Ionis Pharmaceuticals, Inc.

Patent Trials and Appeals Board

Nov 6, 2020

2020002360 (P.T.A.B. Nov. 6, 2020)

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.
15/407,037 01/16/2017 Michael Oestergaard CHEM0084US.C1 4468
130682 7590 11/06/2020
McNeill Baur PLLC/Ionis Pharmaceuticals
125 Cambridge Park Drive
Suite 301
Cambridge, MA 02140
EXAMINER
SHIN, DANA H
ART UNIT PAPER NUMBER
1635
NOTIFICATION DATE DELIVERY MODE
11/06/2020 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):
docketing@mcneillbaur.com
eofficeaction@appcoll.com
rebecca.scarr@mcneillbaur.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte MICHAEL OESTERGAARD,
THAZHA P. PRAKASH, PUNIT P. SETH, and
ERIC E. SWAYZE

Appeal 2020-002360
Application 15/407,037
Technology Center 1600
____________

Before DONALD E. ADAMS, RICHARD M. LEBOVITZ, and
ULRIKE W. JENKS, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
The Examiner rejected the claims under 35 U.S.C. § 103 as obvious.
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the Examiner’s
decision to reject the claims. We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as Ionis
Pharmaceuticals, Inc. Appeal Br. 4.
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STATEMENT OF THE CASE
An oral hearing was held October 1, 2020. A transcript of the hearing
will be entered into the record in due course.
The Examiner rejected the claims2 in the Final Office Action as
follows:
I. Claims 1, 6–11, and 14–22 under pre-AIA 35 U.S.C. § 103(a) as
obvious in view of Seth et al. (US 2011/0130441 A1, published Jun. 2,
2011) (“Seth”) and Thompson et al. (US 2002/0142980 Al, published Oct. 3,
2002) (“Thompson”).
II. Claims 1, 6–11, and 14–22 on the ground of nonstatutory
obviousness-type double patenting over claims 16-47 of U.S. Patent No.
7,399,845 B2 (“the ’845 patent”) in view of Seth and Thompson.
III. Claims 1, 6–11, and 14–22 on the ground of nonstatutory
obviousness-type double patenting over claims 1–5 and 7–22 of U.S. Patent
No. 9,290,534 B2 (“the ’534 patent”) in view of Seth and Thompson.
V. Claims 1, 6–11, and 14–22 on the ground of nonstatutory
obviousness-type double patenting over claim 273, 276–278, 280-282, and
284–294 of Application No. 14/238,441 (now U.S. Patent No. 10,202,599
B2) (“the ’599 patent”).
Claim 1, with indentations added for clarity, is reproduced below:
1. A gapped oligomeric compound comprising a contiguous
sequence of linked monomer subunits having a gap region
located between a 5’-region and a 3’-region
wherein the 5’ and 3’-regions each, independently, have
from 2-5 contiguous modified nucleosides, each independently
selected from a bicyclic nucleoside comprising a bicyclic

2 The claims were also rejected over Application 14/238,439, but this
application is abandoned.
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furanosyl sugar moiety and a modified nucleoside comprising a
furanosyl sugar moiety having a 2’-substituent group selected
from F, OCH3, O(CH2)2-OCH3 and OCH2C(=O)-N(H)CH3,
wherein one or more of the modified nucleosides is a
bicyclic nucleoside, and
wherein the gap region has from 8-10 contiguous β-D-2’-
deoxyribonucleosides and wherein two of the internucleoside
linking groups located between β-D-2’-deoxyribonucleosides in
the gap region have Formula I:

wherein:
each X is O or S;
each Q is, independently, selected from C1-C6 alkyl,
substituted C1-C6 alkyl, C2-C6 alkenyl, C(=O)OH and
CH2C(=O)OH; and
each substituted group comprises one or more optionally
protected substituent groups independently selected from
halogen, OJ1, SJ1 and OC(=O)J1;
each J1 is, independently, H or C1-C6 alkyl;
wherein each internucleoside linking group other than
internucleoside linking groups having Formula I is,
independently, a phosphodiester or a phosphorothioate
internucleoside linking group; and
wherein the gap region comprises only two
internucleoside linking groups having Formula I,
wherein the two internucleoside linking groups having
Formula I are located between nucleosides 1 and 3, counting
from the 5' end of the gap region.

