IMMATICS BIOTECHNOLOGIES GMBH

Patent Trials and Appeals Board

Sep 21, 2020

2020000384 (P.T.A.B. Sep. 21, 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.
14/531,472 11/03/2014 Sabrina KUTTRUFF-COQUI 2912919-037000 4989
84331 7590 09/21/2020
McBee Moore & Vanik, IP, LLC
7900 Westpark Drive, Suite A100
McLean, VA 22102
EXAMINER
FONTAINHAS, AURORA M
ART UNIT PAPER NUMBER
1649
NOTIFICATION DATE DELIVERY MODE
09/21/2020 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@mmviplaw.com
eofficeaction@appcoll.com
smcbee@mmviplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte SABRINA KUTTRUFF-COQUI, TONI WEINSCHENK,
JENS FRITSCHE, STEFFEN WALTER, NORBERT HILF,
OLIVER SCHOOR, COLETTE SONG, and HARPREET SINGH
__________

Appeal 2020-000384
Application1 14/531,472
Technology Center 1600
__________

Before RICHARD M. LEBOVITZ, RYAN H. FLAX, and
RACHEL H. TOWNSEND, Administrative Patent Judges.

TOWNSEND, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
pharmaceutically acceptable salt of a particular peptide sequence, and a
fusion protein, which have been rejected as directed to patent-ineligible
subject matter, and/or as being indefinite and obvious. Oral argument was
held on September 14, 2020. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm in part.

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 Immatics
Biotechnologies GmbH. (Appeal Br. 1.)
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STATEMENT OF THE CASE
Claims 1, 5, 9, 16, 17, and 34 are on appeal. Claims 1 and 34 are
representative and read as follows:
1. A peptide consisting of the amino acid sequence of SEQ ID
NO: 28 wherein said peptide is in the form of a
pharmaceutically acceptable salt.
34. A fusion protein, comprising
(a) a peptide consisting of the amino acid sequence of
SEQ ID NO: 28; and
(b) N-terminal amino acids 1-80 of HLA-DR antigen-
associated invariant chain (Ii) according to SEQ ID No. 133.
(Appeal Br. 43, 48.)

The prior art relied upon by the Examiner is:
Name Reference Date
Singh et al. US 2009/0136528 A1 May 28, 2009
Grifantini et al. WO 2011/051278 A1 May 5, 2011

The following grounds of rejection by the Examiner are before us on
review:
Claims 1, 5, 9, 16, and 17 under 35 U.S.C. § 101 as being directed to
patent-ineligible subject matter.
Claim 34 under 35 U.S.C. §112(b) as being indefinite.2

2 We cite to the post-AIA version of §§ 112 and 103, because the
Application on Appeal was filed on November 3, 2014, based on an
Application filed November 4, 2013, both of which are dates after the AIA
amendments to § 112 took effect on September 16, 2012 and the
amendments to § 103 took effect on March 16, 2013. See, e.g., Leahy-Smith
America Invents Act (“the AIA”), Pub. L. No. 112-29, §§ 3(n), 4(e), 125
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Claim 34 under 35 U.S. C. § 103 as unpatentable over Singh and
Grifantini.
DISCUSSION
I. Patent Eligible Subject Matter
The Dispute
The Examiner finds that claim 1 involves a product of nature, namely
“the COL20A1 protein (collagen, Type XX, alpha 1).” (Final Action 4.)
The Examiner states: “A peptide consisting of the amino acid sequence of
SEQ ID NO: 28 (FLVDGSWSI) . . . is produced by cells expressing human
COL20A1, collagen XX, the protein from which it is derived.” (Ans. 13–
14.) The Examiner notes that “a peptide consisting of the amino acid
sequence of SEQ ID NO: 28 is the same as the peptide that was originally
isolated from the COL20A1 protein, which has this same amino acid
sequence and this same primary structure.” (Id. at 15.)
The Examiner recognizes that “claim 1 calls for a peptide that consists
of SEQ ID NO: 28 wherein the peptide is in the form of pharmaceutically
acceptable salt,” but finds that “the pharmaceutically acceptable salt recited
in instant claim 1 is generic because the claims recite a ‘wherein clause’
limitation that does not change the final structure of the peptide.” (Final
Action 5; see also Ans. 14.) The Examiner finds
[t]he fact that the peptide is in the form of a pharmaceutically
acceptable salt simply means one or more of the amino acid
residues of which the peptide is composed has been ionized and
has formed an ionic bond with whatever cation (e.g., Na+) or

