Ex Parte Bartel

Board of Patent Appeals and Interferences

Jun 9, 2010

10124550 - (D) (B.P.A.I. Jun. 9, 2010)

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.
10/124,550 04/17/2002 Paul Bartel 1629.01 9193
26698 7590 06/09/2010
MYRIAD GENETICS INC.
INTELLECTUAL PROPERTY DEPARTMENT
320 WAKARA WAY
SALT LAKE CITY, UT 84108
EXAMINER
HARRIS, ALANA M
ART UNIT PAPER NUMBER
1643
MAIL DATE DELIVERY MODE
06/09/2010 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte PAUL BARTEL
__________

Appeal 2009-010526
Application 10/124,550
Technology Center 1600
__________

Decided: June 9, 2010
__________

Before TONI R. SCHEINER, FRANCISCO C. PRATS, and STEPHEN
WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to an
isolated protein complex. The Patent Examiner rejected the claims for lack
of written description and enablement. We have jurisdiction under
35 U.S.C. § 6(b). We affirm.
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STATEMENT OF THE CASE
The Specification states: “[i]t has been discovered that Caspase-7
[apoptosis-related cysteine protease caspase-7] interacts with LIPA
(cholesteryl ester hydrolase/lysosomal acid lipase A).” (Spec. 6: 17-19.)
According to the Specification, protein complexes containing Caspase-7 and
LIPA are involved in apoptosis and lipid metabolism (id. at 6:24-26). Such
complexes are said to be useful in screening assays to identify compounds
that can modulate Caspase-7, LIPA, or their complexes (id. at 6:26-31).
Claims 39-48 are on appeal. Claim 39 is representative and reads as
follows:
39. An isolated protein complex comprising a first protein interacting
with a second protein,

wherein said first protein is chosen from:
(a) caspase-7, or a fragment thereof that interacts with LIPA;
(b) a first polypeptide having an amino acid sequence at least
75% identical to that of (a), and that interacts with LIPA;
and
(c) a first fusion protein comprising (a) or (b); and

wherein said second protein is selected from the group consisting of:
(i) LIPA, or a fragment thereof that interacts with caspase-7;
(ii) a second polypeptide having an amino acid sequence at
least 75% identical to that of (i), and that interacts with
caspase-7; and
(iii) a second fusion protein comprising (i) or (ii).

The Examiner rejected the claims as follows:
• claims 39-48 under 35 U.S.C. § 112, first paragraph, as failing to
comply with the written description requirement; and
• claims 39-48 under 35 U.S.C. § 112, first paragraph, as failing to
comply with the enablement requirement.
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Claims 40-48 have not been argued separately and therefore stand or
fall with claim 39. 37 C.F.R. § 41.37(c)(1)(vii).

WRITTEN DESCRIPTION
The Issue
The Examiner’s position is that the Specification “only sets forth first
protein, Caspase-7 which is 254 amino acids long (GenBank Accession
numbers . . .) and second protein, LIPA which is a 399 amino acid protein
GenBank Accession numbers . . .), see Table 1 on page 20. Therefore the
written description is not commensurate in scope with the claims drawn to
an isolated protein complex essentially comprising homologues, derivatives
or fragments” of Caspase-7 and LIPA. (Ans. 4.) The Examiner found that
Appellant was “not in possession of any and all homologues, derivatives or
fragments.” (Id.) The Examiner found that “[t]he homologues and
derivatives more than likely comprise undefined amino acids that would not
resemble the art known proteins, caspase-7 and LIPA.” (Id.)
Appellant contends that the two interacting proteins forming the
claimed complex were well known in the art at the time of filing, and some
homologues and orthologs were also known in the art. (App. Br. 4.)
Appellant further contends that the Specification described fragments that
formed complexes. (Id.) According to Appellant, “the Examiner’s
arguments comprise only allegations, which are not supported by any cited
evidence.” (Id. at 5.) Appellant further argues that the modified LIPA and
Caspase-7 proteins are defined by structural similarity to the respective
native proteins and by the functional feature of binding to the other. (Id. at
7.)
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The issue with respect to this rejection is whether the evidence
supports the Examiner’s finding that the Specification did not provide a
written description of the invention commensurate with the claims.