CLAIM 1
Claim 1 is directed to a “gapped oligomeric compound” having a “gap
region” located between 5’- and 3’- nucleoside regions. The compound is
made up of deoxyribonucleosides, some of which are modified or
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derivatized. At least one bicyclic nucleoside is present in each of the 5’- and
a 3’- nucleoside regions. The gap region has from 8–10 contiguous
deoxyribonucleosides. Two of the internucleoside linkages that attach the
deoxyribonucleosides in the gap region have the structure of Formula I,
where “each internucleoside linking group other than internucleoside linking
groups having Formula I is, independently, a phosphodiester or a
phosphorothioate internucleoside linking group.” The two internucleoside
linkages of Formula I are located between nucleosides 1 and 3, counting
from the 5’ end of the gap region. The reason to include methylphosphonate
linkages between the nucleosides is because of their well-known resistance
to nucleases, making the oligomeric compound more stable when
administered. Thompson ¶¶ 173, 174; Seth ¶ 4.
In response to a requirement by the Examiner to elect a species of
Formula I, Appellant elected the chemical groups in the formula which form
the neutral linkage “methylphosphonate.” Response to Restriction
Requirement (Nov. 17, 2017); Non-final Office Act. 3–4 (Feb. 4, 2018).
Throughout this decision, the internucleoside linkage of Formula I is
referred to as “methylphosphonate.”

I. 103 REJECTION BASED ON SETH AND THOMPSON
Based on the combination of Seth and Thompson, the Examiner
determined that claim 1 would have been obvious to one of ordinary skill in
the art at the time of the invention. Non-final Act. 2–7.
Seth describes an oligomeric compound having a bicyclic nucleoside
attached to the 5’ and 3’ end by a neutral internucleoside linkage. The
oligomeric region inside the 5’ and 3’ ends corresponds to the “gap region”
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of rejected claim 1. The linkage at the 5’ and 3’ end of the gap region of
Seth is, independently, (1) phosphotriester, (2) methylphosphonate, (3)
MMI, (4) amide-3, (5) formacetal, or (6) thioformacetal. Seth, claims 1, 6.
One of the six choices of neutral linkages is (2) methylphosphonate, the
same internucleoside linkage which is claimed. Seth also has bicyclic
nucleosides in the 5’- and 3’-regions as required by claim 1. However, Seth
does not describe the position of the neutral linkages as being between
nucleosides 1 and 3 of the gap region as required by rejected claim 1.
Instead, the neutral linkages are outside this region.
Thompson describes an oligomeric compound (a “nucleic acid
molecule”) comprised of nucleosides. The compound has a three region
structure similar to the claimed three region structure, namely, a gap region
between 5’- and 3’-nucleoside regions. Thompson, claim 4. Claim 4 of
Thompson is reproduced below (annotated with bracketed numbering):
1. A nucleic acid molecule having the formula XIV:
xpxpxpxpxpxpxpDsDsDsDsDsDsDsDsDsxpxpxpxpxpxpx
wherein each x is independently a 2’-O-alkyl-thio-alkyl
nucleotide, each D is independently a deoxyribonucleotide or
2’-arabinofluoro nucleotide, each s is independently [1] a
phosphorothioate[,] [2] phosphorodithioate, [3] 5’-
thiophosphate, [4] 3’-thiophosphate, or [5] methylphosphonate
internucleotide linkage, and each p is independently a
phosphodiester internucleotide linkage and each iB is
independently an inverted abasic moiety.