Stat. 284, 293, 297 (2011). However, the current law and respective pre-
AIA law are, in all aspects relevant to this Decision, the same.
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anion (e.g., Cl-) might be present, as exemplified in the instant
specification, page 91.
(Ans. 15.) However, the Examiner finds that the ionized peptide structure is
the same amino acid sequence and primary structure as that peptide in the
naturally occurring protein. (Id. at 17–18.) The Examiner further finds that
“[t]he pharmacological[ly] acceptable salt also reads on a natural product
because it is still a naturally occurring peptide that is not markedly different
from the naturally protein . . . [and] peptides (composed of amino acids) will
naturally produce a salt.” (Final Action 5–6 (citing Berge3).) The Examiner
thus concludes that “claim 1 reads on naturally occurring polypeptide salts
and thus, this composition reads on a natural product as well.” (Id. at 6.)
According to the Examiner, “[t]he instant claims do not recite any
elements in addition to the natural products that impose meaningful limits on
the claim scope and would substantially foreclose others from using these
natural products.” (Id.)
Appellant argues that “the proper analysis for step 2A is to look at
what is claimed and determine whether it has an identical natural
counterpart. If an identical counterpart to what is claimed does not exist,
that is the end of the analysis.” (Appeal Br. 11. (emphasis omitted)).
Appellant points out that the claimed invention is to a pharmaceutically
acceptable salt of the peptide having SEQ ID No: 28 and that it is an
improper analysis under § 101 to “parse[] [the claim] into i) the 9-amino
acid and ii) a salt.” (Id. at 13–14.)

3 Berge et al., Pharmaeutical Salts, 66 (1) J. Pharmaceutical Sciences, 1–19
(1977).
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Appellant argues that the Examiner’s rejection is in error because
“there is no naturally occurring peptide of SEQ ID NO: 28 either in free
form or in the form of a pharmaceutically acceptable salt.” (Id. at 12.) As a
consequence, Appellant argues, “it is impossible for the claims to be
‘directed’ to a judicial exception.” (Id.) Appellant explains that
[i]t is also impossible for the claimed subject matter to
“monopolize” what occurs in nature, because what occurs in
nature is either a whole 1284 amino acid 3-D protein, or the
peptide complexed with other molecules (where it is never, at
any time, in the form of a pharmaceutically acceptable salt).
(Id.) Undergirding Appellant’s argument is the testimony of Dr. Lawrence
Stern. (Id. at 16–20 (citing Stern Declaration4).)
Appellant further explains, with support from the testimony of
Dr. Stern, that “[t]hese naturally-occurring complexes are both structurally
and functionally different, i.e., ‘markedly different,’ from the peptide salt
claimed.” (Id. at 21–24.) Appellant further notes that “the salt form of the
peptide enables the peptide to be used in vitro where it would otherwise not
be able to be used because of degradation or insolubility.” (Id. at 12–13, 25–
27 (citing Stern Declaration).) Consequently, Appellant points out that
“even if there were a naturally-occurring counterpart, the claimed physical
salt form represents a practical application,” having both structural and
functional differences. (Id. at 13, 25.)
Analysis
35 U.S.C. § 101 defines patent-eligible subject matter. An invention
is patent-eligible if it claims a “new and useful process, machine,

