phosphate-labeled nucleoside polyphosphate contains a base
complementary to the template base at the site of polymerization;
b) detecting said labeled polyphosphate without first separating by
charge of said labeled polyphosphate from the reaction mixture;
c) continuing said polymerization reaction by adding a different
terminal-phosphate-labeled nucleoside polyphosphate selected from
the remaining natural bases or base analogs to said reaction mixture
and repeating step b; and
d) identifying said target region sequence from the identity and order of
addition of terminal-phosphate labeled nucleoside polyphosphates
resulting in production of said labeled polyphosphates.

The Examiner relies on the following evidence:
Bronstein et al. US 5,112,960 May 12, 1992
Keller et al. US 5,656,462 Aug. 12, 1997
Lichtenwalter US 5,683,875 Nov. 4, 1997
Hattori et al. US 5,821,095 Oct. 13, 1998
Williams et al. WO 01/94609 A1 Dec. 13, 2001
Wittwer et al. US 6,174,670 B1 Jan. 16, 2001

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The rejections presented by the Examiner follow:
1. Claims 1-56 stand rejected under the written description provision of 35
U.S.C. § 112, first paragraph.
2. Claims 1-7, 9, 11-18, 20-23, 27-38, 40, 42-45, and 47-56 stand rejected
under 35 U.S.C § 102(b) as being anticipated by Williams1.
3. Claims 8 and 39 stand rejected under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Wittwer.
4. Claims 10 and 41 stand rejected under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Keller.
5. Claims 19 and 46 stand rejected under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Lichtenwalter.
6. Claims 23-25 stand rejected under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Hattori.
7. Claims 25 and 26 stand rejected under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Bronstein.
We reverse the rejection under 35 U.S.C. § 112, first paragraph. We
affirm all other grounds of rejection.

Written Description:
ISSUE

Did the Examiner err in concluding that Appellants’ Specification
does not provide written descriptive support for the detection of detectable

1 The Examiner did not include claims 48 and 51-54 in the statement of the
rejection (Ans. 4). Nevertheless, the Examiner addressed these claims in the
body of the rejection (see Ans. 11-12 and Fin. Rej. 11-12). Accordingly, we
find the Examiner’s failure to include claims 48 and 51-54 in the statement
of the rejection to be a harmless typographical error.
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species/labeled polyphosphate without first separating the detectable species/
labeled polyphosphate from the reaction mixture by charge?

FINDINGS OF FACT
FF 1. The Examiner finds that Appellants’ “specification does not provide
[a] basis for detection without separation based on charge” (Ans. 4).
FF 2. Appellants disclose that
The methods provided by this invention utilize a
nucleoside polyphosphate, . . . with an electrochemical label,
mass tag, or a colorimetric dye, a chemiluminescent label, or a
fluorescent label attached to the terminal-phosphate. When a
nucleic acid polymerase uses this analogue as a substrate, an
enzyme-activatable label would be present on the inorganic
polyphosphate by-product of phosphoryl transfer. Cleavage of
the polyphosphate product of phosphoryl transfer via
phosphatase, leads to a detectable change in the label attached
thereon.

(Spec. 11: 10-18.)
FF 3. Appellants disclose an alternative, wherein “it is possible to
physically separate the labeled polyphosphate product by chromatographic
separation methods before identification by fluorescence, color,
chemiluminescence, or electrochemical detection” (Spec. 13: 32 - 14: 2).

PRINCIPLES OF LAW
Under the written description requirement of 35 U.S.C. § 112, first
paragraph, “the [A]pplicant must . . . convey with reasonable clarity to those
skilled in the art that, as of the filing date sought, he or she was in possession
of the invention.” Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed.
Cir. 1991). “In order to satisfy the written description requirement, the
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disclosure as originally filed does not have to provide in haec verba support
for the claimed subject matter at issue.” Purdue Pharma L.P. v. Faulding,
Inc., 230 F.3d 1320, 1323 (Fed. Cir. 2000).