The region “DsDsDsDsDsDsDsDsDs” of Thompson’s claim 1
corresponds to the claimed gap region. There are five choices for the
internucleotide linkage “s.” One of the five choices is “methylphosphonate,”
the same linkage which is claimed. Unlike Seth, Thompson expressly
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discloses methylphosphonate linkages in the gap region, including at
nucleosides 1 and 3 positions as required by rejected claim 1.
The principal issue in this rejection is whether it would have been
obvious to choose only two methylphosphonate linkages in the gap region of
Seth and Thompson and place them between nucleosides 1 and 3 as required
by rejected claim 1.
Appellant argues that the neutral internucleoside linkages in Seth are
outside the gap region, and thus Seth would not have suggested placing them
inside the gap in the specific number and position as claimed. Appeal Br.
11–12. Appellant also argues that Thompson “does not exemplify any
nucleic acid molecules containing a methylphosphonate internucleoside
linkage, much less a nucleic acid molecule containing exactly two
methylphosphonate internucleoside linkages at the specific positions recited
in the present claims.” Id. at 12. Appellant contends that Thompson’s
statements about methylphosphonate toxicity would have motivated the
skilled worker to use the alternative linkages of “phosphorodithioate, 5’-
thiophosphate, and 3’-thiophosphate internucleoside linkages, in place of
phosphorothioate and methylphosphonate internucleoside linkages.” Id.
Appellant also states there are “9 linkages denoted by ‘s’ in claim 4 of
Thompson, and five possible internucleoside linkages at each position, for a
total of 59, or over 1.9 million possible internucleoside linkage motifs in the
gap” which would provide no reason “to select exactly the motif claimed
from the 1.9 million possible.” Id. at 14.

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Discussion
To make the claimed gap region based on the combination of Seth and
Thompson, the skilled worker would have to pick the methylphosphonate
from the group of five different internucleotide linkages recited in claim 4 of
Thompson, and then choose only the two contiguous positions between
nucleotides 1 and 3 to place them at. The number of possible combinations
to choose from is 1.9 million, which seems like large number, but the
choices are limited with only one of five linkages to choose from and then
place in two of nine different positions. As the Examiner illustrated by
writing out a number of different “predictable” motifs with two
methylphosphonate linkages3 (Final Act. 5, 7), one of ordinary skill in the art
could easily envision all the species within the genus described by
Thompson. While this may not be a case like In re Petering, 301 F.2d 676,
681–682 (CCPA 1962) where the small number of species in the chemical
genus allowed one of ordinary skill in the art to “at once envisage” the
claimed subject matter in the prior art disclosure, it also not In re Baird, 16
F.3d 380, 382 (Fed. Cir. 1994) where the large number of variables, and a
teaching away, precluded a finding that one species would have been
obvious. Here, the structure of the gap region of Thompson’s nucleic acid is
so well defined and limited in the number of choices – one of five different
linkages and at any position(s) of the nine contiguous nucleotides – that the
skilled worker would readily recognize that Thompson’s gap region genus is
shorthand for 1.9 million species as if each had been written out. Of course,
writing out 1.9 million species by hand might be impractical, but this is not
the test of obviousness.
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Appellant contends that Thompson points away from including two
methylphosphonate internucleotide because of their toxicity. Appeal Br. 12.
This argument is based on the following disclosure from Thompson:
While chemical modification of oligonucleotide internucleotide
linkages with phosphorothioate, phosphorothioate, and/or 5’-
methylphosphonate linkages improves stability, too many of
these modifications can cause some toxicity. Therefore when
designing nucleic acid molecules the amount of these
internucleotide linkages should be minimized. The reduction in
the concentration of these linkages should lower toxicity
resulting in increased efficacy and higher specificity of these
molecules.
Thompson ¶ 173 (emphasis added).
We have considered this disclosure and do not agree it would dissuade
the skilled worker from using a methylphosphonate linkage. Above all,
Thompson expressly describes a nucleic acid compound with
methylphosphonate. Therefore, it is inconsistent to argue that Thompson
would motivate the skilled worker to use other linkages as alternatives to
methylphosphonate (Appeal Br. 12) when methylphosphonate is expressly
recited as a choice in a compound which Thompson claims as its invention.
Thompson, claim 4.
Thompson does not identify what number is “too many of” the
methylphosphonate linkages. Thompson ¶ 173. But Thompson’s claim 4 has
at least one methylphosphonate because it is one of the five possible choices.