4 Declaration of Dr. Lawrence Stern, dated Dec. 19, 2017 (“Stern
Declaration”).)
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manufacture, or composition of matter.” 35 U.S.C. § 101. The Supreme
Court, however, has carved out exceptions to what would otherwise appear
to be within the literal scope of § 101, e.g., “[l]aws of nature [and] natural
phenomena” such as products of nature that are considered “buildin[g]
block[s] of human ingenuity.” Alice Corp. v. CLS Bank Int’l, 573 U.S. 208,
216 (2014) (citing Ass’n for Molecular Pathology v. Myriad, 569 U.S. 576
(2013) and Mayo Collaborative Servs. v. Prometheus Labs, Inc., 566 U.S.
66, 89 (2012)). “The ‘manifestations of laws of nature’ are ‘part of the
storehouse of knowledge,’ ‘free to all men and reserved exclusively to
none.’” Manual of Patent Examiner Procedure (“MPEP”) § 2106.04 (b)
(quoting Funk Bros. Seed Co. v. Kalo Inoculant Col, 33 U.S. 127, 130
(1948)). “When a law of nature or natural phenomenon is claimed as a
physical product, the courts have often referred to the exception as a
‘product of nature.’” MPEP § 2106.04(b)(II).
The Supreme Court has established a two-step framework for
“distinguishing patents that claim laws of nature, natural phenomena, and
abstract ideas from those that claim patent-eligible applications of those
concepts.” Alice, 573 U.S. at 216. “First, we determine whether the claims
at issue are directed to” a patent-ineligible concept. Id. If so, “we consider
the elements of each claim both individually and ‘as an ordered
combination’ to determine whether the additional elements ‘transform the
nature of the claim’ into a patent-eligible application.” Id. (quoting Mayo,
566 U.S. at 78–79).
The United States Patent and Trademark Office (“PTO”) issued the
2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”),
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indicating how the PTO would analyze patent eligibility under the Supreme
Court’s two-step framework. 84 Fed. Reg. 50–57 (January 7, 2019).5
Under the Guidance, in determining what concept the claim is
“directed to,” we first look to whether the claim recites any judicial
exceptions, including laws of nature, natural phenomena, and/or abstract
ideas. (Guidance, 84 Fed. Reg. at 53–54.) (“Step 2A, Prong One”). If it
does, then we look to whether the claim recites additional elements that
integrate the recited judicial exception into a practical application. (Id. at
54–55 (citing MPEP § 2106.05(a)–(c), (e)–(h)).) (“Step 2A, Prong Two”).
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, i.e., it is found to be
“directed to” a judicial exception, do we then look to whether the claim
contains an “‘inventive concept’ sufficient to ‘transform’” the claimed
judicial exception into a patent-eligible application of the judicial exception.
Guidance, 84 Fed. Reg. at 56; see also Alice, 573 U.S. at 221 (quoting Mayo,
566 U.S. at 82).
Claims alleged to be patent-ineligible because they recite products of
nature are properly analyzed under the framework of the Guidance. See
Guidance, 84 Fed. Reg. at 54 n.20 (“This notice does not change the type of
claim limitations that are considered to recite a law of nature or natural

