Ex Parte Turner et al

Board of Patent Appeals and Interferences

Sep 24, 2004

09770643 (B.P.A.I. Sep. 24, 2004)

The opinion in support of the decision being entered today was not written
for publication and is not binding precedent of the Board.

Paper No. 23

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte C. ALEXANDER TURNER JR., ERIN HILBUN.
GREGORY DONOHO, JOHN SCOVILLE,
FRANK WATTLER, GLENN FRIEDFRICH,
ALEJANDRO ABUIN, BRIAN ZAMBROWICZ,
and ARTHUR T. SANDS
__________

Appeal No. 2004-1040
Application No. 09/770,643
__________

ON BRIEF
__________

Before WILLIAM F. SMITH, SCHEINER, and GRIMES, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL

This is a decision on appeal under 35 U.S.C. § 134 from the examiner’s final
rejection of claims 1-3 and 6-8, all of the claims in the application. Claims 1 and 3 are
representative and read as follows:
1. An isolated nucleic acid molecule comprising the nucleotide sequence of
SEQ ID NO:1.

3. An isolated nucleic acid molecule comprising a nucleotide sequence that
encodes the amino acid sequence shown in SEQ ID NO:2.

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The examiner relies on the following references:
Bork, (Bork I), “Go hunting in sequence databases but watch out for the traps,” Trends
in Genetics, Vol. 12, No. 10, pp. 425-427 (1996)

Smith et al. (Smith), “The challenges of genome sequence annotation or ‘the devil is in
the details,’” Nature Biotechnology, Vol. 15, pp. 1222-1223, (1997)

Doerks et al. (Doerks), “Protein annotation: detective work for function prediction,”
Trends in Genetics, Vol. 14, No. 6, pp.248-250 (1998)

Brenner, “Errors in genome annotation,” Trends in Genetics, Vol. 15, No. 4, p.132-133,
(1999)

Bork, (Bork II), “Powers and pitfalls in sequence analysis: the 70% hurdle,” Genome
Research, Vol. 10, pp. 398-400 (2000)

Skolnick et al. (Skolnick), “From genes to protein structure and function: novel
applications of computational approaches in the genomic era,” Trends in Biotechnology,
Vol. 18, No. 1, pp.34-39 (2000)

Claims 1-3 and 6-8 stand rejected under 35 U.S.C. §§ 101 and 112, first
paragraph, as lacking patentable utility.
We affirm.
Technical Background
The specification discloses “polynucleotides encoding human proteins (referred
to generically as ‘novel human proteins’ or NHPs) that share sequence similarity with
animal neurexin proteins and contactin associated proteins.” Page 1. See also page
15: “The described sequences share limited structural similarity with a variety of
proteins, including, but not limited to, neurexins (including secreted types) and contactin
associated proteins.”
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The specification also discloses that “[a] polymorphism was identified that results
in a C-or-T transition at, for example, the position corresponding to nucleotide 812 of
SEQ ID NO:1 that can result in a ser or leu being present at, for example, amino acid
position 271 of SEQ ID NO:2.
“Neurexins have been associated with, inter alia, mediating neural processes,
seizures, signaling, exocytosis, cancer, and development. Neurexins can also serve as
receptors for latrotoxins.” Page 1. The specification does not disclose what role the
protein of SEQ ID NO:2 plays in any physiological process, but contemplates
“processes for identifying compounds that modulate, i.e., act as agonists or antagonists,
of NHP expression and/or NHP activity that utilize purified preparations of the described
NHPs and/or NHP product, or cells expressing the same. Such compounds can be
used as therapeutic agents for the treatment of a wide variety of symptoms associated
with biological disorders or imbalances.” Page 2.
The specification also discloses that “suitably labeled NHP nucleotide probes can
be used to screen a human genomic library using appropriately stringent conditions or
by PCR. The identification and characterization of human genomic clones is helpful for
identifying polymorphisms . . . , determining the genomic structure of a given
locus/allele, and designing diagnostic tests.” Page 10.
The specification discloses that “[t]he NHP proteins or peptides, NHP fusion
proteins, NHP nucleotide sequences, host cell expression systems, antibodies,
antagonists, agonists and genetically engineered cells and animals can be used for
screening for drugs . . . effective in the treatment of the symptomatic or phenotypic
manifestations of perturbing the normal function of NHP in the body.” Page 14. Or “the
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NHP products can be used as therapeutics. For example, soluble derivatives such as
NHP peptides/domains corresponding to the NHPs, . . . NHP antibodies . . .,
antagonists or agonists . . . can be used to directly treat diseases or disorders.” Id.
The specification discloses that “[n]ucleotide constructs encoding functional
NHPs, mutant NHPs, as well as antisense and ribozyme molecules can also be used in
‘gene therapy’ approaches for the modulation of NHP expression.” Page 15.
The NHP protein is disclosed to have “a variety of uses. These uses include, but
are not limited to, the generation of antibodies, as reagents in diagnostic assays, for the
identification of other cellular gene products related to a NHP, [and] as reagents in
assays for screening for compounds that can be [used?] as pharmaceutical reagents
useful in the therapeutic treatment of mental, biological, or medical disorders and
disease.” Pages 15-16.
The specification discloses that NHP-binding antibodies “may be used, for
example, in the detection of NHP in a biological sample and may, therefore, be utilized
as part of a diagnostic or prognostic technique whereby patients may be tested for
abnormal amounts of NHP. . . . Such antibodies may additionally be used as a method
for the inhibition of abnormal NHP activity. Thus, such antibodies may, therefore, be
utilized as part of treatment methods.” Page 23.
Procedural Background
On June 19, 2004, Appellants were notified of certain similarities between the
present case and commonly assigned, previously decided Appeal 2004-0343
(application no. 09/564,557). Appellants were ordered (pursuant to 37 CFR § 1.196(d))
to explain why the appeal in this case should not be affirmed on the same basis as
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previous appeal. On July 19, 2004, Appellants responded to the Rule 196(d) order,
pointing out two aspects in which the facts of the present application differ from those at
issue in Appeal 2004-0343. See Paper No. 22. “[I]n order to preserve such issues for
appeal to the Federal Circuit, . . . Appellants respectfully request[ed] the Board to
address all of the assertions of utility set forth by Appellants in the Appeal Brief.” Id.,
pages 3-4. We therefore proceed to the merits of the appeal.
Discussion
The examiner rejected all of the claims as lacking a disclosed utility sufficient to
satisfy 35 U.S.C. § 101.1 The examiner bears the initial burden of showing that a
claimed invention lacks patentable utility. See In re Brana, 51 F.3d 1560, 1566, 34
USPQ2d 1436, 1441 (Fed. Cir. 1995) (“Only after the PTO provides evidence showing
that one of ordinary skill in the art would reasonably doubt the asserted utility does the
burden shift to the applicant to provide rebuttal evidence sufficient to convince such a
person of the invention’s asserted utility.”).
The seminal decision interpreting the utility requirement of § 101 is Brenner v.
Manson, 383 U.S. 519, 148 USPQ 689 (1966). At issue in Brenner was a claim to “a
chemical process which yields an already known product whose utility—other than as a
possible object of scientific inquiry—ha[d] not yet been evidenced.” Id. at 529, 148
USPQ at 693. The Patent Office had rejected the claimed process for lack of utility, on
the basis that the product produced by the claimed process had not been shown to be
useful. See id. at 521-22, 148 USPQ at 690. On appeal, the Court of Customs and