Findings of Fact
1. The Summary of the Invention states:
In accordance with a first aspect of the present invention,
isolated protein complexes are provided comprising Caspase-7 and
LIPA. In addition, homologues, derivatives, and fragments of
Caspase-7 and of LIPA may also be used in forming protein
complexes. In a specific embodiment, fragments of Caspase-7 and
LIPA containing the protein domains responsible for the interaction
between Caspase-7 and LIPA are used in forming a protein complex
of the present invention. In another embodiment, an interacting
protein member in the protein complexes of the present invention is a
fusion protein containing Caspase-7 or a homologue, derivative, or
fragment thereof. A fusion protein containing LIPA or a homologue,
derivative, or fragment thereof may also be used in the protein
complexes. In yet another embodiment, a protein complex is provided
from a hybrid protein, which comprises Caspase-7 or a homologue,
derivative, or fragment thereof covalently linked, directly or through a
linker, to LIPA or a homologue, derivative, or fragment thereof. In
addition, nucleic acids encoding the hybrid protein are also
encompassed by the present invention.

(Spec. 7:1-14.)
2. The Detailed Description of the Invention provides this definition of
the terms “polypeptide,” “protein,” and “peptide”:
The terms “polypeptide,” “protein,” and “peptide” are used
herein interchangeably to refer to amino acid chains in which the
amino acid residues are linked by peptide bonds or modified peptide
bonds. The amino acid chains can be of any length of greater than two
amino acids. Unless otherwise specified, the terms “polypeptide,”
“protein,” and “peptide” also encompass various modified forms
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thereof. Such modified forms may be naturally occurring modified
forms or chemically modified forms. Examples of modified forms
include, but are not limited to, glycosylated forms, phosphorylated
forms, myristoylated forms, palmitoylated forms, ribosylated forms,
acetylated forms, ubiquitinated forms, etc. Modifications also include
intra-molecular cross-linking and covalent attachment to various
moieties such as lipids, flavin, biotin, polyethylene glycol or
derivatives thereof, etc. In addition, modifications may also include
cyclization, branching and cross-linking. Further, amino acids other
than the conventional twenty amino acids encoded by genes may also
be included in a polypeptide.

(Id. at 12:30 – 13:12.)
3. The Detailed Description of the Invention provides this definition of
the term “protein fragment”:
The term “protein fragment” as used herein means a
polypeptide that represents a portion of a protein. When a protein
fragment exhibits interactions with another protein or protein
fragment, the two entities are said to interact through interaction
domains that are contained within the entities.
As used herein, the term “domain” means a functional portion,
segment or region of a protein, or polypeptide.

(Id. at 14:15-20.)
4. The Detailed Description of the Invention provides this definition of
“interaction”:
As used herein, the term “interacting” or “interaction” means
that two protein domains, fragments or complete proteins exhibit
sufficient physical affinity to each other so as to bring the two
“interacting” protein domains, fragments or proteins physically close
to each other.
(Id. at 13:13-16.)
5. The Detailed Description of the Invention provides this definition of
the term “homologue”:
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As used herein, the term “homologue,” when used in
connection with a first native protein or fragment thereof that is
discovered, according to the present invention, to interact with a
second native protein or fragment thereof, means a polypeptide that
exhibits an amino acid sequence homology and/or structural
resemblance to the first native interacting protein, or to one of the
interacting domains of the first native protein such that it is capable of
interacting with the second native protein. Typically, a protein
homologue of a native protein may have an amino acid sequence that
is at least 50%, preferably at least 75%, more preferably at least 80%,
85%, 86%, 87%, 88% or 89%, even more preferably at least 90%,
91%, 92%, 93% or 94%, and most preferably 95%, 96%, 97%, 98%
or 99% identical to the native protein. Examples of homologues may
be the ortholog proteins of other species including animals, plants,
yeast, bacteria, and the like. Homologues may also be selected by,
e.g., mutagenesis in a native protein. For example, homologues may
be identified by site-specific mutagenesis in combination with assays
for detecting protein-protein interactions, e.g., the yeast two-hybrid
system described below, as will be apparent to skilled artisans
apprised of the present invention. Other techniques for detecting
protein-protein interactions include, e.g., protein affinity
chromatography, affinity blotting, in vitro binding assays, and the
like.