5 “All USPTO personnel are, as a matter of internal agency management,
expected to follow the guidance.” Id. at 51; see also USPTO, October 2019
Update: Subject Matter Eligibility 1 (the “October 2019 Update”) (available
at https://www.uspto.gov/sites/default/files/documents/peg_oct_2019_
update.pdf).
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phenomenon. For more information about laws of nature and natural
phenomena, including products of nature, see MPEP 2106.04(b) and (c).”).
Applying the Guidance and binding legal precedent, we disagree with
the Examiner’s conclusion that the claims are directed to patent-ineligible
subject matter. We address independent claim 1 as the representative claim
for our analysis. There is no dispute that claim 1, which recites a peptide in
the form of a pharmaceutically acceptable salt, is a composition and, thus,
falls squarely within the “composition of matter” statutory category.
Consequently, we proceed to the next steps of the analysis.
STEP 2A, Prong One:
In Step 2A, Prong One of the Guidance, we evaluate whether claim 1
recites a judicial exception, i.e., whether it sets forth or describes a product
of nature in accordance with the guidance in MPEP 2106.04 (b) and (c).
Guidance, 84 Fed. Reg. at 54; October 2019 Update.
a. Product of Nature Analysis
Claim 1 includes recitation of a peptide sequence that is undisputedly
found in nature as part of a larger sequence. SEQ ID No: 28 is a peptide
sequence from a protein encoded by the COL20A1 gene, a collagen gene
mapped to the human chromosome 20q13.33. (Spec. 5 (Table 1a), 33.)
However, as Appellant points out, the claim does not recite a free peptide,
but rather a pharmaceutically acceptable salt of that peptide.
According to Examiner, because the claim does not specify a
particular “anionic or cationic constituent[] of the salt, apart from the peptide
itself, it is the peptide, not the salt, that is the invention; and therefore the
anion or cation (i.e., the ‘counterion’) that forms a salt with the ionized
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peptide is unrelated to the invention.” (Ans. 14 n.3 (emphasis added).) We
disagree with the Examiner’s claim interpretation.
The claim requires a peptide “consisting of the amino acid sequence
of SEQ ID NO: 28” where that peptide is a pharmaceutically acceptable salt.
In other words, the amino acid sequence of the peptide salt cannot be
anything other than SEQ ID NO: 28, but that sequence must be in ionic
combination with another ion to form a pharmaceutically acceptable salt.
The claimed salt is a structurally different chemical composition than a free
peptide, as even the Examiner recognizes. (See Ans. 15 (“The fact that the
peptide is in the form of a pharmaceutically acceptable salt simply means
one or more of the amino acid residues of which the peptide is composed has
been ionized and has formed an ionic bond with whatever cation (e.g., Na+)
or anion (e.g., Cl-) might be present.” (footnote omitted)); see also Stern
Declaration ¶ 20 (“Salts are formed when a compound that is ionized in
solution forms a strong ionic interaction with an oppositely charged
counterion, leading to neutralization of the charges. . . .”), id. ¶¶ 23–24
(“[P]eptides of any length . . . will therefore have a one free amino group
(NH2,) referred to as the amino terminus or N-terminus and one free
carboxyl group (COOH) referred to as the carboxyl or C-terminus . . . .
[T]here can also be ionizable groups in the side chains (‘R’) of the amino
acid residues within the peptide.”).)
Appellant’s expert explained, with reference to numerous articles, that
the amino acid sequence of SEQ ID NO: 28 would not exist in the body as a
salt. (Stern Declaration ¶¶ 32–34.) Dr. Stern explained that peptide
fragments, such as amino acid sequence SEQ ID NO: 28, that arise when
proteins are degradedare themselves degraded within a few seconds if not
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associated with other proteins involved in degradation, ER transport and
loading of the peptide onto MHC-1 molecules. (Stern Declaration ¶ 32.)
Dr. Stern notes that “[i]n the absence of peptide binding, neither the peptide
nor the MHC molecule by itself is stable, or persists.” (Id. ¶ 33.)
Dr. Stern further explains that even if the free peptide existed in the
cell, “there is no acid-base reaction that could occur in the cytoplasm or ER
of a cell . . . that would result in formation of a peptide salt.” (Id. ¶ 34.)
That is because “[t]he formation of salts requires specific combinations of
acids or bases in specific concentrations, at a defined ratio (stoichiometry),
so that there is a set number of moles of acid and moles of base in a
controlled environment[, and] [t]he cytoplasm of a cell is not such an
environment.” (Id.) Dr. Stern notes that the cytoplasm “would not contain
either the peptides or the acid or base counterpart in sufficient quantities in
sufficient proximity to each other to form a peptide salt.” (Id.) Furthermore,
Dr. Stern explains that “[e]ven if all the water in cell were removed, specific
salts would not form, because of the highly complex mixtures of anions and
cations present.” (Id.)
The Examiner has not provided any evidence in contravention of the
foregoing testimony by Dr. Stern. Rather, the Examiner asserts that peptides
will form salts because (1) “Amino acids will naturally produce a salt.
Berge et al., 1977 (IDS, 2/22/2017) teaches that salt formation is an acid-
base reaction involving a proton-transfer or neutralization reaction (see page
1, 1st column) and amino acids are also used as salt forming agents (see page
2, 2nd column, 3rd paragraph)” (Final Action 6); and because (2)“The human
cell cytosol comprises ions of pharmaceutically acceptable salts, e.g. Na+,
Cl-, K+, HCO3-. One of ordinary skill is aware that at physiological pH, both
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the amino and carboxy groups of a peptide are ionized” (Final Action 9).
Relying on general principles of chemistry, the Examiner posits that because
the peptide is present in an aqueous solution in vivo within the cytosol, the
endoplasmic reticulum, and at the surface of cells in complex with an HLA
class I molecule, it will be ionized and because there are “counterions of the
appropriate charge” naturally present in each situation in the body, a salt will
form. (Ans. 16–21.)
The Examiner does not assert that Berge describes in vivo salt
formation of peptides. Berge is a review article concerned with providing
information about salts to those in the pharmaceutical industry to have a
rational basis for selecting a suitable salt form of a drug for administration.
In particular, Berge states
[t]his review surveys literature of the last 25 years, emphasizing
comparisons between the properties of different salt forms of
the same compound. Included also is a discussion of
potentially useful salt forms. Our purpose is twofold: to
present an overview of the many different salts from which new
drug candidates can be chosen and to assemble data that will
provide, for the student and practitioner alike, a rational basis
for selecting a suitable salt form.
(Berge 1–2.)
Moreover, the Examiner’s assertion that the peptide fragments of the
collagen protein degraded by a proteasome will naturally form a salt in the
cytosol, the ER, or the MHC because there are counterions such as sodium,
chloride and potassium present around lacks any evidentiary foundation.
And, it is contradicted by the testimony of Dr. Stern that salt formation
requires specific combinations of acids or bases in specific concentrations, at
a defined ratio (stoichiometry), so that there is a set number of moles of acid
and moles of base in a controlled environment. It cannot be disputed that the
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cytosol, the ER and the MHC in vivo is not such a controlled environment
with respect to peptide fragments of the collagen protein degraded by a
proteasome.
In addition, the Examiner’s position that the free peptide is extant in
the first place for long enough to form a salt is contradicted by Dr. Stern’s
testimony that any free peptide of the collagen protein degraded by a
proteasome would be rapidly degraded if it is not associated with certain
other proteins in the cytosol or in transport to the endoplasmic reticulum or
when bound in the MHC.
While an amino acid sequence consisting of SEQ ID NO: 28 is
unquestionably identical to a peptide sequence found in COL20A1, which
Appellant does not dispute, we conclude that the preponderance of the
evidence favors finding that the claimed pharmaceutically acceptable salt of
the peptide consisting of the amino acid sequence of SEQ ID NO: 28 is not a
compound that occurs in nature.
Thus, we disagree with the Examiner’s conclusion that the claimed
invention is not markedly different from a naturally occurring peptide
consisting of an amino acid sequence of SEQ ID NO: 28.6 The Examiner’s
analysis does not properly address the claimed structure, as discussed above.
It cannot be said that the pharmaceutically acceptable salt of amino acid
peptide of SEQ ID NO: 28 is merely an isolated component of a larger
structure known to be present in nature, similar to DNA isolated from the