3

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It has no limitation as to how many can be included in the nine nucleoside
member region. Seth’s compound can have at least two methylphosphonate
because claim 6 of Seth has at neutral linkage at each end of the gap region,
and methylphosphonate is one of the six possible linkages in its compound.
Seth, claims 1, 6. Consequently, the evidence supports the Examiner’s
determination that Seth and Thompson reasonably suggests that at least
several methylphosphonate linkages may be in the gap region of an
oligomeric compound without concerns about toxicity.
While there is no explicit embodiment disclosed in Seth and
Thompson of a compound with at least two methylphosphonate linkages, a
reference disclosure is not limited to its preferred embodiments, but is
available for all that it discloses and suggests to one of ordinary skill in the
art. In re Lamberti, 545 F.2d 747, 750 (CCPA 1976); Merck & Co v.
Biocraft Laboratories, 874 F.2d 804, 807 (Fed. Cir. 1989) (“[A]ll
disclosures of the prior art, including unpreferred embodiments, must be
considered.”). Thus, Appellant’s argument about the lack of specific
exemplification of an oligomer with a methylphosphonate linkage is
unavailing. Appeal Br. 15.
With respect to placing these two methylphosphonate linkages
between nucleosides 1 and 3, while there is no specific embodiment with the
linkages at these positions, Thompson discloses a genus which includes
them. There is a presumption of obviousness when a claimed invention
recites range of values falls within a range of values disclosed in the prior
art. In re Peterson, 315 F.3d 1325, 1329 (Fed. Cir. 2003). This same
principle applies here when the “range” is the number and position of
internucleotide linkages in Thompson’s gap region. It would have been
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routine optimization to determine the number of linkages and their position
to enhance the compound’s stability without producing toxicity. Final Act. 7.

Unexpected results
One way for a patent applicant to rebut a prima facie case of
obviousness is to make a showing of ‘unexpected results,’ i.e.,
to show that the claimed invention exhibits some superior
property or advantage that a person of ordinary skill in the
relevant art would have found surprising or unexpected.
In re Soni, 54 F.3d 746, 750 (Fed. Cir. 1995).
Appellant contends that the nonobviousness of the claim 1 is
supported by “unexpected results.” Appeal Br. 15. Specifically, Appellant
states that Examples 26 and 27 of the Specification “describe administration
to mice of gapped oligomeric compounds comprising two internucleoside
linking groups of Formula I located between positions 1 and 3 of the gap,
and corresponding ‘parent’ gapped oligomeric compounds with
phosphorothioate internucleoside linkages at those positions.” Id. at 16.
Summarizing the results in the Specification, Appellant explains that “ALT
[alanine transferase] levels, which are a measure of toxicity, were about 5 to
over 100 fold lower following administration of a compound of the present
claims, compared to same compound with phosphorothioate in place of
linking groups of Formula I.” Appeal Br. 16. See Specification at page 102,
lines 21-32; and page 105, lines 8-28.
The Examiner responded that “it was known and expected that at least
one neutral linkage in place of a phosphorothioate linkage significantly
reduces ALT (alanine aminotransferase) levels when compared to a full-
phosphorothioate modified oligomer as demonstrated by Seth.” Ans. 10. As
evidence, the Examiner pointed to Seth’s teaching that MMI, a neutral
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internucleotide linkage, in an oligomeric compound with the remaining
linkages being phosphorothioate, was less toxic than an oligomeric
compound with all phosphorothioate linkages. Id. at 10–11.
The experiment relied upon Appellant in support of nonobviousness
involved a compound with all phosphorothioate internucleoside linkages
except for two methylphosphonates. The claimed oligomeric compound is
not limited to such a compound. Claim 1 is broader, specifically reciting
“each internucleoside linking group other than internucleoside linking
groups having Formula I is, independently, a phosphodiester or a
phosphorothioate internucleoside linking group” (emphasis added). Thus,
the claim covers a compound with no phosphorothioate linkages, but the
comparison is between a compound with all phosphorothioates and a
compound with all but 2 linkages being phosphorothioate. Thompson ¶ 173
(reproduced above) teaches that phosphorothioate linkages also have
toxicity. A showing of unexpected must be “commensurate in scope with the
degree of protection sought by the claimed subject matter.” In re Harris,
409 F.3d 1339, 1344 (Fed. Cir. 2005). Appellant did not demonstrate that
the asserted reduced toxicity would be observed when compared to an
oligomeric compound with fewer that all, or no phosphorothioate linkages.
In addition to this, Appellant did not demonstrate the criticality of
placing methylphosphonate linkages at the recited positions between
nucleosides 1 and 3. The comparison described in the Specification is
between a compound with no methylphosphonates and a compound with
two. However, as discussed above, the cited combination of Seth and
Thompson reasonably suggests the presence of methylphosphonate linkages
in a gap region of an oligomeric compound. The data described by Appellant
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in the Specification does not show that methylphosphonates at the recited
positions is any less toxic, or otherwise superior, to a compound with
methylphosphonates at any other position, such as at the positions described
in Seth at the linkage to the bicyclic nucleotide. “To be particularly
probative, evidence of unexpected results must establish that there is a
difference between the results obtained and those of the closest prior art, and
that the difference would not have been expected by one of ordinary skill in
the art at the time of the invention.” Bristol-Myers Squibb Co. v. Teva
Pharm. USA, Inc., 752 F.3d 967, 977 (Fed. Cir. 2014). A compound with all
phosphorothioate linkages is not the closest prior art to the claimed
compound with two methylphosphonates, with no requirement that any
phosphorothioate is present.
The rejection of claim 1 as obvious in view of Seth and Thompson is
affirmed. Claims 6–11 and 14–22 fall with claim 1 because separate reason
for their patentability were not provided. 37 C.F.R. § 41.37(c)(1)(iv).