1 The examiner also rejected all of the claims under 35 U.S.C. § 112, first paragraph, for lack of
enablement, but that rejection is merely as a corollary of the finding of lack of utility. See the Examiner’s
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Patent Appeals reversed, on the basis that “where a claimed process produces a known
product it is not necessary to show utility for the product.” Id. at 522, 148 USPQ at 691.
The Brenner Court noted that although § 101 requires that an invention be
“useful,” that “simple, everyday word can be pregnant with ambiguity when applied to
the facts of life.” Id. at 529, 148 USPQ at 693. Thus,
[it] is not remarkable that differences arise as to how the test of usefulness
is to be applied to chemical processes. Even if we knew precisely what
Congress meant in 1790 when it devised the “new and useful”
phraseology and in subsequent re-enactments of the test, we should have
difficulty in applying it in the context of contemporary chemistry, where
research is as comprehensive as man’s grasp and where little or nothing
is wholly beyond the pale of “utility”—if that word is given its broadest
reach.

Id. at 530, 148 USPQ at 694.2
The Court, finding “no specific assistance in the legislative materials underlying §
101,” based its analysis on “the general intent of Congress, the purposes of the patent
system, and the implications of a decision one way or the other.” Id. at 532, 148 USPQ
at 695. The Court concluded that “[t]he basic quid pro quo contemplated by the
Constitution and the Congress for granting a patent monopoly is the benefit derived by
the public from an invention with substantial utility. Unless and until a process is refined
and developed to this point—where specific benefit exists in currently available form—
there is insufficient justification for permitting an applicant to engross what may prove to
be a broad field.” Id. at 534-35, 148 USPQ at 695.

