Ex Parte Hayes et al

Patent Trial and Appeal Board

Feb 13, 2017

13748964 (P.T.A.B. Feb. 13, 2017)

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.
13/748,964 01/24/2013 Thomas K. Hayes ONGX.P-001-DV 2743
57381 7590 02/14/2017
Larson & Anderson, LLC
P.O. BOX 4928
DILLON, CO 80435
EXAMINER
CHONG, KIMBERLY
ART UNIT PAPER NUMBER
1674
MAIL DATE DELIVERY MODE
02/14/2017 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 THOMAS K. HAYES, NICOLE D. KRILLA, and LORI NIXON1
__________

Appeal 2015-000614
Application 13/748,964
Technology Center 1600
__________

Before JACQUELINE T. HARLOW, BRIAN D. RANGE, and
JOHN E. SCHNEIDER, Administrative Patent Judges.

SCHNEIDER, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to an
oligonucleotide liquid formulation which have been rejected as directed to
ineligible subject matter. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm.
STATEMENT OF THE CASE
The present invention a room temperature storage-stable
oligonucleotide liquid formulation containing a phosphorothioate

1 Appellants identify the Real Party in Interest as OncoGenex
Pharmaceuticals, Inc. Br. 1. Oral argument was heard on February 6, 2017.
A transcript of the hearing will be entered into the record when available.
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oligonucleotide designed to bind to Hsp27 mRNA. Spec. 1, ll. 3–5. The
oligonucleotide is used to inhibit the production of human hsp27 protein.
Spec. 1, ll. 9–10. The liquid formulation contains mono or disaccharides or
a sugar alcohol to prevent agglomeration of the oligonucleotides. Spec. 2, l.
26–3, l. 8.
Claims 13–20 and 28–32 are on appeal. Claim 13 is the sole
independent claim and reads as follows:
13. A liquid formulation comprising
(a) an oligonucleotide consisting of Seq ID No. 1: or
consisting of a variant oligonucleotide in which no more than 3
non-sequential bases are different from Seq. ID NO. 1 and
(b) an aqueous carrier comprising an aggregation-
preventing compound selected from the group consisting of
mono and disaccharides and/or sugar alcohols, wherein the
amount of the aggregation-preventing compound is sufficient to
solubilize the oligonucleotide and maintain it in solution
without aggregation for a period in excess of 6 hours at room
temperature, wherein the oligonucleotide is a present in the
formulation at a concentration of at least 25 mg/ml.