(Id. at 16:20 - 17:4.)

6. The Detailed Description of the Invention provides this definition of
the term “derivative”:
The term “derivative,” when used in connection with a first
native protein (or fragment thereof) that is discovered, according to
the present invention, to interact with a second native protein (or
fragment thereof), means a modified form of the first native protein
prepared by modifying the side chain groups of the first native protein
without changing the amino acid sequence of the first native protein.
The modified form, i.e., the derivative should be capable of
interacting with the second native protein. Examples of modified
forms include glycosylated forms, phosphorylated forms, myristylated
forms, ribosylated forms, ubiquitinated forms, and the like.
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Derivatives also include hybrid or fusion proteins containing a native
protein or a fragment thereof. Methods for preparing such derivative
forms should be apparent to skilled artisans. The prepared derivatives
can be easily tested for their ability to interact with the native
interacting partner using techniques known in the art, e.g., protein
affinity chromatography, affinity blotting, in vitro binding assays,
yeast two-hybrid assays, and the like.

(Id. at 17:26 – 18:6.)
7. According to the Specification, “[s]pecific fragments capable of
conferring interacting properties on Caspase-7 and LIPA have been
identified, which are summarized in Table 1.” (Id. at 20:10-12.)
8. Table 1 is reproduced here:

(Id. at 20.)
9. We find that Table 1 identifies the binding region of Caspase-7 as its
amino acids 1 through 254, and the binding region of LIPA as its
amino acids 33 through 215.
10. The Detailed Description of the Invention provides this definition of
the term “fusion protein”:
The terms “hybrid protein,” “hybrid polypeptide,” “hybrid peptide,”
“fusion protein,” “fusion polypeptide,” and “fusion peptide” are used
herein interchangeably to mean a non-naturally occurring protein
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having a specified polypeptide molecule covalently linked to one or
more polypeptide molecules that do not naturally link to the specified
polypeptide.

(Id. at 18:23-27.)

Principles of Law
When an Applicant claims a class, the Applicant “must describe that
class in order to meet the description requirement of the statute.” In re
Lukach, 442 F.2d 967, 968 (CCPA 1971). In assessing whether the written
description requirement is satisfied, “[t]he primary consideration is factual
and depends on the nature of the invention and the amount of knowledge
imparted to those skilled in the art by the disclosure.” Vas-Cath, Inc. v.
Mahurkar, 935 F.2d 1555, 1562 (Fed. Cir. 1991) (citation omitted, emphasis
in original). The amount of description needed to meet the requirement can
vary with the scientific and technologic knowledge already in existence.
Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005).
A claim will not be invalidated on section 112 grounds simply
because the embodiments of the specification do not contain
examples explicitly covering the full scope of the claim
language. That is because the patent specification is written for
a person of skill in the art, and such a person comes to the
patent with the knowledge of what has come before. Placed in
that context, it is unnecessary to spell out every detail of the
invention in the specification; only enough must be included to
convince a person of skill in the art that the inventor possessed
the invention and to enable such a person to make and use the
invention without undue experimentation.

Falkner v. Inglis, 448 F.3d 1357, 1366 (Fed. Cir. 2006); see also Capon v.
Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005) (“It is not necessary that every
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permutation within a generally operable invention be effective in order for
an inventor to obtain a generic claim, provided that the effect is sufficiently
demonstrated to characterize a generic invention.”).
If an Examiner has notified an Applicant exactly what the Examiner
found was missing, “the burden was then properly shifted to [the Applicant]
to cite to the examiner where adequate written description could be found, or
to make an amendment to address the deficiency.” Hyatt v. Dudas, 492 F.3d
1365, 1371 (Fed. Cir. 2007).