Answer, page 7. Therefore, our conclusion with respect to the § 101 issue also applies to this § 112
issue.
2 The invention at issue in Brenner was a process, but the Court expressly noted that its holding “would
apply equally to the patenting of the product produced by the process.” Id. at 535, 148 USPQ at 695-96.
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The Court considered and rejected the applicant’s argument that attenuating the
requirement of utility “would encourage inventors of new processes to publicize the
event for the benefit of the entire scientific community, thus widening the search for
uses and increasing the fund of scientific knowledge.” The Court noted that, while there
is value to encouraging disclosure, “a more compelling consideration is that a process
patent in the chemical field, which has not been developed and pointed to the degree of
specific utility, creates a monopoly of knowledge which should be granted only if clearly
commanded by the statute. Until the process claim has been reduced to production of a
product shown to be useful, the metes and bounds of that monopoly are not capable of
precise delineation. It may engross a vast, unknown, and perhaps unknowable area.
Such a patent may confer power to block off whole areas of scientific development.” Id.
at 534, 148 USPQ at 695.
The Court took pains to note that it did not “mean to disparage the importance of
contributions to the fund of scientific information short of the invention of something
‘useful,’” and that it was not “blind to the prospect that what now seems without ‘use’
may tomorrow command the grateful attention of the public.” Id. at 535-36, 148 USPQ
at 696. Those considerations did not sway the Court, however, because “a patent is not
a hunting license. It is not a reward for the search, but compensation for its successful
conclusion.” Id.
Subsequent decisions of the CCPA and the Court of Appeals for the Federal
Circuit have added further layers of judicial gloss to the meaning of § 101’s utility
requirement. The first opinion of the CCPA applying Brenner was In re Kirk, 376 F.2d
936, 153 USPQ 48 (CCPA 1967). The invention claimed in Kirk was a set of steroid
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derivatives said to have valuable biological properties and to be of value “in the
furtherance of steroidal research and in the application of steroidal materials to
veterinary or medical practice.” Id. at 938, 153 USPQ at 50. The claims had been
rejected for lack of utility. In response, the applicants submitted an affidavit which
purportedly “show[ed] that one skilled in the art would be able to determine the
biological uses of the claimed compounds by routine tests.” Id. at 939, 153 USPQ at
51.
The court held that “nebulous expressions [like] ‘biological activity’ or ‘biological
properties’” did not adequately convey how to use the claimed compounds. Id. at 941,
153 USPQ at 52. Nor did the applicants’ affidavit help their case: “the sum and
substance of the affidavit appear[ed] to be that one of ordinary skill in the art would
know ‘how to use’ the compounds to find out in the first instance whether the
compounds are—or are not—in fact useful or possess useful properties, and to
ascertain what those properties are.” Id. at 942, 153 USPQ at 53.
The Kirk court held that an earlier CCPA decision, holding that a chemical
compound meets the requirements of § 101 if it is useful to chemists doing research on
steroids, had effectively been overruled by Brenner. “There can be no doubt that the
insubstantial, superficial nature of vague, general disclosures or arguments of ‘useful in
research’ or ‘useful as building blocks of value to the researcher’ was recognized, and
clearly rejected, by the Supreme Court” in Brenner. See Kirk, 376 F.2d at 945, 153
USPQ at 55.
More recently, in In re Ziegler, 992 F.2d 1197, 26 USPQ2d 1600 (Fed. Cir. 1993),
the Federal Circuit considered the degree of specificity required to show utility for a
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claim to polypropylene. The U.S. application on appeal in Ziegler claimed priority to a
German application filed in 1954. “In the German application, Ziegler disclosed only
that solid granules of polypropylene could be pressed into a flexible film with a
characteristic infrared spectrum and that the polypropylene was ‘plastic-like.’” Id. at
1203, 26 USPQ2d at 1605. “Ziegler did not assert any practical use for the
polypropylene or its film, and Ziegler did not disclose any characteristics of the
polypropylene or its film that demonstrated its utility.” Id. The court held that the
German application did not satisfy the requirements of § 101 and therefore could not be
relied on to overcome a rejection based on an intervening reference. See id., 26
USPQ2d at 1606. “[At] best, Ziegler was on the way to discovering a practical utility for
polypropylene at the time of the filing of the German application; but in that application
Ziegler had not yet gotten there.” Id., 26 USPQ2d at 1605.
On the other hand, the CCPA reversed a rejection for lack of utility in In re Jolles,
628 F.2d 1322, 206 USPQ 885 (CCPA 1980). The applicant in Jolles claimed
pharmaceutical compositions that were disclosed to be useful in treating acute
myeloblastic leukemia. See id. at 1323, 206 USPQ at 886. The active ingredients in
the compositions were closely related to daunorubicin and doxorubicin, both of which
were “well recognized in the art as valuable for use in cancer chemotherapy.” Id., 206
USPQ at 887. The applicant also submitted declaratory evidence showing that eight of
the claimed compositions were effective in treating tumors in a mouse model, and one
was effective in treating humans. See id. at 1323-24, 206 USPQ at 887-88. The court
noted that the data derived from the mouse model were “relevant to the treatment of
humans and [were] not to be disregarded,” id. at 1327, 206 USPQ at 890, and held that
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the evidence was sufficient to support the asserted therapeutic utility. See id. at 1327-
28, 206 USPQ at 891.
The Federal Circuit held in Cross v. Iizuka, 753 F.2d 1040, 224 USPQ 739 (Fed.
Cir. 1985), that in vivo testing (as in Jolles) was not necessarily required to show utility
in the pharmaceutical context. The Cross court stated that “[it] is axiomatic that an
invention cannot be considered ‘useful,’ in the sense that a patent can be granted on it,
unless substantial or practical utility for the invention has been discovered and disclosed
where such utility would not be obvious.” Id. at 1044, 224 USPQ at 742 (citing Brenner
v. Manson). The court “perceive[d] no insurmountable difficulty, under appropriate
circumstances, in finding that the first link in the screening chain, in vitro testing, may
establish a practical utility for the compound in question.” Id. at 1051, 224 USPQ at
748. Successful in vitro testing could provide an immediate benefit to the public, by
“marshal[ling] resources and direct[ing] the expenditure of effort to further in vivo testing
of the most potent compounds . . ., analogous to the benefit provided by the showing of
an in vivo utility.” Id. On the facts of that case – successful in vitro testing
supplemented by similar in vitro and in vivo activities of structurally similar compounds –
the court held that in vitro activity was sufficient to meet the requirements of § 101.
See id.
The Federal Circuit confirmed in In re Brana, 51 F.3d 1560, 34 USPQ2d 1436
(Fed. Cir. 1995), that human testing is not necessary to establish utility for a method of
treatment. The invention claimed in Brana was a group of compounds disclosed to
have antitumor activity. See id. at 1562, 34 USPQ2d at 1437-38. The claimed
compounds were disclosed to have higher antitumor activity than related compounds
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known to have antitumor activity, and the applicants provided declaratory evidence of in
vivo activity against tumors in a mouse model. See id., 34 USPQ2d at 1438. The court
held that these data were sufficient to satisfy § 101; usefulness in patent law does not
require that the invention be ready to be administered to humans. See id. at 1567, 34
USPQ2d at 1442.
Several lessons can be drawn from Brenner and its progeny. First, § 101’s
requirement that an invention be “useful” is not to be given its broadest reach, such that
little or nothing of a chemical nature would be found to lack utility. See Brenner, 383
U.S. at 530, 148 USPQ at 694. Thus, not every “use” that can be asserted will be
sufficient to satisfy § 101. For example, the steroid compound at issue in Brenner was
useful as a possible object of scientific inquiry, and the polypropylene claimed in Ziegler
was useful for pressing into a flexible film, yet both lacked sufficient utility to satisfy
§ 101. See Brenner, 383 U.S. at 529, 148 USPQ at 696; Ziegler, 992 F.2d at 1203, 26
USPQ2d at 1605.
Rather than setting a de minimis standard, § 101 requires a utility that is
“substantial”, i.e., one that provides a specific benefit in currently available form.
Brenner, 383 U.S. at 534-35, 148 USPQ at 695. This standard has been found to be
met by pharmaceutical compositions shown to be useful in mouse models and in
humans for treating acute myeloblastic leukemia (Jolles, 628 F.2d at 1327-28, 206
USPQ at 891); by evidence showing successful in vitro testing supplemented by similar
in vitro and in vivo activities of structurally similar compounds (Cross, 753 F.2d at 1051,
224 USPQ at 748); and by evidence showing in vivo antitumor activity in mice,
combined with a disclosure that the claimed compounds had higher antitumor activity
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than a related compound known to have antitumor activity (Brana, 51 F.3d at 1567, 34
USPQ2d at 1442).
By contrast, Brenner’s standard has been interpreted to mean that “vague,
general disclosures or arguments of ‘useful in research’ or ‘useful as building blocks of
value to the researcher’” would not satisfy § 101. See Kirk, 376 F.2d at 945, 153 USPQ
at 55 (interpreting Brenner). Likewise, a disclosure of a “plastic-like” polypropylene
capable of being pressed into a flexible film was held to show that the applicant was “at
best . . . on the way to discovering a practical utility for polypropylene at the time of the
filing,” but not yet there. Ziegler, 992 F.2d at 1203, 26 USPQ2d at 1605.
In this case, the examiner found the specification’s disclosure to be inadequate:
[T]he instant claims are drawn to a nucleic acid molecule which has a yet
undetermined function or biological significance, or correlation to a specific
disease state. . . . In the absence of a knowledge of the natural ligands or
biological significance of this protein, or any significance of the nucleic
acid molecule of the present invention, . . . there is no immediately
obvious patentable use for them. To employ the nucleic acid molecule of
the instant invention to treat [sic], to better understand disease, or to use it
to produce a receptor protein to identify substances which bind to and/or
mediate activity of the said receptor is clearly to use it as the object of
further research.