II. OBVIOUSNESS-TYPE DOUBLE-PATENTING OVER CLAIMS OF
’845 PATENT
Claim 16 of the ’845 patent is directed to an oligomeric compound
comprising a bicyclic nucleoside as claimed and internucleoside linkages
between the nucleoside monomers. See Appeal Br. 18. The claim does not
specific the type of linkage, but the disclosure lists methylphosphonate
linkages as example of a useful linkage. ’845 patent, col. 16, ll. 44-50. The
Examiner found it would have been obvious to have incorporated
methylphosphonate linkages into the compound of the claims of the ’845
patent to enhance its therapeutic properties and stability as described by Seth
and Thompson. Non-final Act. 9
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Appellant states that the Examiner “relied on Seth and Thompson for
inclusion of methylphosphonate linkages in the oligonucleotides of the ’845
patent claims.” Appeal Br. 18. However, the linkages in the patented claims,
when read in light of the ’845 patent disclosure, would be understood to
encompass methylphosphonate linkages between the nucleosides. In an
obviousness-type double-patenting analysis, while the earlier patent’s
specification cannot be used as prior art to the later patent application
claims, it can be consulted to ascertain the meaning of the words in the claim
to interpret the patented claim’s proper scope. Sun Pharmaceutical
Industries Ltd. v. Eli Lilly and Co., 611 F.3d 1381, 1387 (Fed. Cir. 2010).
With respect to the teachings of Seth and Thompson, Appellant relies
on the same arguments for the obviousness rejection which we find
unpersuasive. Consequently, for the same reasons, we affirm the
obviousness-type double patenting rejection of claim 1 over the claims of the
’845 patent in view of Seth and Thompson. Claims 6–11 and 14–22 fall with
claim 1 because separate reason for their patentability were not provided. 37
C.F.R. § 41.37(c)(1)(iv).

III. OBVIOUSNESS-TYPE DOUBLE-PATENTING OVER CLAIMS OF
’534 PATENT
The ’534 patent is based on the Seth application. Claim 1 of the patent
is similar to claim 1 of Seth, where a neutral internucleoside linkage attaches
a gap region to a bicyclic nucleoside. The neutral linkage is the same six
recited in Seth’s claim 1, where the methylphosphonate is one of the
choices. The Examiner’s rejection is the same as that set forth for the
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obviousness-type double-patenting rejection based on the ’845 patent, Seth,
Thompson. Non-final Act. 10.
Appellant argues that because
Seth and Thompson would not have rendered obvious the
specific number and position of internucleoside linking groups
of Formula I recited in the present claims, the present claims
also would not have been obvious over claims 1–5 and 7–22 of
the '534 patent in view of Seth and Thompson.
Appeal Br. 18. These arguments have been addressed and found to be
unavailing. Consequently, for the same reasons, we affirm the obviousness-
double patenting rejection of claim 1 over the claims of the ’534 patent in
view of Seth and Thompson. Claims 6–11 and 14–22 fall with claim 1
because separate reason for their patentability were not provided. 37 C.F.R.
§ 41.37(c)(1)(iv).