Analysis
The claimed complex comprises two proteins, the first “interacting
with” the second, and each defined in part as a protein “that interacts.”
There is no dispute that native Caspase-7 and native LIPA function in that
way, and that a complex comprising them has been adequately described.
Like the Examiner, we find a description of native Caspase-7 and native
LIPA, and a description of a functional, i.e., “binding,” fragment of each, as
shown in Table 1 by reference to GenBank Accession numbers. (FF-7 and
8.)
The Examiner found, and we agree, that the claim includes many
complexes other than the complex of native Caspase-7 with LIPA. The
complex’s components in parts (a) and (i) of claim 39 may comprise not
only the native proteins and the fragment of each identified in Table 1, but
may comprise instead other fragments each of which may be of any length
greater than two amino acids. (FF-2.) The complex’s components in parts
(b) and (ii) of claim 39 may comprise not only the native proteins, but may
comprise instead many others defined in the Specification as including
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modified forms and nonconventional amino acids (FF-2), homologues (FF-
5) or derivatives (FF-6). The complex’s components in parts (c) and (iii) of
claim 39 may comprise not only the native proteins but any of those in parts
(a), (b), (i) or (ii) covalently linked to one or more polypeptides. (FF-10.)
The Examiner found, and we agree, that the description in the
Specification was not commensurate with the claims. The Specification’s
definitions mean that the claim terms cover broad classes of compounds, but
the definitions themselves do not identify any compounds.
Appellant contends that the Examiner’s position is not supported by
evidence. (App. Br. 5.) However, the Examiner (i) identified the
descriptions that were present (Ans. 5, noting the two full length sequences
and the two fragments listed in Table 1); (ii) indicated that Appellant was
“not required to disclose every species encompassed by a genus” (id.); and
indicated the missing descriptive information (id.). We find the Examiner
properly shifted the burden to Appellant to cite where the missing
descriptions can be found or amend the claims. See Hyatt v. Dudas,
492 F.3d at 1371.
Rather than provide evidence that the Specification in fact did
describe the compounds listed by category in the claims, or provide evidence
that the missing descriptive information was known in the art, or provide
evidence that those of skill in the art would not have required more to
recognize an adequate description and credit Appellant with possession
commensurate with the claims, Appellant argues the facts here are directly
analogous to those in another case and/or in the Office’s training materials.
Appellant cites Invitrogen Corp. v. Clontech Labs., Inc., 429 F.3d
1052 (Fed. Cir. 2005), where, according to Appellant, a single example in
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the Specification provided adequate written description for a generic claim.
(App. Br. 6.) In that case, a district court ruled that (1) the written
description, (2) testimony from an expert, and (3) and a journal article
“established a sufficiently known correlation between RNase H activity in
RT (function) and the RT gene made by deletion mutation (structure) to
satisfy the PTO test for written description.” 429 F.3d at 1072. On those
facts, the Federal Circuit affirmed. We find the facts in this appeal are not
directly analogous to those in Invitrogen. Here, although the Caspase-7
binding region and LIPA binding region sequences were identified in Table
1, no correlation between the structure and the function of complex
formation has been made of record. The 255 amino acid fragment of
Caspase-7 and the 183 amino acid fragment of LIPA identified in Table 1
(FF-8), do not inform us that a person of ordinary skill in the art would have
understood that information to be representative of a genus of fragments as
small as 3 amino acids, under Appellant’s definitions of protein and
fragment (FF-2 and 3). Further, there is no evidence in this record, in
contrast to the expert testimony and literature evidence in Invitrogen, that a
person of ordinary skill in the art would have accepted Appellant’s
disclosure of the native sequences as representative for the scope of the
modified forms, including, e.g, nonconventional amino acids, of the proteins
in the claimed complex. In short, Appellant’s analogy to Invitrogen is based
on factual premises not supported on this record.
Appellant alleges that orthologs of Caspase-7 and LIPA were well
known in the art, but Appellant refers us to no evidence to support the
argument. (App. Br. 7.) Appellant also argues that an example in the
USPTO’s training materials supports finding written description for a
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hypothetical claim drawn to active variants having 95% identity to a known
sequence (App. Br. 8), and that Appellant’s claims are similarly described.
Because written description is a fact question, each case must be decided on
its own merits. In this case, Appellant’s definitions of variants are expansive
(FF-5 and 6), and we are not persuaded that the facts in the training material
example are so similar to Appellant’s claims.
“[T]he specification must demonstrate that the applicant has made a
generic invention that achieves the claimed result and do so by showing that
the applicant has invented species sufficient to support a claim to the
functionally-defined genus.” Ariad Pharmaceuticals, Inc. v. Eli Lilly & Co.,
598 F.3d 1336, 1349 (Fed. Cir. 2010). “[A]n adequate written description of
a claimed genus requires more than a generic statement of an invention’s
boundaries.” Id. We find that the Examiner made an “objective inquiry into
the four corners of the specification from the perspective of a person of
ordinary skill in the art,” as required by Ariad. See id. at 1351. Appellant’s
response does not persuade us that the Specification, taken with available
knowledge in the art evidenced on this record, provided an adequate written
description commensurate with the claims. As Ariad’s claims did,
Appellant’s claims effectively recite a description of the problem to be
solved while claiming the solutions—leaving it to those in the art to
complete an unfinished invention. See id. at 1353.