Examiner’s Answer, page 5.3 The examiner noted Appellants’ evidence that the
claimed polynucleotides encode a member of the neurexin superfamily or a contactin-
associated protein (caspr), but concluded that the evidence did not suggest a utility that
would satisfy § 101. See id., pages 6-7:

3 The examiner also criticized the specification’s reliance on sequence similarity as a basis for inferring
the function of the claimed NHP. See the Examiner’s Answer, pages 4-5. Appellants argue that
sequence comparisons are well-accepted, although perhaps not universally accepted, in the art as a
reasonable basis on which to predict function. See the Appeal Brief, pages 6-11. We need not decide the
issue because, even assuming Appellants are correct, the specification does not adequately disclose the
utility of the claimed nucleic acids.
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Subsequent references (GenBank NM_130773 and AB077881) by others
do teach proteins which are 99% identical to that of the claimed invention.
These proteins are named “Caspr” proteins and are members of the
neurexin superfamily. . . . While it is known, as Applicants disclose in the
specification, that the superfamily of neurexins mediate neuronal processes,
the specific neur[on]al processes of the proteins and genes of the present
invention have not been disclosed. . . . Therefore, one of ordinary skill in
the art would not know how to use a protein, or a gene, which is only known
to generally be involved in neuronal processes, along with potentially
hundreds or thousands of proteins.

Appellants argue that the claimed nucleic acids encode a protein that would be
accepted as a caspr by those skilled in the art, because
two sequences sharing nearly 100% percent identity at the protein level
over the entire length of the claimed sequence are present in the leading
scientific repository for biological sequence data (GenBank), and have
been annotated by third party scientists wholly unaffiliated with Appellants
as “Homo sapiens caspr5 protein.” . . . Given these GenBank
annotations, there can be no question that those skilled in the art would
clearly believe that Appellants’ sequence is a caspr protein.

