Ex Parte Stender

Board of Patent Appeals and Interferences

May 4, 2012

10917013 (B.P.A.I. May. 4, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte HENRIK STENDER
__________

Appeal 2011-010844
Application 10/917,013
Technology Center 1600
__________

Before DONALD E. ADAMS, JEFFREY N. FREDMAN, and
STEPHEN WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) from the rejection of
claims directed to a PNA oligomer, an oligomer set, and a kit. The Patent
Examiner rejected the claims for obviousness. We have jurisdiction under
35 U.S.C. § 6(b). We affirm.
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STATEMENT OF THE CASE
“This invention is related to the field of probe-based determination of
microorganisms such as Enterococcus faecalis and other Enterococcus
species.” (Spec. 2, ll. 14-15.) The invention concerns peptide nucleic acid
(PNA) probes. “PNA is a non-naturally occurring polyamide that can
hybridize to nucleic acid (DNA and RNA) with sequence specificity.” (Id.
at ll. 26-27.)
Claims 1, 4-13, 15-18, 21-31, and 43-65 are on appeal. Claim 1 is
representative and reads as follows:
1. A PNA oligomer having a nucleobase sequence selected from the
group consisting of CCT-CTG-ATG-GGT-AGG (SEQ ID NO: 1), CCT-
TCT-GAT-GGG-CAG (SEQ ID NO: 2), exactly the complement to SEQ ID
NO: 1 and exactly the complement to SEQ ID NO: 2.

The Examiner rejected the claims as follows:
 claims 1, 4-6, 8, 13, 15-18, 21-23, 25, 30, 31, 48, 52-56, 60, and 61
under 35 U.S.C. § 103(a) as unpatentable over Hogan ‘789,1 Apfel,2
and search reports AC AAH20853 and AC AAH20848;3
 claims 43-47 and 62-65 under 35 U.S.C. § 103(a) as unpatentable over
Hogan ‘789, Apfel, search reports AC AAH20853 and AC
AAH20848, and Hogan ‘484;4 and

1 James J. Hogan, WO 00/66789, published Nov. 9, 2000.
2 Heiko Apfel et al., DE 19955303 A1, published May 31, 2001.
3 The search reports are said to be attached to an Office Action mailed June
21, 2006. (Office Action, June 21, 2006, at 5.) We cannot find the search
reports in the file, but they appear to be only cumulative with Apfel’s
disclosures. (See, e.g., Ans. 4, directing attention to Apfel “pg. 16, table 4
and the search report.”) As the search reports are not mentioned in the
arguments, we conclude that a remand to obtain the missing search reports is
not required.
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 claims 7, 9-12, 24, 26-29, 49-51, and 57-59 under 35 U.S.C. § 103(a)
as unpatentable over Hogan ‘789, Apfel, and search reports AC
AAH20853 and AC AAH20848, and Rigby.5

OBVIOUSNESS
The Issue
The Examiner’s position is that Hogan ‘789 taught identifying
microbes including Enterococcus, in biological samples, by hybridizing
sample nucleic acid with a collection of probes having binding specificity
for microbe nucleic acid. (Ans. 3.) The Examiner found that Hogan taught
using PNA probes (id.), but Hogan did not teach a PNA having SEQ ID
NO:1 or 2 (id. at 4). Like Hogan, Apfel also taught a method for directly
identifying organisms in a biological sample by using a labeled
hybridization probe. (Id.) Apfel disclosed Enterococcus specific probe
sequences SEQ ID NO:17 and 22, which comprise Appellant’s SEQ ID
NO:2 and 1 respectively. The Examiner concluded it would have been
obvious to make a PNA probe “which has a nucleobase sequence of either
SEQ ID NO:1 or 2 because Apfel et al. disclose that the method for the
direct identification of organisms by using these nucleic acid sequences as
hybridization probes is sensitive and specific.” (Id.)
Appellant contends that the claims “have been amended and each now
uses the closed transitional phrase ‘consisting of,’” and “the PNA oligomer
that is claimed cannot include any additional elements.” (App. Br. 11-12.)
Appellant argues that Apfel’s “SEQ IDs NOs: 17 and 22 comprise,