The claims stand rejected under 35 U.S.C. § 101 as directed to patent
ineligible subject matter.
Issue
The issue with respect to this rejection is whether the Examiner has
established by a preponderance of the evidence that claims 13–20 and 28–32
are directed to patent ineligible subject matter under 35 U.S.C. § 101.
The Examiner finds that the claims are directed to a naturally
occurring nucleic acid fragment which is not patent eligible as the nucleic
acid sequence is a product of nature. Ans. 3. The Examiner finds that the
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combination of the nucleic acid sequence with water and a sugar does not
recite something significantly different from a product of nature. Ans. 4–5.
Appellants contend that the isolated DNA fragment is not a product of
nature in that the segment itself does not exist in nature apart from the gene
encoding for hsp27. Br. 4. Appellants argue that the isolated sequence is a
new structure with a new function and is therefore patent eligible. Br. 5–6.
Appellants argue that the combination of the nucleotide sequence with water
and a sugar or sugar alcohol does not exist in nature, especially where the
concentration of the nucleotide is 25 mg/ml. Br. 6–7. Appellants argue that
the Examiner misapplied the March 2014 Guidelines for determining
patentable subject matter and that a roper application of the guidelines shows
the claimed invention is patentable subject matter. Br. 8–10. With respect
to claim 15, Appellants argue that the Tris buffer recited in the claims is not
naturally occurring and that a product containing the buffer cannot be a
product of nature. Br. 7.
35 U.S.C. § 101 states that “[w]hoever invents or discovers any new
and useful process, machine, manufacture, or composition of matter, or any
new and useful improvement thereof, may obtain a patent therefor, subject to
the conditions and requirements of this title.”
The Supreme Court has “long held that this provision contains an
important implicit exception: Laws of nature, natural phenomena, and
abstract ideas are not patentable.” Alice Corp. Pty. Ltd. v. CLS Bank Intern.,
134 S. Ct. 2347, 2354 (2014).
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The Federal Circuit has summarized the Supreme Court’s two-part
test for distinguishing between claims to patent-ineligible exceptions, and
claims to patent-eligible applications of those exceptions, as follows:
Step one asks whether the claim is “directed to one of
[the] patent-ineligible concepts.” [Alice, 134 S. Ct. at 2354]. If
the answer is no, the inquiry is over: the claim falls within the
ambit of § 101. If the answer is yes, the inquiry moves to step
two, which asks whether, considered both individually and as
an ordered combination, “the additional elements ‘transform the
nature of the claim’ into a patent-eligible application.” Id.
(quoting Mayo [Collaborative Services v. Prometheus Labs,
Inc., 132 S. Ct. 1289, 1297 (2012)]).
Step two is described “as a search for an ‘inventive
concept.’” Id. (quoting Mayo, 132 S.Ct. at 1294). At step two,
more is required than “well-understood, routine, conventional
activity already engaged in by the scientific community,” which
fails to transform the claim into “significantly more than a
patent upon the” ineligible concept itself. Mayo, 132 S.Ct. at
1294.

Rapid Litigation Mgmt. Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1047 (Fed.
Cir. 2016) (paragraphing added).
We believe a preponderance of the evidence supports the Examiner’s
conclusion that the claims are directed to patent ineligible subject matter.
With respect to step one above, we conclude that the claims are
directed to a product of nature. As Appellants admit, the claimed nucleotide
sequence is part of the naturally occurring sequence that encodes for hsp27.
Br. 4. Appellants have made no change to the naturally occurring sequence
other than isolating the sequence from the naturally existing gene sequence.
See Br. 5 (Sequence created by cutting the naturally occurring gene.) Thus,
following the Supreme Court’s precedent in Myriad, the claimed nucleotide
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is a product of nature. Assoc. for Molecular Pathol. v. Myriad Genetics,
Inc., 133 S. Ct. 2107, 2117 (2013).
Appellants argue that the claimed sequence is analogous to the cDNA
molecule found to be patentable in Myriad. Appellants contend that the
inventor’s selection of the claimed sequence from the naturally occurring
gene is similar to the creation of a cDNA sequence. Br. 6. We are
unpersuaded. As the Court noted in Myriad, “the lab technician
unquestionably creates something new when cDNA is made.” Myriad, 133
S. Ct. at 2119. In creating a cDNA sequence, the technician starts with an
mRNA sequence and uses the mRNA sequence to create a new
complimentary DNA sequence. Id. In the instant case, the segment is not
created from scratch but merely isolated from the larger sequence. Br. 5.
Thus, the sequence recited in the claims is more closely analogous to the
BRCA sequences isolated in Myriad than the cDNA sequences.
Appellants contend that the short sequence recited in the claims
should be considered an article of manufacture and not a product of nature in
that sequence represents a new structure having a new function. Br. 5.
Appellants’ argument is unpersuasive. As the Federal Circuit has stated “the
Supreme Court made clear, neither naturally occurring compositions of
matter, nor synthetically created compositions that are structurally identical
to the naturally occurring compositions, are patent eligible.” In re BRCA1-
and BRCA2-Based Hereditary Cancer Test Patent Litigation, 774 F.3d 755,
760 (Fed. Cir. 2014) (citing Myriad, 133 S. Ct. at 2117.); see also Myriad,
133 S. Ct. at 2118 (“Nor are Myriad’s claims saved by the fact that isolating
DNA from the human genome severs chemical bonds and thereby creates a
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nonnaturally occurring molecule.”). Here Appellants have not shown that
the claimed sequence is structurally different from what occurs in nature.
Having found that the claims are directed to a product of nature we
turn to the second step of the analysis, do the claims present an inventive
concept. We agree with the Examiner that they do not.
The use of sugars and sugar alcohols to prevent agglomeration of
DNA fragments was well known in the art. Madden,2 abstract. Madden
teaches a method of administering a therapeutic oligonucleotide comprising
the steps of
(a) treating a composition comprising the therapeutic
oligonucleotide in multimeric aggregate form to convert
substantially all of the therapeutic oligonucleotide to a
monomeric form or to substantially prevent the formation of
multimeric aggregates; and
(b) administering the composition in which substantially
all of the therapeutic oligonucleotide is in monomeric form to a
mammal in need of therapy provided by the oligonucleotide.
The composition can be treated by beating, preferably no more
than 24 hours prior to administration, or using chemical species
such as mannitol which disrupt aggregates.

