Ex Parte Ach et al

Patent Trial and Appeal Board

Jul 7, 2016

12243585 (P.T.A.B. Jul. 7, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
12/243,585 10/01/2008
22878 7590 07111/2016
Agilent Technologies, Inc, in care of:
CPA Global
P. 0. Box 52050
Minneapolis, MN 55402
FIRST NAMED INVENTOR
Robert A. Ach
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
20080261-01 1470
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
07/11/2016 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):
IPOPS.LEGAL@agilent.com
Agilentdocketing@cpaglobal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ROBERT A. ACH and N. ALICE YAMADA
Appeal2013-009191
Application 12/243,585
Technology Center 1600
Before DONALD E. ADAMS, RICHARD M. LEBOVITZ, and
RICHARD J. SMITH, Administrative Patent Judges.
ADAMS, Administrative Patent Judge.
DECISION ON APPEAL 1
This appeal under 35 U.S.C. § 134(a) involves claims 1 and 4--15 (see
generally Ans. 3).2 Examiner entered rejections under 35 U.S.C. § 101 and
35 U.S.C. § 103(a). We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
1 Appellants identify the Real Party in Interest as "Agilent Technologies,
Inc." (App. Br. 3.)
2 "Claims 16-20 [stand] withdrawn from further consideration ... as being
drawn to a nonelected invention" (Ans. 3).
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Application 12/243,585
STATEMENT OF THE CASE
The claims are directed to "a method of sample analysis" (Spec. 1 ).
Claim 1 is representative and reproduced in the Claims Appendix of
Appellants' Brief.
Claims 1 and 4--15 stand rejected under 35 U.S.C. § 101 as directed to
non-statutory subject matter.
Claims 1and4--15 stand rejected under 35 U.S.C. § 103(a) as
unpatentable over the combination of Hyldig-Nielsen,3 Tafas,4 Ishiguro,5 and
Appellants' admitted prior art.
Utility:
ISSUE
Does the evidence of record support Examiner's finding that
Appellants' claimed invention is directed to non-statutory subject matter?
FACTUAL FINDINGS (FF)
FF 1. Examiner finds that Appellants' claimed methods requirethe use of
"probes" that "hybridize to different RNA molecules of [a] microbe at sites
that are unique to [the] microbe" and that "RNA has a naturally-occurring
relationship with [a microbial] cell," wherein the RNA "sequence [has] a
naturally-occurring ordering of nucleotides found within the genetic material
of each microbe" (Ans. 8).
FF 2. Examiner finds that Appellants' "claimed method fairly
encompasses any of the admittedly well-known and routine conditions
3 Hyldig-Nielsen et al., US 2006/0003332 Al, published Jan. 5, 2006.
4 Tafas et al., US 2008/0213769 Al, published Sept. 4, 2008.
5 Ishiguro et al., US 7,112,407 B2, issued Sept. 26, 2006.
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where in situ hybridization of probes to different RNA molecules occurs"
(Ans. 8-9; see also id. at 22).
FF 3. Examiner finds that, for the reasons set forth in the obviousness
rejection below, "the use of oligonucleotide probes, including those that are
differently labeled, was routine in the art at the time of filing" (Ans. 9).
FF 4. Examiner finds that "the aspect of using in situ hybridization
conditions,' [together with] reading and determining [steps,] amount to
instructions that are well-understood, routine, conventional activity,
previously engaged in by those in the field [and] add nothing specific to the
natural principle that would render it patent-eligible" (Ans. 9; see generally
id. at 22 (Appellants' "claimed method does not specify the conditions under
which the hybridization is to take place [or the] conditions under which one
is to perform the step of 'reading said contacted sample,' much less require
any device to perform any one or combinations of steps recited in the
claimed method")).
FF 5. Examiner finds that Appellants' Specification discloses that the
selection of labels, such as fluorophores, that "do not interfere with the
detection characteristic of any other label" are known in the art (Ans. 9,
citing Spec. 25).
FF 6. Examiner finds that the term "microbe" encompasses "any microbe,
be it bacteria and/or virus[], including those that are known as well as those
that are yet to be discovered (Ans. 1 O; see also id. at 8).