6 We note, but do not find it necessary to respond to, Appellant’s arguments
concerning any alleged misapplication of law in the MPEP. (Appeal Br. 9.)
We need not address this argument because we conclude that the Examiner
erred in evaluating the claimed invention as a whole.
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human genome. Cf. Myriad, 569 U.S. at 593 (“Nor are Myriad’s claims
saved by the fact that isolating DNA from the human genome severs
chemical bonds and thereby creates a nonnaturally occurring molecule.”);
see also Roche Molecular Sys., Inc. v. CEPHEID, 905 F.3d 1363 (Fed. Cir.
2018) (finding similar to the claimed DNA at issue in Myriad, that the
claimed primers were necessarily present in the natural genome of Mtb).
The markedly different characteristic for the claimed invention here is
not merely due to the breaking of chemical bonds, but is rather based on
chemical differences attributable to the fact that the peptide of SEQ ID
NO: 28 is in strong ionic interaction with an oppositely charged counterion.
In Myriad, the Supreme Court determined that naturally occurring, but
isolated, DNA fell within the product of nature exception because “Myriad’s
claims . . . do [not] rely in any way on the chemical changes that result from
the isolation of a particular section of DNA.” Myriad, 569 U.S. at 593
(emphasis added). The Court in Myriad, however, also noted that “creation
of a cDNA sequence from mRNA results in an exons-only molecule that is
not naturally occurring” and determined that such a chemical construct is
patent-eligible. Id. at 594. We conclude that, like the cDNA in Myriad, the
pharmaceutically acceptable salt of the peptide consisting of amino acid
SEQ ID NO: 28 is markedly different from the peptide consisting of amino
acid SEQ ID NO: 28 because the claimed pharmaceutically acceptable salt is
a chemical construct that does not exist in nature. Accord MPEP
2106.04(c)(II) (“Markedly different characteristics can be expressed as the
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product’s structure, function, and/or other properties, and are evaluated
based on what is recited in the claim on a case-by-case basis.”).7
Accordingly, under Guidance Step 2A, Prong 1, we conclude that the
composition of claim 1 does not recite a product of nature, and thus is not
directed to a patent ineligible judicial exception. Our analysis of the issue
need not proceed further.
Thus, we do not affirm the Examiner’s rejection of claims 1, 5, 9, 16
and 17 under 35 U.S.C. § 101 as being directed to patent-ineligible subject
matter.
II. Rejection of Claim 34 as Indefinite
The Examiner finds that the claim language of claim 34, the fusion
protein claim, is “confusing and unclear” because “there are multiple
interpretation[s] of the instant claim” because it uses both “comprising” and
“consisting of” language. (Final Action 3.) The Examiner indicates that the
following two interpretations are possible.