ANALYSIS
The Examiner finds that Appellants’ “specification does not provide
[a] basis for detection without separation based on charge” (FF 1).
Appellants contend that when their Specification is read as a whole it
“describes sequencing methods which do not require a separation step, prior
to the detecting step, of either the detectable species or the labeled
polyphosphate from the reaction mixture” (App. Br. 5). We agree (FF 2-3).
It is evident from the examples that the detection of the label occurs without
chromatographic separation. While Appellants also disclose the use of
chromatographic separation methods (e.g., separation by charge) prior to
detection, Appellants make clear that this is an alternative method to
detection without chromatographic separation (FF 3).

CONCLUSION OF LAW
The Examiner erred in concluding that Appellants’ Specification does
not provide written descriptive support for the detection of detectable
species/labeled polyphosphate without first separating the detectable species/
labeled polyphosphate from the reaction mixture by charge. The rejection of
claims 1-56 under the written description provision of 35 U.S.C. § 112, first
paragraph is reversed.

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Anticipation:
ISSUE
Does the evidence of record support the Examiner’s finding that
Williams anticipates Appellants’ claimed invention?

FINDINGS OF FACT
FF 4. The Examiner finds that Williams teaches a method wherein a
“detectable moiety is released as a charged detectable moiety when the NP
[(nucleotide phosphate)] is incorporated into the primer nucleic acid” (Ans.
5).
FF 5. The Examiner finds that Williams teaches that “[u]pon incorporation
by a polymerase, the dNTP is hydrolyzed as usual and the liberated
pyrophosphate-dye moiety diffuses into the surrounding medium. The free
dye molecule is fluorescent and its appearance is imaged at video-rate under
a microscope . . . (page 22, lines 31 to top of page 23)” (Ans. 27). Therefore
the Examiner finds that “Williams teaches detection without separation by
charge” (Ans. 28).
FF 6. The reaction scheme encompassed by the claims is disclosed on page
11 of Appellants’ Specification is reproduced below:

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(Spec. 11: 24-25.) Appellants disclose that the foregoing scheme “shows the
most relevant molecules in the methods of this invention; namely the
terminal-phosphate-labeled nucleotide, the labeled polyphosphate by-
product and the enzyme-activated label” (Spec. 11: 21-23).
FF 7. Appellants disclose that the label (L) “is a phosphatase activatable
label which may be a chromogenic, fluorogenic, chemiluminescent
molecule, mass tag or electrochemical tag” (Spec. 12: 1-3).
FF 8. Williams teaches “charge-switch nucleotide phosphate probes” of
the following formula:

(Williams 15: 1-2.) “In Formula I, F is a fluorophore or dye” (Williams 15:
22).
FF 9. Williams teaches that “[m]any dyes or labels are suitable for charge-
switch nucleotide phosphates of the present invention” including
“fluorescent and chromogenic molecules” (Williams 16: 2-4).
FF 10. Appellants disclose a method wherein reagents are incubated
[I]n the presence of a nucleic acid polymerizing enzyme, a
phosphatase and a terminal-phosphate-labeled nucleoside
polyphosphate, which reaction produces labeled polyphosphate
if the nucleotide present is complementary to the target
sequence at the site of polymerization. The labeled
polyphosphate then reacts with phosphatase or a phosphate or
polyphosphate transferring enzyme to produce free label with a
signal readily distinguishable from the phosphate bound dye.

(Spec. 4: 3-9 (emphasis added).)
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FF 11. Williams teaches “the use of a phosphatase enhances the charge-
switch magnitude by dephosphorylating the [phosphate detectable moiety,]
PPi-F[2]” (Williams 25: 12-13).
FF 12. Appellants disclose that “while RNA and DNA polymerases are able
to recognize nucleotides with modified terminal phosphoryl groups, the
inventors have determined that this starting material is not a template for
phosphatases” (Spec. 11: 18-21).
FF 13. “In certain aspects [of Williams’ invention], a change in charge sign
. . . is utilized to separate the γ -dNTP-Dye from the PPi-Dye” (Williams 21:
18-19).
FF 14. Williams also teaches that “[u]pon incorporation by a polymerase,
the dNTP is hydrolyzed as usual and the liberated pyrophosphate-dye moiety
diffuses into the surrounding medium. The free dye molecule is fluorescent
and its appearance is imaged at video-rate under a microscope. A flowing
stream sweeps the dye away from the parent DNA molecule” (Williams 22:
31-34).
FF 15. Williams teaches another embodiment, wherein an intact NP probe is
separated from a phosphate detectable moiety, which comprises “applying
an electric field to the sample stream, thereby separating the labeled NP
from the charged detectable moiety” (Williams 22: 3-4 (emphasis added)).