Appeal Brief, pages 4-5. Appellants cite sequence comparison data that purportedly
show that “caspr proteins are distinct members of the neurexin superfamily,” id., page 5,
and conclude that, “[a]s the Examiner admits that casprs have a specific utility, due to
their association with ‘myelinated axons and potassium channels’ (the Final Action at
page 3), the claimed sequence clearly meets the requirements of 35 U.S.C. § 101.” Id.,
page 6.
We do not agree that the characterization of the claimed nucleic acids as
encoding a contactin-associated protein (caspr) is sufficient to establish their utility. The
specification admits that “[n]eurexins have been associated with, inter alia, mediating
neural processes, seizures, signaling, exocytosis, cancer, and development. Neurexins
can also serve as receptors for latrotoxins.” Page 1. The specification does not
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disclose any biological processes that have been associated with casprs and, more
specifically, the specification provides no information regarding what biological functions
or activities involve the polypeptides encoded by the instantly claimed nucleic acids.
Nor have Appellants provided other evidence to show that the biological activity
or role of the protein of SEQ ID NO:2 would have been apparent to those skilled in the
art at the time this application was filed.4 The only prior art cited by Appellants that
bears on the activity of caspr proteins is Poliak,5 of which only the abstract is of record.
Poliak discloses that the protein Caspr2 is found in a particular part (the “juxtaparanodal
region”) of nerve cells (myelinated axons) and suggests that Caspr family members may
have a role in “the local differentiation of the axon into distinct functional subdomains.”
Appellants have provided no explanation of how Poliak’s disclosure would have
suggested a well-established utility for other caspr proteins to those skilled in the art,
and no such utility is apparent to us.
Appellants argue that the examiner “admit[ted] that casprs have a specific utility,
due to their association with ‘myelinated axons and potassium channels,’” citing the
Final Action (Paper No. 14) at page 3. We have reviewed the Final Action and do not
find that the examiner has admitted that the instantly claimed invention has utility.

4 Whether a claimed invention is supported by a disclosure of utility sufficient to satisfy 35 U.S.C. § 101 is
determined as of the filing date of the application. See In re Brana, 51 F.3d 1560, 1566 n.19, 34 USPQ2d
1436, 1441 n.19 (Fed. Cir. 1995) (“Enablement, or utility, is determined as of the application filing date.”).
Therefore, we have not considered any of the references cited by the examiner or by Appellants that were
published after the effective filing date of the present application.
5 Poliak et al., “Caspr2, a new member of the neurexin superfamily, is localized at the juxtaparanodes of
myelinated axons and associates with K+ channels,” Neuron, Vol. 24, pp. 1037-1047 (1999).
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Granted, the examiner states that “Casprs, for example, appear to associate with
myelinated axons and potassium channels and it is the involvement with these functions
which confer[s] a specific utility to Caspr proteins.” Page 3. However, the examiner
provided no further explanation of precisely what “specific utility” is conferred on casprs
by virtue of their association with myelinated axons and potassium channels.
Moreover, the above-quoted statement must be read in context. The examiner
concluded that, despite what was known about casprs generally, “one of ordinary skill in
the art, only knowing that the proteins of the present invention are caspr proteins, . . .
would still not know what the specific utility of these proteins was, other than the fact
that they mediate neuronal processes. Therefore, one of ordinary skill in the art would
not know how to use a protein, or a gene, which is only known to generally be involved
in neuronal processes, along with potentially hundreds or thousands of proteins.” Id.,
pages 3-4. These statements, along with the examiner’s decision to maintain rejections
of lack of utility, show that he did not intend to admit that the presently claimed invention
has patentable utility.
Thus, the record does not support Appellants’ position that the characterization of
a polypeptide as neurexin-like or as a caspr protein would have suggested a specific
biological function, or any other basis for patentable utility, to a person skilled in the art
at the time the application was filed. In the terms used by the Brenner Court, such a
characterization does not provide a specific utility in currently available form. We are
not persuaded Appellants’ argument that the claimed polynucleotides have utility by
virtue of the “sequence similarity” of the encoded polypeptide to neurexins and
contactin-associated proteins (casprs).
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Appellants also argue that the claimed polynucleotides are useful because of the
disclosed polymorphism at position 812 of SEQ ID NO:1: “As polymorphisms such as
this are the basis for forensic analysis, which is undoubtedly a ‘real world’ utility, the
presently claimed sequences must in themselves be useful.” Appeal Brief, page 11.
“The fact that forensic biologists use polymorphic markers such as that described by
Appellants every day provides more tha[n] ample support for the assertion that forensic
biologists would also be able to use the specific polymorphic marker described by
Appellants in the same fashion.” Id., page 13. The lack of information regarding
biological function is irrelevant to this utility, Appellants argues, because “[f]orensic
analysis requires no information regarding the function of the protein encoded by the
polymorphic DNA sequence.” Id., pages12-13.
This argument is not persuasive because, among other things, it has no support
in the specification or in the evidence of record. The specification discloses the
presence of a polymorphism in SEQ ID NO:1 (page 14) but discloses no utilities based
on detection of the polymorphism. In particular, the specification does not disclose that
the polymorphism is a useful marker for forensic analysis.
Appellants cite the specification at page 10, lines 15-19, as disclosing that “the
present nucleic acids sequences have utility in forensic analysis.” Appeal Brief, page
11. We do not agree that this passage supports Appellants’ argument. The sentence
cited by Appellants reads as follows:
The identification and characterization of human genomic clones is helpful
for identifying polymorphisms (including, but not limited to, nucleotide
repeats, microsatellite alleles, single nucleotide polymorphisms, or coding
single nucleotide polymorphisms), determining the genomic structure of a
given locus/allele, and designing diagnostic tests.
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Thus, the cited passage makes no reference to the specific polymorphism in
SEQ ID NO:1 or to forensic analysis. It therefore does not support the utility asserted in
the Appeal Brief. Appellants have cited no other evidence of record to show that such a
use was well-established as of the effective filing date of the present application
(January 26, 2000). Nor have Appellants provided any evidence to show that those
skilled in the art would have found the specific polymorphism present in SEQ ID NO:1 –
without analysis of its degree of variability in the human population and without
associating it with any other genetic marker – to be useful as argued. Thus, the
polymorphism-based utility asserted in the Appeal Brief lacks evidentiary support and
cannot be relied on to overcome the rejection.
In addition to the polymorphism-based argument, Appellants also argue that the
claimed nucleic acids are useful in “gene chip” methods of tracking gene expression.
See the Appeal Brief, pages 15-16:
Such “DNA chips” clearly have utility, as evidenced by hundreds of issued
U.S. Patents. . . . Clearly, compositions that enhance the utility of such
DNA chips, such as the presently claimed nucleotide sequences, must in
themselves be useful.