Madden ¶¶ 7– 9. Madden teaches that “a chemical additive ((such as
mannitol or sucrose) can be added to the beated material to
substantially prevent the reformation of monomers.” Madden ¶ 23.
Madden also teaches that the nucleotides were mixed with saline.
Madden ¶ 30. Thus Madden teaches the use of saccharides and sugar
alcohols to prevent aggregation and the combination nucleotides and

2 Madden et al., US 2003/0119768 A1, published June 26, 2003
(“Madden”).
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water. One skilled in the art faced with the need to prevent
agglomeration of the sequence recited in the claims would have been
motivated to use the sugars and sugar alcohols of Madden. The
combination of the claimed combination of the recited
oligonucleotide, water and sugar or sugar alcohol would have been
obvious. Thus, the claims do not present something significantly more
than a product of nature.
Appellants also argue that the concentration of 25 mg/ml limitation
also renders the claim patentable. Br. 6. We are not persuaded. While the
solution with the recited concentration may not exist in nature, the Examiner
has established a prima facie case that the claims do not present something
significantly more than a product of nature. Ans. 4-6. Appellants have
pointed to nothing in the record that shows that the recited concentrations
render the claimed subject matter patentable.
Appellants go on to argue that the fact that the combination of
components results in a mixture where agglomeration is prevented for at
least 6 hours at room temperature is another factor in favor of patentability.
Br. 7. We remain unpersuaded. We agree with the Examiner’s reasoning
and conclusion that “the claimed products are not markedly different from
naturally occurring products.” Ans. 6. Appellants have offered no credible
evidence to rebut the Examiner’s conclusion.
The limitations regarding concentration and stability do not transform
the claims into something significantly more to render the claims patentable
because those limitations merely represent “well-understood, routine,
conventional activity already engaged in by the scientific community,” and
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do not transform the claim into “significantly more than a patent upon the”
ineligible concept itself. Mayo, 132 S.Ct. at 1294. Stated plainly, the
addition of a well-known anti-agglomeration composition to a product of
nature is insufficient to confer patent eligibility here.
Appellants argue that others are not substantially foreclosed from
using the naturally occurring product and that this favors a finding that the
subject matter of the claims is patentable. Br. 10. We are not persuaded.
The Federal Circuit has expressly rejected similar contentions regarding
preemption, stating that a patentee’s “attempt to limit the breadth of the
claims by showing alternative uses . . . outside of the scope of the claims
does not change the conclusion that the claims are directed to patent
ineligible subject matter.” Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788
F.3d 1371, 1379 (Fed. Cir. 2015). The court explained that, “[w]hile
preemption may signal patent ineligible subject matter, the absence of
complete preemption does not demonstrate patent eligibility. . . . Where a
patent’s claims are deemed only to disclose patent ineligible subject matter
under the Mayo framework . . . preemption concerns are fully addressed and
made moot.” Id.
SUMMARY
We affirm the rejection under 35 U.S.C. § 101.
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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