ENABLEMENT
The Issue
The Examiner’s position is that “[t]he claims encompass undefined
and uncharacterized protein fragments, fusion proteins, peptides,
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homologues, derivatives and sequence variants ranging from 75%-95%
sequence identity.” (Ans. 6.) “While one of ordinary skill in the art can
theoretically produce all of these proteins with art known techniques such as
site-directed mutagenesis it would still be burdensome to . . . determine their
activity.” (Id. at 6-7.) “[T]his would require a level of ingenuity beyond
what is expected from on[e] of ordinary skill in the field.” (Id. at 7.)
According to the Examiner,
[s]ince the amino acid sequence of a polypeptide determines its
structural and functional properties, predictability of which
changes can be tolerated in a polypeptide’s amino acid
sequence and still retain activity requires a knowledge of and
guidance with regard to which amino acids in the polypeptide’s
sequence, if any are tolerant of modification . . . and detailed
knowledge of the ways in which the protein’s structure relates
to its function.

(Id.) The Examiner found the peptide art “unpredictable” and found that the
Specification did not provide sufficient guidance (id. at 7-8), citing the Lazar
article1 for the state of the art (id. at 8). The Examiner concluded that the
amount of experimentation required to identify working variants was undue.
(Id. at 8.)
Appellant points again to the Invitrogen case (App. Br. 10-11) and
contends that the enablement rejection is “clearly incorrect in view of
Invitrogen” (id. at 11). Appellant argues that orthologs of Caspase-7 and
LIPA were known from other species, that fragments were disclosed in the
Specification, and that a person having ordinary skill would know how to

1 Eliane Lazar et al., Transforming Growth Factor α: Mutation of Aspartic
Acid 47 and Leucine 48 Results in Different Biological Activities, 8 MOL.
CELL. BIOL. 1247-1252 (1988).
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make modified proteins by routine molecular biology techniques. (Id.)
Appellant argues that a person of ordinary skill could “readily determine the
minimal fragment of LIPA that retains the ability to interact with caspase-7
using routine experimentation.” (Id. at 12.) According to Appellant, “[o]nly
routine experiments are required” and “undue experimentation is simply not
required . . . especially in view of the high level of skill.” (Id. at 13.)
The issue with respect to this rejection is whether the evidence
supports the conclusion that it would be unduly burdensome for a person of
ordinary skill in the art to determine the activity of Caspase-7 and LIPA
fragments, fusion proteins, peptides, homologues, derivatives and of
sequence variants at least 75% identical to the native sequences.

Additional Findings of Fact
11. According to Appellant
one of ordinary skill would know how to (1) perform
alignments of amino acid sequences of homologous proteins,
(2) identify conserved amino acid residues, (3) introduce
conservative changes to specific residues in regions of proteins
not exhibiting significant conservation, and (4) test whether the
engineered variant proteins are still capable of interacting.