Appellants argue that, in addition to their use in “DNA chips”, the claimed
sequences are also useful “in determining the genomic structure of the corresponding
human chromosome, for example mapping the protein encoding regions.” Id., page 16.
More particularly, Appellants argue that
[t]he presently claimed polynucleotide sequence provides biologically
validated empirical data (e.g., showing which sequences are transcribed,
spliced, and polyadenylated) that specifically define that portion of the
corresponding genomic locus that actually encodes exon sequence.

Appeal No. 2004-1040 Page 18
Application No. 09/770,643

Id., page 17. Appellants argue that “the practical scientific value of expressed, spliced,
and polyadenylated mRNA sequences is readily apparent to those skilled in the relevant
biological and biochemical arts.” Id. Finally, Appellants argue that “the present
nucleotide sequence has a specific utility in mapping the claimed sequence to the
corresponding human chromosome, specifically chromosome 2.” Id.
We are not persuaded by Appellants’ argument. We find that the asserted uses
of the claimed polynucleotides—as a component of a DNA chip for monitoring gene
expression, as a marker for a given chromosomal locus, or for defining the exon splice-
junctions of a gene—do not satisfy the utility requirement of § 101. Such uses do not
provide a specific benefit in currently available form.
For example, with regard to the asserted “DNA chip” utility, we accept for
argument’s sake that a person skilled in the art could attach one of the claimed
polynucleotides (or a part of it) to a solid substrate, in combination with other
polynucleotides, to form a DNA chip, and that such a DNA chip could be used to
monitor changes in expression of the corresponding gene. However, the specification
provides no guidance to allow a skilled artisan to use data relating to the expression of
the gene comprising SEQ ID NO:1 in any practical way. The specification provides no
guidance regarding what the SEQ ID NO:1-specific information derived from a DNA chip
would mean.
For example, assume that a fragment of SEQ ID NO:1 was attached to a DNA
chip and the researcher observed that expression of the corresponding gene was
increased when a cell was treated with a particular agent. The specification provides no
basis on which a skilled worker would be able to determine what, if anything, that result
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Application No. 09/770,643