IV. OBVIOUSNESS-TYPE DOUBLE-PATENTING OVER CLAIMS OF
’599 PATENT
Application 14/238,441 has issued as the ’599 patent. The Examiner
made note that the application matured into a patent, but referred to the
claim numbers in the application. We have focused on claim 1 of the issued
patent.
The key difference between the oligomeric compound of the ’599
patent claim 1 and rejected claim 1 is the lack of an explicit recitation of
methylphosphonate linkages in the claims of the ’599 patent. The claims of
the ’599 patent are directed to oligomeric compounds, but they do not
specify the type of internucleotide linkage between the nucleosides. The
’599 patent claims also recite a specific motif to the 5’ region, but rejected
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claim 1 is broader and we understand it to include oligomeric compounds
with such motifs.
Although the claims of the patent do not identify the nature of the
linkages between the nucleosides of the oligomeric compound, the
specification of the ’599 patent describes the presence of two
methylphosphonate linkage. ’599 patent, col. 19 (Embodiment 219). The
Examiner found:
That is, any type of linkages can be used when making the
gapmer claimed in the ’599 patent, and furthermore, when one
of ordinary skill in the art sets out to determine which gapmer
structures are encompassed by such broad claims in support of
the specification of the issued patent, one of ordinary skill in
the art would readily determine that the broad scope of the ’599
patent claims does encompass a gapmer “comprising two
methylphosphonate internucleoside linkages” (see
“Embodiment 219”), wherein “at least one of the 3rd, 4th, 5th,
6th, and/or 7th internucleoside from the 5’ end is a
methylphosphonate internucleoside linkage” (see “Embodiment
220”). Now, note that the gapmer of the ‘599 patent claims has
a 5-mer 5’ wing region. As such, the scope of the gapmer
having a 5-mer 5’ wing region as claimed in the ‘599 patent
claims embodies a gapmer having “two methylphosphonate
internucleoside linkages” at positions 6th and 7th “from the 5’
end” of the gapmer (see the aforementioned “Embodiments”
disclosed in the ’559 patent specification), wherein such
positions are located in the first two positions within the gap
region as claimed in the instant case, thereby rendering the
instant claims an obvious variation/embodiment of the broadly
written ’599 patent claims.
Ans. 16 (bold in original).
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Appellant did not dispute the Examiner’s findings in Reply Brief.4
Appellant argues that the Examiner pointed to unclaimed Embodiment
219, which is improper. Appeal Br. 14. Appellant argues:
While the Examiner may consider the specification of the
reference application to determine a definition of a claim term,
the Examiner may not import specific structural elements from
the specification into the claims of the reference application
under the guise of determining what the claims “read on.” The
Examiner must explain how the claims, and not the
specification, of the cited application render obvious the claims
of the present application.
Appeal Br. 22.
Appellant’s argument does not persuade us that Examiner erred. The
Examiner clearly used the ’599 patent specification to ascertain the scope of
the claims of the ’599 patent. Because the patented ’599 claims do not
specifically identify the type of linkage between the recited “linked
nucleosides,” the Examiner properly consulted its specification to determine
what types of linkages are covered by the claims. Sun Pharmaceutical, 611
F.3d at 1387. The Examiner determined that methylphosphonate linkages in
the same positions as claimed are described in the ’599 patent. Appellant did
not identify a defect in the Examiner’s findings. See Reply Br. 14.