4 James J. Hogan, US 6,235,484 B1, issued May 22, 2001.
5 Susan Rigby et al., WO 02/057493 A2, published July 25, 2002.
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respectively, SEQ IDs NOs: 1 and 2, plus three extra bases each. Since the
language of the instant claims excludes any sequences other than precisely
SEQ IDs NOs: 1 and 2, even if Hogan and Apfel were combined, the
combination would fail to recite every element of the instant claims.” (Id. at
12.) Appellant further argues that the rejection failed to establish that it
would have been obvious to modify Apfel’s 18-mer sequences by truncating
them to the 15-mer sequences recited in the claims. (Id. at 12-17.) Claims
43-47 and 62-65 and claims 7, 9-12, 24, 26-29, 49-51, and 57-59 were
separately rejected over Hogan ‘789 and Apfel in combination with other
references, but Appellant relies on the same arguments for the additional
rejections. (Id. at 17-18.)
The Examiner responds that as the claims recite “a PNA oligomer
having a nucleobase sequence,” and “[s]ince ‘having’ is considered to be
open language, the claimed PNA oligomer encompasses the sequence of
SEQ ID NO:1, SEQ ID NO:2, or their complement sequences, as well as
larger sequences comprising them.” (Ans. 8.) The Examiner contends that
the fact patterns in the obviousness cases Appellant cites are not closely
related to the facts in this case. (Id. at 9.)
The issue is whether the term “having” in claim 1 is properly
interpreted as open language, thus allowing claim 1’s PNA to read on the
18-mer Apfel sequences.

Findings of Fact
1. Apfel disclosed two probing sequences for detecting Enterococcus
faecalis, SEQ ID NO:17 and SEQ ID NO:22. (Apfel at 16, Table 4.)
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2. The first of Appellant’s probing sequences aligns with Apfel’s SEQ
ID NO:22 as follows:
Apfel’s SEQ ID NO:22 CCCTCTGATGGGTAGGTT
Appellant’s SEQ ID NO:1 CCTCTGATGGGTAGG

(Id.)
3. The second of Appellant’s probing sequences aligns with Apfel’s
SEQ ID NO:17 as follows:
Apfel’s SEQ ID NO:17 CCCCTTCTGATGGGCAGG
Appellant’s SEQ ID NO:2 CCTTCTGATGGGCAG

(Id.)
4. Appellant’s Specification states:
The probing nucleobase sequence suitable for determining
Enterococcus faecalis and/or other Enterococcus species can have a
length of 18 or fewer PNA subunits. . . . The PNA oligomers can
comprise a nucleobase sequence that is one hundred percent
homologous to Seq. ID No. 1 or Seq. ID No. 2 or even be exactly Seq.
ID No. 1 or Seq. ID No. 2.

(Spec. 17, ll. 4-10.)
5. Appellant’s Specification provides this definition:
b. As used herein, "nucleobase sequence" means any segment, or
aggregate of two or more segments, of a polymer that comprises
nucleobase-containing subunits. Non-limiting examples of suitable
polymers include oligodeoxynucleotides (e.g. DNA),
oligoribonucleotides (e.g. RNA), peptide nucleic acids (PNA), PNA
chimeras, PNA oligomers, nucleic acid analogs and/ or other nucleic
acid mimics.

(Id. at 4, ll. 17-21.)

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Principles of Law
“During patent examination the pending claims must be
interpreted as broadly as their terms reasonably allow.” In re Zletz,
893 F.2d 319, 321 (Fed. Cir. 1989) (citations omitted). Limitations
are not to be read into the claims from the specification. Id.
The term “‘[h]aving’ . . . does not create a presumption that the body
of the claim is open.” The full context must be examined to determine if
“having” limits a claim to recited elements. Crystal Semiconductor Corp. v.
TriTech Microelectronics Intern., Inc., 246 F.3d 1336, 1348 (Fed. Cir.
2001). See also, Regents of the University of California v. Eli Lilly & Co.,
119 F.3d 1559, 1573 (Fed. Cir. 1997) (“‘having’ still permitted inclusion of
other moieties”); In re Crish, 393 F.3d 1253, 1257 (Fed. Cir. 2004) (“The
reasonable interpretation of the claims containing both of the terms
‘comprising’ and ‘consists’ is that the term ‘consists’ limits the ‘said
portion’ language to the subsequently recited numbered nucleotides, but the
earlier term ‘comprising’ means that the claim can include that portion plus
other nucleotides. Read in context, the claims thus do not preclude a DNA
sequence having additional nucleotides.”).
The term “group consisting of” is a closed term when it defines a
Markush group. Abbott Labs. v. Baxter Pharm. Products, Inc., 334 F.3d
1274, 1280-81 (Fed. Cir. 2003).