means. Perhaps a change in expression of the gene would mean different things,
depending on other factors, but again the specification provides no hint what other
factors might be important. Would it depend on what agent is used, what cell type is
used, the behavior of other genes (if so, which genes and what behavior is significant),
or the degree of increase? Because the specification provides no information about the
activity of the protein encoded by SEQ ID NO:1, it provides no guidance as to how to
interpret the results of a DNA chip-based gene expression assay based on the claimed
polynucleotides.
The same problem afflicts Appellants’ assertions that the claimed polynucleotides
can be used to map a particular chromosomal locus or to define the exon splice-
junctions of the genomic gene: the specification provides no meaningful guidance
regarding how to use such information in any practical way. What would it mean, for
example, if SEQ ID NO:1 hybridizes to a specific part of human chromosome 2, or if
SEQ ID NO:1 can be used to show that the chromosomal gene has an exon splice
junction between nucleotides 103 and 104? The specification provides no guidance on
how such information would allow those skilled in the art to use the claimed
polynucleotides in a specific, substantial way. By contrast, if the specification disclosed,
for example, that SEQ ID NO:1 hybridized adjacent to a chromosomal locus associated
with a known disease (e.g., a locus susceptible to a cancer-causing translocation), the
sequence would have an apparent utility in disease diagnosis. However, without
disclosure of a specific use for the resulting data, using the claimed sequences for
mapping or determining exon splice-junctions amounts to research on the claimed
polynucleotides themselves.
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In effect, Appellants’ position is that the claimed polynucleotides are useful
because those of skill in the art could experiment with them and figure out for
themselves what any observed experimental results might mean. We do not agree that
such a disclosure provides a “specific benefit in currently available form.” Rather, the
instant case seems analogous to Brenner. In Brenner, the applicant claimed a method
of making a compound but disclosed no utility for the compound. 383 U.S. at 529, 148
USPQ at 693. The Court held that a process lacks utility if it produces a product that
lacks utility. Id. at 534, 148 USPQ at 695. Here, Appellants claim a product asserted to
be useful in a method of generating gene-expression or gene-mapping data, but the
specification does not disclose how to interpret those data. Just as the process claimed
in Brenner lacked utility because the specification did not disclose how to use the end-
product, the product claims here lack utility, based on their use in, e.g., DNA chips,
because the specification does not disclose how to use the SEQ ID NO:1-specific gene
expression data generated by a DNA chip.
Appellants argue that the claimed polynucleotides could potentially be part of a
DNA chip; since DNA chips have utility, compounds that “enhance the utility of such
DNA chips, such as the presently claimed nucleotide sequence, must in themselves be
useful.” Appeal Brief, pages 15-16. We disagree.
Assuming arguendo that a generic DNA chip—one comprising a collection of
uncharacterized or semi-characterized gene fragments—would provide a useful tool for,
e.g., drug discovery, it does not follow that each one of the polynucleotides represented
in the DNA chip individually has patentable utility. Although each polynucleotide in the
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DNA chip contributes to the data generated by the DNA chip overall, the contribution of
a single polynucleotide—its data point—is only a tiny contribution to the overall picture.
The Brenner Court held that § 101 sets more than a de minimis standard for
utility. Therefore, the patentable utility of a DNA chip, for example, does not necessarily
mean that every one of the components of the DNA chip also has patentable utility. A
patentable utility divided by a thousand does not necessarily equal a thousand
patentable utilities. Each claimed invention must be shown to meet § 101’s utility
requirement in order to be patentable; it must provide a specific benefit in currently
available form. Providing a single data point among thousands, even if the thousands
of data points collectively are useful, does not meet this standard.
The Supreme Court noted that the patent system contemplates a basic quid pro
quo: in exchange for the legal right to exclude others from his invention for a period of
time, an inventor discloses his invention to the public. See Brenner, 383 U.S. at 534,
148 USPQ at 695. The Brenner Court held that the grant of patent rights to an applicant
is justified only by disclosure of an invention with substantial utility – a specific benefit in
currently available form. Until the invention has been refined and developed to this
point, the Court held, the applicant has not met his side of the bargain, and has not
provided a disclosure that justifies granting him the right to exclude others. See id.
Thus, the basic quid pro quo of the patent system is the grant of a valuable legal
right in exchange for a meaningful disclosure of the claimed invention. In this case, the
generic utilities disclosed for the claimed products do not entitle Appellants to the legal
right they claim to exclude others from using those products.
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We note that this application is one of several on appeal that share the same
assignee.6 In each of these cases, regardless of the specific facts of the case, the
Appellants have asserted the same DNA chip, gene-mapping, and exon splice junction
arguments. Apparently, Appellants view these potential uses as utilities that can be
asserted for any cDNA they isolate, regardless of how little is known about it, which
(they hope) will nonetheless serve as a basis for patent protection and secure for
Appellants any value that might become apparent in the future, after they or others have
further characterized the claimed products. This is precisely the type of result that the
Brenner Court sought to avoid by requiring disclosure of a substantial utility to satisfy
§ 101. See 148 U.S. at 535-36, 148 USPQ at 696: [The Court was not] “blind to the
prospect that what now seems without ‘use’ may tomorrow command the grateful
attention of the public. But a patent is not a hunting license. It is not a reward for the
search, but compensation for its successful conclusion.” Id.
The polynucleotides of the instant claims may indeed prove to be useful (and
valuable), after the in vivo role of the encoded protein is discovered. The work required
to confer value on the claimed products, however, remains to be done. The instant
specification’s disclosure does not justify a grant of patent rights. See Brenner, 383
U.S. at 534, 148 USPQ at 695: “[A] process patent in the chemical field, which has not
been developed and pointed to the degree of specific utility, creates a monopoly of
knowledge which should be granted only if clearly commanded by the statute. Until the
process claim has been reduced to production of a product shown to be useful, the