FF 7. Examiner finds that Appellants' "probe set" encompasses "probes
that are known as well as unknown, and that the labels and their associated
signals encompass that which is known and that which is yet to be
discovered" (Ans. 10; see also id. at 22).
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ANALYSIS
Examiner finds that Appellants': "claim[ed] the[ir] invention in such
general terms, [that] the claims fairly encompass embodiments that are not
only known, but also seek to block future development in the area of art"
and "claimed method is deemed to focus on the use of natural laws and does
not 'also contain other elements or a combination of elements ... to ensure
that the patent in practice amounts to significantly more than a patent upon
the natural law itself'" (Ans. 11). We are not persuaded.
Appellants' claimed method requires, inter alia, the use of a first and
second population of labeled oligonucleotides that produce first and second
distinguishable signals, respectively (see Appellants' claim 1 ). Appellants'
claimed method further requires that the identity of a microbe is determined
"on the basis of [a] predetermined optically detectable signature"
(Appellants' claim 1). The method of Appellants' claim 1 defines a
"predetermined optically detectable signature" as "a composite signal of said
first and second signals" (id.).
Examiner established that labeled oligonucleotides that meet the
foregoing criteria are known in the art (see FF 5). Examiner did not,
however, establish that such labeled oligonucleotides were naturally
occurring, mental processes, or abstract intellectual concepts (cf Ans. 6,
citing Mayo Collaborative Services v. Prometheus Laboratories, Inc., 132
S.Ct. 1289, 1293 (2012) ("Phenomena of nature ... , mental processes, and
abstract intellectual concepts are not patentable").
Examiner does not address and, thereby, failed to establish that the
steps of Appellants' claimed method, which, inter alia, require the
production of a composite signal of a first and second signal to obtain an
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optically detectable signature that is used to identify a microbe fails to
transform the use of natural phenomena (i.e. the sequence of microbial
mRNA) or known reagents (i.e. labeled probes) into patent-ineligible subject
matter. Id. at 1294. Thus, on this record, Examiner failed to establish that
Appellants' claimed subject matter, when read as a whole, is nothing more
than a recitation of "a nonpatentable phenomenon, process, or concept" with
the additional "words 'apply it'." Id.; see Ans. 6 and 8. For the same
reasons, Examiner failed to establish that Appellants' claimed invention,
when read as a whole, is nothing more than "post-solution activity that is
purely conventional or obvious." Id. at 1299.
As Appellants explain, their:
claims are directed to a method in which a microbe is
hybridized in situ with a particular set of labeled
oligonucleotides that produce a composite signal. Specifically,
the claims use oligonucleotides (which are man-made), the
hybridization is done in situ (which does not happen in nature),
and the signal produced is a composite signal ( \vhich does not
occur in nature).
(App. Br. 5; see Reply Br. 2-3.)
CONCLUSION OF LAW
The evidence of record fails to support Examiner's finding that
Appellants' claimed invention is directed to non-statutory subject matter.
The rejection of claims 1 and 4--15 under 35 U.S.C. § 101 as directed to non-
statutory subject matter is reversed.
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Obviousness:
ISSUE
Does the preponderance of evidence relied upon by Examiner support
a conclusion of obviousness?
FACTUAL FINDINGS (FF)
FF 8. Hyldig-Nielsen discloses "PNA probes, probe sets, methods and kits
useful for detecting, identifying and/ or quantitating one or more organisms
of interest in a sample wherein the organisms are members of the bacterial
species of E.coli, Staphylococcus aureus, Pseudomonas aeruginosa,
Pseudomonas cepatia, Pseudomonas fluorescens or organisms of a bacterial
genus including the Salmonella genus, Bacillus genus or Pseudomonas
genus" (Hyldig-Nielsen i-f 10; Ans. 14--15; see also Ans. 19-20, citing
Appellants' admissions).
FF 9. Hyldig-Nielsen's "PNA probes ... may comprise ... detectable
moieties (labels)," which "are used in in-situ hybridization (ISH) and
fluorescence in-situ hybridization (FISH) assays" (Hyldig-Nielsen i-fi-1 46 and
4 7; see also id. i-f 31; Ans. 15-16; see Ans. 20, citing Appellants'
admissions).