PRINCIPLES OF LAW
“A claim is anticipated only if each and every element as set forth in
the claim is found, either expressly or inherently described, in a single prior

2 Williams defines “F” as “a fluorophore or dye” (Williams 15: 22).
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art reference.” Verdegaal Bros. v. Union Oil Co. of California, 814 F.2d
628, 631 (Fed. Cir. 1987).

ANALYSIS
Appellants provide separate arguments for the following groups of
claims: (I) claims 1-7, 9, 11-18, 20-23, 27-31 and (II) claims 32-38, 40, 42-
45, and 47-56. Claims 1 and 32 are representative. See 37 C.F.R. §
41.37(c)(1)(vii).

Claim 1:
Appellants contend that while Williams “suggests the use of a
phosphatase to enhance the charge-switch magnitude of the labeled
polyphosphate, the property/detectability of the label in Williams et al.
remains the same before and after the phosphatase treatment” (App. Br. 6-7).
Accordingly, Appellants contend that “[t]he only change phosphatase
treatment brings to the label in Williams et al. is a change in charge” (App.
Br. 7; see also FF 11).
In contrast, Appellants contend that their claim 1 requires the
phosphatase treatment “to generate a detectable species” (App. Br. 6).
We are not persuaded. Appellants’ claims and Williams both use a
terminal-phosphate-labeled nucleotide (FF 6 and 8). Appellants’ claims and
Williams both teach the use of a chromagenic or fluorogenic label (FF 7 and
9). We recognize the requirement in Appellants’ claim 1 that the terminal-
phosphate-labeled nucleoside polyphosphate “is substantially non-reactive to
phosphatase” (Claim 1). In that regard, we recognize Appellants’ disclosure
that they “have determined that . . . [the terminal-phosphate-labeled
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nucleotide] is not a template for phosphatases” (FF 12). This is, however, a
property of the terminal-phosphate-labeled nucleotide. Therefore, Williams’
terminal-phosphate-labeled nucleotide, which appears to be identical, would
also not be a template for phosphatases. Appellants have not provided
persuasive argument or evidence on this record to support a conclusion that
their terminal-phosphate-labeled nucleotide is different from that taught by
Williams.
Appellants and Williams both treat the by-product of the polymerase
reaction with a phosphatase (FF 6 and 11). Appellants have failed to
establish that the product resulting from their phosphatase treatment differs
from the product obtained by Williams’ phosphatase treatment.
We recognize Appellants’ contention that “[w]ithout physical
separation, it is impossible to distinguish the reaction product [of Williams’
method] from the dye-labeled nucleotide” (App. Br. 7). We are not
persuaded. As discussed above, Appellants have failed to establish a
structural difference between the reaction products of their claim 1 and those
taught by Williams. We recognize Appellants’ disclosure that phosphatase
treatment produces “free label with a signal readily distinguishable from the
phosphate bound dye” (FF 10), However, absent evidence to the contrary, it
would appear that if Appellants’ detectable species generated by
phosphatase treatment is readily distinguishable from untreated labeled
polyphosphate, or labeled nucleotide, then the same would be true of
Williams as it has the same structure.
In this regard, we note that certain aspects of Williams’ invention
utilize separation based on charge (FF 13 and 15). Williams also teaches a
method wherein “[u]pon incorporation by a polymerase, the dNTP is
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hydrolyzed as usual and the liberated pyrophosphate-dye moiety diffuses
into the surrounding medium. The free dye molecule is fluorescent and its
appearance is imaged at video-rate under a microscope. A flowing stream
sweeps the dye away from the parent DNA molecule” (FF 14).
Notwithstanding Appellants’ contention to the contrary (App. Br. 7 and 9),
there is no disclosure of charge separation in this embodiment of Williams’
invention. Instead, Williams makes clear that the “free dye molecule is
fluorescent and its appearance is imaged at video-rate under a microscope”,
implying that the liberated pyrophosphate-dye moiety can be distinguished
from the labeled nucleotide also present in the solution (FF 14). There is no
persuasive argument or evidence on this record to support a contrary
conclusion.