6 Such applications include 09/460,594 (Appeal No. 2003-1528), 09/804,969 (2003-1794); 09/802,116
(2003-2017); 09/822,807 (2003-2028); and 09/564,557 (2004-0343).
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metes and bounds of that monopoly are not capable of precise delineation. It may
engross a vast, unknown, and perhaps unknowable area. Such a patent may confer
power to block off whole areas of scientific development.” We consider the Brenner
Court’s concern about the “power to block off whole areas of scientific development” to
be equally applicable here.
Finally, adopting the per se rule that Appellants seek—that any expressed
human gene has utility because it can be used in a DNA chip—would mean that almost
any naturally occurring nucleic acid would be patentable. Appellants’ reasoning does
not depend on the biological function of the protein encoded by the claimed nucleic
acids, and so would apparently apply to any expressed human gene, as well as
fragments of them (see, e.g., the specification at page 6, lines 3-12).
Nor can the rationale be confined to expressed human genes. We can take
judicial notice of the fact that other organisms are of interest for many different reasons,
such that gene expression assays could conceivably be used in their research. For
example, some organisms are of interest to researchers because they have been
historically well-studied (e.g., yeast and Arabidopsis). Others are of interest because
they are used as animal models (e.g., mice and chimpanzees), because they are
commercially valuable (e.g., pigs and tomatoes), because they are pests (e.g., ragweed
and corn borers), or because they are pathogens (e.g., Candida and various bacteria).
Under Appellants’ proposed rule, hybridizable fragment of any gene of any of these
organisms—and probably most other organisms—would be found to have patentable
utility because it could be attached to a chip and used in “research” to see what
happens to expression of that gene under various conditions.
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Appellants’ reasoning would also vitiate the enablement requirement, since “[t]he
enablement requirement is met if the description enables any mode of making and
using the invention.” Johns Hopkins Univ. v. CellPro Inc., 152 F.3d 1342, 1361, 47
USPQ2d 1705, 1714 (Fed. Cir. 1998) (quoting Engel Indus., Inc. v. Lockformer Co.,
946 F.2d 1528, 1533, 20 USPQ2d 1300, 1304 (Fed. Cir. 1991)). If we were to agree
with Appellants that any expressed gene and any hybridizable fragment thereof is useful
in a DNA chip, then we would also have to hold that the specification has taught those
skilled in the art one mode of using the invention. Thus, Appellants’ rule of per se utility
would also require a corresponding rule of per se enablement.
Under Appellants’ rule, then, any polynucleotide from an expressed gene would
be patentable if it was adequately described in the specification and was not disclosed
or suggested in the prior art. This standard, however, is not the one set by Congress,
which requires that a patentable invention also be useful and fully enabled, nor is it the
standard that has been consistently applied by the courts.
In addition, the flood of DNA patents that would result from adoption of
Appellants’ rule could doom the potential contribution of microarrays to biological
research. Appellants argue that “[g]iven the widespread utility of such ‘gene chip’
methods using public domain gene sequence information, there can be little doubt that
the use of the presently described novel sequences would have great utility in such
DNA chip applications.” Appeal Brief, page 15. “[T]here is an entire industry
established based on the use of gene sequences or fragments thereof in a gene chip
format.” Id.
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The practical effect of Appellants’ utility standard, however, would be that making
a microarray with 1000 genes represented on it would require investigating each of the
DNA sequences (and subsequences) on the gene chip to ensure that it was not the
subject of someone else’s patent. For each of the DNAs that was the subject of
someone else’s patent claim, a license would have to be negotiated – potentially
thousands of such negotiations for the finished product. These transaction costs would
have to be incurred for each new product that an aspiring gene chip manufacturer
wished to market. The industry gridlock likely to result has been termed a “tragedy of
the anticommons”:
By conferring monopolies in discoveries, patents necessarily increase
prices and restrict use—a cost society pays to motivate invention and
disclosure. The tragedy of the anticommons refers to the more complex
obstacles that arise when a user needs access to multiple patented inputs
to create a single useful product. Each upstream patent allows its owner
to set up another tollbooth on the road to product development, adding to
the cost and slowing the pace of downstream biomedical innovation.

Heller, page 698.7
The Supreme Court has warned against allowing too many “tollbooths” on
the road to innovation:
Patents . . . are meant to encourage invention by rewarding the inventor
with the right, limited to a term of years fixed by the patent, to exclude
others from the use of his invention. . . . But in rewarding useful invention,
the “rights and welfare of the community must be fairly dealt with and
effectually guarded.” Kendall v. Winsor, 21 How. 322, 329 (1859). . . . To
begin with, a genuine “invention” or “discovery” must be demonstrated
“lest in the constant demand for new appliances the heavy hand of tribute
be laid on each slight technological advance in an art.”

Sears, Roebuck & Co. v. Stiffel Co., 376 U.S. 225, 230, 140 USPQ 524, 527 (1964).
Appeal No. 2004-1040 Page 26
Application No. 09/770,643

Summary
The basic quid pro quo of the patent system requires disclosure of an invention
having substantial utility. Appellants’ disclosure in this case does not provide a specific
benefit in currently available form, and therefore lacks the substantial utility required by
35 U.S.C. § 101. The rejections for lack of utility are affirmed.
No time period for taking any subsequent action in connection with this appeal
may be extended under 37 CFR § 1.136(a).

AFFIRMED

William F. Smith )
Administrative Patent Judge )
)
)
) BOARD OF PATENT
Toni R. Scheiner )
Administrative Patent Judge ) APPEALS AND
)
) INTERFERENCES
)
Eric Grimes )
Administrative Patent Judge )

7 Heller et al., “Can patents deter innovation? The anticommons in biomedical research,” Science, Vol. 280,
pp. 698-701 (1998). Accessible online at www.sciencemag.org/cgi/content/full/280/5364/698.
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