7 In addition to this structural difference, Dr. Stern contends that the free
peptide would be poorly soluble in aqueous solution (Stern Declaration ¶ 38)
whereas “[s]alts of hydrophobic peptides have been shown improve their
solubility in aqueous solutions, just as salts of other compounds improve
their solubility” (Id. ¶ 40). He also contends that “[p]eptides are not very
stable in free form, without modifications” (Id. ¶ 41) and that “the peptide
claimed in the Immatics application can undergo hydrolysis in aqueous
solution in free form” (Id. ¶ 42), whereas “[f]ormation of peptide salts
stabilizes the peptides from physical degradation, discussed above, to some
extent” (Id. ¶ 45). In light of our conclusion regarding the marked structural
difference, we need not address Appellant’s additional argument and
testimony of Dr. Stern that the physical properties of the pharmaceutically
acceptable salt of the claimed peptide fragment is markedly different than a
free peptide fragment if it existed in nature.
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One interpretation is that the “the fusion protein is composed of only
SEQ ID NO: 28, the N-terminal amino acids 1-80 of HLA-DR antigen-
associated invariant chain and other components.” (Id.) The second
interpretation is that fusion protein is composed of any peptides/proteins
including up to the full length of COL20A1 and the HLA-DR antigen-
associated invariant chain as long as they include the specific peptides in
SEQ ID NOs: 28 and 133. (Id.)
Appellant argues that the use of the phase “fusion protein comprising”
“does not mean that the term applies to the individual elements within the
claim that are further limited by the term ‘consisting of.’” (Appeal Br. 40.)
Appellant explains, therefore, that because clause (a) of the claim uses the
term “consisting of,” it “cannot include anything beyond the peptide of SEQ
ID NO: 28 and certainly not the whole protein, which is not a peptide as
would reasonably be understood.” (Appeal Br. 40.)
We disagree with Appellant’s claim construction. We find the claim
language issue similar to that present in In re Crish, 393 F.3d 1253 (Fed.
Cir. 2004). In that case, our reviewing Court explained that a claim to an
“oligonucleotide comprising at least a portion of . . . SEQ ID NO:1, . . .
wherein said portion consists of nucleotides 521 to 2473” reads on a plasmid
that includes more than just the recited portion of SEQ ID NO:1. 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.” Id.
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Here the language “consisting of” limits clause (a) to the amino acid
sequence specified in SEQ ID NO: 28 being present in the fusion protein
without any variation to that sequence. It does not limit the other amino
sequences that may be present in the claimed fusion protein. Nor is there
other limiting language in the claim requiring the amino acid sequence of
clause (a) to be directly fused to the amino acid sequence recited in clause
(b). “‘Comprising’ is a term of art used in claim language which means that
the named elements are essential, but other elements may be added and still
form a construct within the scope of the claim.” Genentech, Inc. v. Chiron
Corp., 112 F.3d 495, 501 (Fed. Cir. 1997). Thus, the use of the term fusion
protein comprising means that the claim can include SEQ ID NO: 28
including up to the full length of COL20A1, as the Examiner recognized.
Nevertheless, we disagree with the Examiner that the claim is
indefinite. Breadth is not equated with indefiniteness. In re Miller, 441 F.2d
689, 693 (CCPA 1971). That the claim can be read to encompass up to the
full length of COL20A1 as a fusion protein with the “N-terminal amino
acids 1–80 of HLA-DR antigen-associated invariant chain (Ii) according to
SEQ ID No. 133” is an issue of claim breadth. The fact that the claim
encompasses as much as an entire protein that includes a specifically recited
peptide sequence where that protein is fused to another amino acid sequence
or as little as just a specific peptide sequence fused to another amino acid
sequence does not make it indefinite.
Consequently, we reverse the Examiner’s rejection of claim 34 as
being indefinite.