Analysis
When a composition claim uses two transitional terms, and the first is
more inclusive than the second, the broader first term may effectively
broaden the claim beyond the scope of the narrower second term. E.g,
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Crish, 393 F.3d at 1257. In Appellant’s claim 1, the first transitional term is
“having,” which may or may not be open language depending on the
context, see Crystal Semiconductor, 246 F.3d at 1348, and the second
transitional term is “group consisting of,” which is closed language, see
Abbott Labs., 334 F.3d at 1280-81.
The plain language of claim 1 does not impose a narrow meaning on
“having.” The Specification did not define “having” narrowly, and
expressly stated that the “probing nucleobase sequence . . . can have a length
of 18 or fewer PNA subunits.” (FF 4.) Apfel’s sequences are 18-mers. (FF
2 and 3.) The Specification further explained that the “PNA oligomers can
comprise a nucleobase sequence that is one hundred percent homologous to
Seq. ID No. 1 or Seq. ID No. 2 or even be exactly Seq. ID No. 1 or Seq. ID
No. 2” (FF 4), meaning that Appellant’s oligomers could comprise Apfel’s
18-mers. In the context of the Specification’s options, there is no reason to
infer that “having” is a closed term. Using the broadest reasonable
interpretation in light of the Specification, we conclude that “having” is open
language. Like the claim in Crish, claim 1 includes PNAs that comprise
sequences selected from the group consisting of SEQ ID NO:1, etc.
We acknowledge that Appellant replaced the open term “comprising”
with the potentially open or potentially closed term “having.” Interpreting
the claim in light of the Specification leads us to conclude that Appellant
replaced one open term with another open term, and that the amendment was
ineffective to avoid the prior art. Appellant could have claimed narrowly by
claiming, for example, a “PNA selected from the group consisting of SEQ
ID NO:1 . . . ,” etc., or a “PNA that is exactly SEQ ID NO:1”, etc., an option
listed in the Specification. That is, there were ways to avoid using the open
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language “having,” and no compelling reason to interpret the term opposite
the open meaning indicated in the context of the Specification.
Claims 4-6, 8, 13, 15-18, 21-23, 25, 30, 31, 48, 52-56, 60, and 61 have
not been argued separately and therefore fall with claim 1. 37 C.F.R.
§ 41.37(c)(1)(vii). Although claims 43-47 and 62-65 and claims 7, 9-12, 24,
26-29, 49-51, and 57-59 were separately rejected over Hogan ‘789 and Apfel
in combination with other references, Appellant has relied on the claim 1
arguments to address those rejections. Accordingly, claims 43-47 and 62-65
and claims 7, 9-12, 24, 26-29, 49-51, and 57-59 also fall with claim 1.

SUMMARY
We affirm the rejection of claims 1, 4-6, 8, 13, 15-18, 21-23, 25, 30,
31, 48, 52-56, 60, and 61 under 35 U.S.C. § 103(a) as unpatentable over
Hogan ‘789, Apfel, and search reports AC AAH20853 and AC AAH20848.
We affirm the rejection of claims 43-47 and 62-65 under 35 U.S.C.
§ 103(a) as unpatentable over Hogan ‘789, Apfel, search reports AC
AAH20853 and AC AAH20848, and Hogan ‘484.
We affirm the rejection of claims 7, 9-12, 24, 26-29, 49-51, and 57-59
under 35 U.S.C. § 103(a) as unpatentable over Hogan ‘789, Apfel, search
reports AC AAH20853 and AC AAH20848, and Rigby.

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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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