FF 10. Hyldig-Nielsen discloses the use of "one or more distinct
independently detectable moieties ... to label two or more different probes
... in an assay," wherein
the ability to differentiate between and/ or quantitate each of the
independently detectable moieties provides the means to
multiplex a hybridization assay because the data which
correlates with the hybridization of each of the distinctly
(independently) labeled probe to a particular nucleic acid
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sequence can be correlated with the presence, absence or
quantity of each organism sought to be detected in the sample.
(Hyldig-Nielsen i-f 35; Ans. 15.)
FF 11. Hyldig-Nielsen's "multiplex assays ... may be used to
simultaneously detect the presence, absence or quantity of two or more
organisms in the same sample and in the same assay" (Hyldig-Nielsen i-f 35;
see also id. i-f 62; Ans. 16).
FF 12. Hyldig-Nielsen discloses "[t]he grouping of PNA probes within
probe sets to be used with methods for detecting specific groups of
organisms (e.g., classification within species, genus, or USP bacteria)"
(Hyldig-Nielsen i-f 62; Ans. 16).
FF 13. Examiner finds that Hyldig-Nielsen fails to disclose the use of
"probes to RNA that is not rRNA" and relies on Ishiguro to disclose the
"detection of bacterial mRNA via hybridization reaction" (Ans. 17 and 19).
FF 14. Examiner finds that Hyldig-Nielsen fails "to teach basing the
determination of a specific bacteria ... on a pattern of signals emanating
from a single bacterial cell" and relies on Tafas to make up for this
deficiency in Hyldig-Nielsen (Ans. 18).
FF 15. Examiner finds that Tafas discloses "fluorescence in situ
hybridization (FISH)," wherein a "multicolor probe set ... permit[ s]
simultaneous analysis of[] three genomic markers within a single cell"
(Ans. 17; Tafas i-f 17; see also Ans. 24--25).
FF 16. Appellants contend that a "composite signal" can be detected as two
separate signals or as a single signal which is a combination of two separate
signals, wherein:
Using[] Examiner's example, if purple is detected, then red and
blue signals must be present[, i.e., purple is a combination of
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red and blue]. Alternatively, one could detect red and blue
signals separately, which would also indicate that red and blue
signals are present. Composite signals can be detected both
ways")
(App. Br. 8.)
FF 17. Appellants' Specification discloses that an "' [ o ]ptically detectable
signature' may be made up of one or more signals, where the signal(s) is
produced by a label(s). An optically detectable signature may be made up
of: a single signal, a combination of two or more signals, ratio of magnitude
of signals, etc." (Spec. 6: 16-21 ).
FF 18. Appellants' Specification discloses that "[ t ]he hybridization of [the
label] set to a target microbe provides an optically detectable signature to the
microbe where the signature is the combination of the first and the second
signal" (Spec. 11: 1-3).
FF 19. Appellants' Specification discloses that "each microbe has a
different signature comprised of [] different combination[ s] of signals"
(Spec. 13:5---6).
FF 20. Appellants' Specification discloses that the "'distinguishable labels"'
used for the probes "can be independently detected and measured, even
when the labels are mixed. In other words, the amounts of label present
(e.g., the amount of fluorescence) for each of the labels are separately
determinable, even when the labels are co-located (e.g., in the same tube or
in the same duplex molecule or in the same cell)."
ANALYSIS
Based on the combination of Hyldig-Nielsen, Tafas, Ishiguro, and
Appellants' admitted prior art, Examiner concludes that, at the time
Appellants' invention was made, it would have been prima facie obvious "to
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use a combination of [labeled] probes that hybridize to a nucleotide
sequence [(i.e. RNA that is not rRNA)] that is conserved across variants of a
given species ... [,] whereby identification of the specific organism is based
upon the pattern of labels/signals detected" (Ans. 18-19). In this regard,
Examiner finds that Hyldig-Nielsen discloses "that one can use a
combination of probes that hybridize [in situ] to nucleic acids in a common
bacterial cell and that the detection can result in the identification of species"
and Tafas discloses "that one can use a plurality of probes, each bearing a
different label, in a common assay where simultaneous hybridization to
different nucleic acids in a common cell is conducted" (Ans. 18; see also id.
at 20-21).