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III. Rejection of Claim 34 as Obvious
Appellant contests the Examiner’s rejection of claim 34 as being
obvious on the grounds that “no reasonable interpretation of ‘consisting of’
encompasses the whole protein from which SEQ ID NO: 28 is derived” and
the prior art does not teach or suggest a fusion protein of SEQ ID NO: 28.
(Appeal Br. 41.) As explained above, we do not agree with Appellant’s
claim interpretation. So long as the amino acid sequence of SEQ ID NO: 28
is present in a fusion protein, the limitation in dispute would be met.
Furthermore, Appellant does not dispute the Examiner’s findings that
“[t]he sequences taught by Grifantini, COL20A1 in it[s] variant isoforms
SEQ ID NOs: 32, 35-37 or with a sequence identity of at least 80-95% (see
page 10) encompass the instantly claimed SEQ ID NO: 28” or that
“Grifantini teaches a fusion protein of COL20A1 (see page 34, Figures 25-
26 and page 41, lines 5-6).” (Final Action 16.) Nor does Appellant dispute
the Examiner’s findings regarding Singh as to fusion proteins “which
comprises the 80 N-terminal amino acids of the HLA-DR antigen associated
invariant chain (see paragraph 105).” (Id. at 15.) Appellant also does not
challenge the Examiner’s findings concerning the reason to combine the
teachings of Grifantini and Singh to arrive at a fusion protein that would
include the full length of COL20A1 in its variant isoforms and the 80 N-
terminal amino acids of the HLA-DR antigen associated invariant chain.
(Id. at 16–17.) Consequently, we affirm the Examiner’s rejection of claim
34 as obvious over Singh and Grifantini.
Appeal 2020-000384
Application 14/531,472

18
DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1, 5, 9, 16,
17
101 Eligibility 1, 5, 9, 16,
17
34 112(b) Indefinite 34
34 103 Singh, Grifantini 34
Overall
Outcome
34 1, 5, 9, 16,
17

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). See 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED IN PART