Claim 32:
For clarity, we emphasize that claim 32 does not require phosphatase
treatment. Appellants contend that “the property/detectability of the label in
Williams et al. remains the same before and after the polymerase reaction”
(App. Br. 8). In contrast, Appellants contend that in their claim 32, the
labeled polyphosphate produced from the polymerase reaction is readily
detectable (id.). For the reasons set forth above, we are not persuaded. For
the same reasons, we are not persuaded by Appellants’ contentions regarding
the requirement in Williams for a separation by charge of the dye-labeled
pyrophosphate product of the polymerase reaction from the dye-labeled
nucleotides, prior to detection (id.).

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CONCLUSION OF LAW
The evidence of record supports the Examiner’s finding that Williams
anticipates Appellants’ claimed invention. The rejection of claims 1 and 32
under 35 U.S.C § 102(b) as being anticipated by Williams is affirmed.
Claims 2-7, 9, 11-18, 20-23, 27-31 fall together with claim 1. Claims 33-38,
40, 42-45, and 47-56 fall together with claim 32.

Obviousness:
ISSUE
Did the Examiner err in concluding that Appellants’ claimed
invention would have been prima facie obvious to a person of ordinary skill
in this art in view of the evidence of record?

PRINCIPLES OF LAW
“[T]he [E]xaminer bears the initial burden, on review of the prior art
or on any other ground, of presenting a prima facie case of unpatentability.”
In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992). “The ‘prima facie
case’ serves as a procedural mechanism that shifts the burden of going
forward to the applicant, who must produce evidence and/or argument
rebutting the case of unpatentability.” Ex parte Frye,
http://www.uspto.gov/ip/boards/bpai/decisions/prec/fd09006013.pdf, slip
op. at 8 (BPAI Feb. 26, 2010) (precedential).
An appellant may attempt to overcome an examiner’s
obviousness rejection on appeal to the Board by submitting
arguments and/or evidence to show that the examiner made an
error in either (1) an underlying finding of fact upon which the
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final conclusion of obviousness was based, or (2) the reasoning
used to reach the legal conclusion of obviousness. Similarly,
the applicant may submit evidence of secondary considerations
of non-obviousness.

Id. at 9. “[T]he Board will generally not reach the merits of any issues
not contested by an appellant.” Id. at 10.

ANALYSIS
For each rejection under 35 U.S.C § 103(a) Appellants contend that
the secondary reference relied upon by the Examiner fails to make up for the
deficiency in Williams discussed above (App. Br. 9-11). For the reasons set
forth above, we find no deficiency in the Examiner’s reliance on Williams.
Accordingly, we are not persuaded by Appellants’ contention to the
contrary.

CONCLUSION OF LAW
The Examiner did not err in concluding that Appellants’ claimed
invention would have been prima facie obvious to a person of ordinary skill
in this art in view of the evidence of record.
The rejection of claim 8 under 35 U.S.C § 103(a) as unpatentable over
the combination of Williams and Wittwer is affirmed. Because the claims
were not separately argued claim 39 falls together with claim 8. See 37
C.F.R. § 41.37(c)(1)(vii).
The rejection of claim 10 under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Keller is affirmed. Because the
claims were not separately argued claim 41 falls together with claim 10.
See 37 C.F.R. § 41.37(c)(1)(vii).
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The rejection of claim 19 under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Lichtenwalter is affirmed. Because
the claims were not separately argued claim 46 falls together with claim 19.
See 37 C.F.R. § 41.37(c)(1)(vii).
The rejection of claim 23 under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Hattori is affirmed. Because the
claims were not separately argued claims 24 and 25 fall together with claim
23. See 37 C.F.R. § 41.37(c)(1)(vii).
The rejection of claim 25 under 35 U.S.C § 103(a) as unpatentable
over the combination of Williams and Bronstein is affirmed. Because the
claims were not separately argued claim 26 falls together with claim 25.
See 37 C.F.R. § 41.37(c)(1)(vii).

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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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