(App. Br. 12.)
12. We do not find amino acid sequences of homologous proteins
disclosed in the Specification.
13. Appellant has not pointed us to evidence in the record that amino acid
sequences of homologous proteins were known in the art.
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Principles of Law
“To be enabling, the specification of a patent must teach those skilled
in the art how to make and use the full scope of the claimed invention
without undue experimentation.” Genentech, Inc. v. Novo Nordisk, A/S, 108
F.3d 1361, 1365 (Fed. Cir. 1997). “While every aspect of a generic claim
certainly need not have been carried out by an inventor, or exemplified in
the specification, reasonable detail must be provided in order to enable
members of the public to understand and carry out the invention.”
Id. at 1366. “The test [for undue experimentation] is not merely
quantitative, since a considerable amount of experimentation is permissible,
if it is merely routine, or if the specification in question provides a
reasonable amount of guidance with respect to the direction in which the
experimentation should proceed to enable the determination of how to
practice a desired embodiment of the invention claimed.” PPG Indus., Inc.
v. Guardian Indus. Corp., 75 F.3d 1558, 1564 (Fed. Cir. 1996) (quotation
and citation omitted).

Analysis
The Examiner’s conclusion that undue experimentation would have
been required was based mainly on a finding that the Specification did not
provide structural and functional guidance commensurate with the claims.
Appellant does not dispute that a person of ordinary skill in the art would
have required such guidance, but argues that the skilled artisan could derive
the information needed from the amino acid sequences of homologues, i.e.,
Caspase-7 and LIPA from other species. (FF-11.) Although Appellant
asserts that such sequences were known in the art, Appellant has not pointed
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us to evidence supporting that assertion. (FF-12 and 13.) A Specification
need not disclose what is well known in the art, e.g., Genentech, 108 F.3d at
1366, but in the absence of evidence that the amino acid sequences
Appellant relies on were in fact well known in the art, we conclude that the
Examiner has established that undue experimentation would have been
required to make complexes commensurate with the scope of the claims.
Appellant also argues that the Invitrogen case should lead us to
reverse the enablement rejection. (App. Br. 10-11.) In that case,
Invitrogen’s claims were to “genetically engineered RT without regard for
the method used to mutate the genes.” 429 F.3d at 1070. The patent
described how to make the product by deletion mutation, and Clontech
argued the claims were not enabled because the patent did not teach how to
make the product by point mutation. Id. The court found that Clontech’s
argument “overlooks the fact that the claims are not limited by the method of
achieving the mutation,” and concluded that the patent’s teaching regarding
deletion mutation was sufficient. Id. at 1071.
The fact pattern here is not similar to the Invitrogen pattern. The
Examiner found that adequate guidance was missing, and Appellant argues
that a person of ordinary skill could have derived the needed guidance from
known homologues. Appellant has not provided evidence that usable
homologues were known to the art. In contrast to the evidence available in
Invitrogen, the available evidence here does not support Appellant’s
argument. We find nothing in the Invitrogen decision that suggests we
should excuse the missing sequence information in Appellant’s case.

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CONCLUSIONS
The evidence supports the Examiner’s finding that the Specification
did not provide a written description of the invention commensurate with the
claims.
The evidence supports the conclusion that it would be unduly
burdensome for a person of ordinary skill in the art to determine the activity
of Caspase-7 and LIPA fragments, fusion proteins, peptides, homologues,
derivatives and of sequence variants at least 75% identical to the native
sequences.

SUMMARY
We affirm the rejection of claims 39-48 under 35 U.S.C. § 112, first
paragraph, as failing to comply with the written description requirement; and
We affirm the rejection of claims 39-48 under 35 U.S.C. § 112, first
paragraph, as failing to comply with the enablement requirement.

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

lp

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MYRIAD GENETICS INC.
INTELLECTUAL PROPERTY DEPARTMENT
320 WAKARA WAY
SALT LAKE CITY UT 84108