4 In the Oral Hearing, Appellant’s attorney, Dr. Scarr, stated that the species
with the two methylphosphonate linkages between positions 1 and 3 do not
fall within the claims of the ’599 patent. Record of Oral Hearing, pages 15–
16. This argument was not made in the Appeal or Reply Briefs. New
arguments or evidence is not permitted in an oral hearing. 37 C.F.R. § 41.47.
Nonetheless, the Examiner’s finding indicates that methylphosphonate
linkages at the claimed positions were considered to be part of the invention
of the ’599 patent.
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In an obviousness-type double-patenting analysis, while the earlier
patent’s specification cannot be used as prior art to the later patent
application claims, it can be consulted to ascertain the meaning of the words
in the claim to interpret the patented claim’s proper scope. As explained in
Sun Pharmaceutical, 611 F.3d at 1387:
In Geneva [Pharmaceuticals, Inc. v. GlaxoSmithKline PLC, 349
F.3d 1373 (Fed. Cir. 2003)], we acknowledged the general rule
that an earlier patent’s specification is not available to show
obviousness-type double patenting. 349 F.3d at 1385. We have
held, however, that there are “certain instances” where the
specification of an earlier patent may be used in the
obviousness-type double patenting analysis. In re Basell
[Poliolefine Italia S.P.A., 547 F.3d 1371, 1378 (Fed. Cir.
2008).] Specifically, the specification’s disclosure may be used
to determine whether a claim “merely define[s] an obvious
variation of what is earlier disclosed and claimed,” “to learn the
meaning of [claim] terms,” and to “interpret [ ] the coverage of
[a] claim.” Id. As we recognized in Geneva, a court
considering a claim to a compound must examine the patent’s
specification to ascertain the coverage of the claim, because a
claim to a compound “[s]tanding alone . . . does not adequately
disclose the patentable bounds of the invention.” 349 F.3d at
1385. Id.
Claim 1 of the ’599 patent is directed to an oligomeric compound,
which when the patent specification is examined, indicates that claim covers
compounds with methylphosphonate linkages between the recited
nucleosides, including methylphosphonates at the claimed positions (Ans.
16). The ’599 claim is unrestricted as to the type of internucleoside linkage,
and because the ’599 patent specification teaches embodiments where
methylphosphonate linkages are incorporated (Ans. 16), the Examiner
reasonably interpreted the scope of the claim to include these disclosed
embodiments. It is not reasonable to read a claim to exclude embodiments
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described in the written description of it in the specification.5 The
Specification is therefore properly being used to ascertain the scope of the
claim and obvious variations encompassed by the scope. A compound with
methylphosphonate would infringe the claim.
When the patent specification is consulted, based on the disclosure of
methylphosphonate linkages at the same positions as claimed, the skilled
worker would interpret claim 1 of the ’599 patent make rejected claim 1
obvious. For this reason, we agree with the Examiner that it is not justified
to extend Appellant’s right to exclude through claims in this later application
when it has not been established that the later claim is patentably distinct
from the claims in the ’599 patent. As explained in Basell, 547 F.3d at 1375:
“The doctrine of double patenting is intended to prevent a
patentee from obtaining a time-wise extension of [a] patent for
the same invention or an obvious modification thereof.” In re
Lonardo, 119 F.3d 960, 965 (Fed. Cir. 1997). The judicially
created doctrine of obviousness-type double patenting
“prohibit[s] a party from obtaining an extension of the right to
exclude through claims in a later patent that are not patentably
distinct from claims in a commonly owned earlier patent.” Eli
Lilly & Co. v. Barr Labs., Inc., 251 F.3d 955, 967 (Fed. Cir.
2001).
Consequently, we affirm the obviousness-double patenting rejection
of claim 1 over the claims of the ’599 patent. Claims 6–11 and 14–22 fall

5 “We normally do not interpret claim terms in a way that excludes
embodiments disclosed in the specification. . . . At leas[t] where claims can
reasonably [be] interpreted to include a specific embodiment, it is incorrect
to construe the claims to exclude that embodiment, absent probative
evidence on the contrary.” Oatey Co. v. IPS Corp., 514 F.3d 1271, 1276–77
(Fed. Cir. 2008).
Appeal 2020-002360
Application 15/407,037

19
with claim 1 because separate reason for their patentability were not
provided. 37 C.F.R. § 41.37(c)(1)(iv).
CONCLUSION
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 6–11, 14–
22
103 Seth, Thompson 1, 6–11, 14–
22

1, 6–11, 14–
22
101 Obviousness-type
double-patenting;
’845 patent, Seth,
Thompson
1, 6–11, 14–
22

1, 6–11, 14–
22
101 Obviousness-type
double-patenting;
’534 patent, Seth,
Thompson
1, 6–11, 14–
22

1, 6–11, 14–
22
101 Obviousness-type
double-patenting;
’599 patent
1, 6–11, 14–
22

Overall
Outcome
1, 6–11, 14–
22

TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv).

AFFIRMED