Appellants contend that Hyldig-Nielsen suggests a "'one fluorophore
=one microbe' system," which fails to suggest a "composite signal of the
first and second signals" as is required by Appellants' claimed invention
(App. Br. 10-11; cf FF 14). In this regard, Appellants contend that
Examiner failed to establish that Ishiguro makes up for the foregoing
deficiency in Hyldig-Nielsen (App. Br. 12). Appellants further contend that
Tafas does not provide a "composite signal" (App. Br. 11-12).
Appellants contend that "Tafas' i-f 17 [] is the only paragraph[, in
Tafas,] that refers to a multicolor probe set that can be used to identify three
markers within a cell" (App. Br. 11; see FF 15). In this regard, Appellants
contend that "Tafas fails to provide ... a signal that is a composite of two
other signals" (App. Br. 11 ). Instead, Appellants contend, Tafas discloses
that the multicolor probe set referred to in [Tafas' i-f 17]
contains three probes, each labeled with a different fluorophore
(where the emitted colors are referred to as "orange", "green"
and "aqua"). The different probes hybridize to different parts
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of chromosome 8 to produce a ... signal pattern (i.e., a pattern
that has two green bands sandwiched between two orange
bands and two aqua bands).
(App. Br. 11.) Therefore, Appellants contend that "Tafas teaches away from
using composite signals because [Tafas'] method relies on an ability to
distinguish the different fluorophores separately from one another in order to
identify [] cells" (id.). We are not persuaded.
Appellants concede that their Specification "does not contain an
explicit definition for what is meant by the term 'composite signal"' (App.
Br. 7). Nonetheless, Appellants contend that a "composite signal" can be
detected as two separate signals or as a single signal which is a combination
of two separate signals (FF 16). Thus, as Examiner explains, Appellants'
contention regarding Tafas "is in direct conflict with what [A]ppellant's [sic]
representative[] asserted at page 8 of the Brief' (Ans. 25; cf FF 16).
For the foregoing reasons, we are not persuaded by Appellants'
contention that the term "'composite signal' ... should be interpreted as a
'blend' of two or more other signals" or that Tafas' "chromosome banding
pattern that contains different colored bands is not a 'composite signal"'
(Reply Br. 3 and 4).
We are not persuaded by Appellants' contention that Examiner
"interpreted the term 'composite signal' in a way that is not consistent [with
Appellants'] [S]pecification" (Reply Br. 4). To the contrary, Examiner
interpreted the term in a manner that is consistent with Appellants'
interpretation of the term, which is not defined by their Specification (see FF
16; see also App. Br. 7). We recognize, but are not persuaded by
Appellants' contention that, when read in light of their Specification the
undefined term "composite signal" is clear to a person of ordinary skill in
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this art and "has a plain meaning in the English language," which is contrary
to Examiner's interpretation of the term (Reply Br. 5; FF 17-20).
Notwithstanding Appellants' contentions to the contrary, Examiner
provided Appellants an opportunity to interpret the term "composite signal"
in light of their Specification (see July 30, 2012 Office Action 9 (wherein
Examiner rejected Appellants claimed invention under the second paragraph
of 35 U.S.C. 112 as "indefinite with respect to what constitutes the metes an
bounds of a 'composite signal of said first and second signals'")). In
response, Appellants contended that when interpreted in light of their
Specification, the term "composite signal" means that a signal can be
detected as two separate signals or as a single signal which is a combination
of two separate signals (FF 16). Relying upon Appellants' definition of the
term composite signal, Examiner withdrew the rejection under 35 U.S.C.
112, second paragraph (see Ans. 4).
Thus, notwithstanding Appellants' contentions to the contrary, the
combination of Hyldig-Nielson, Tafas, and Ishiguro makes obvious the
subject matter of Appellants' claim 1.
CONCLUSION OF LAW
The preponderance of evidence relied upon by Examiner supports a
conclusion of obviousness. The rejection of claim 1 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Hyldig-Nielson, Tafas, and
Ishiguro is affirmed. Claims 4--15 are not separately argued and fall with
claim 1.
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TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).
AFFIRMED
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