Ex Parte Kido et al

Patent Trial and Appeal Board

May 18, 2016

10556679 (P.T.A.B. May. 18, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
10/556,679 0612912007
23373 7590 05/20/2016
SUGHRUE MION, PLLC
2100 PENNSYLVANIA A VENUE, N.W.
SUITE 800
WASHINGTON, DC 20037
FIRST NAMED INVENTOR
Hiroshi Kido
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.
Q91487 4266
EXAMINER
BOESEN, CHRISTIAN C
ART UNIT PAPER NUMBER
1639
NOTIFICATION DATE DELIVERY MODE
05/20/2016 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):
PPROCESSING@SUGHRUE.COM
sughrue@sughrue.com
USPTO@sughrue.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte HIROSHI KIDO,
MINEYOSHI HIYOSHI, MIW A BANDO,
MORITOSHI KINOSHITA, YOJI FUKUDA,
and HIROSHI MIZUGUCHI
Appeal2013-004404 1
Application 10/556,679
Technology Center 1600
Before FRANCISCO C. PRATS, MELANIE L. McCOLL UM, and
RICHARD J. SMITH, Administrative Patent Judges.
PRATS, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134(a) involves claims to a
transcription chip to which a polynucleotide is bound. The Examiner
rejected the claims for anticipation and obviousness.
We have jurisdiction under 35 U.S.C. § 6(b). We affirm.
1 Otsuka Pharmaceutical Co., Ltd., is the real party in interest. App. Br. 2.
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Application 10/556,679
STATEMENT OF THE CASE
The Specification discloses a "transcription chip where single or
double-stranded DNA comprising one or more element sequences of
transcription factors are immobilized on a substrate." Spec. 2. The
Specification discloses that expression levels of a "transcription factor or a
substance which interacts with the factor can be profiled by the chip based
on a biological function such as DNA binding capacity." Id.
The Specification explains that, using the disclosed chips, binding to
DNA of a number of transcription factors, such as NFKB, can be evaluated.
Id. at 5. The Specification explains further:
The [bound] transcription factor can be quantified by
immunologically measuring using an antibody against the
transcription factor and a publicly known method such as
ELISA or measuring using mass spectrometer. For example,
the transcription factor may be directly measured by mass
spectrometer, but it is preferable to identify and quantify the
bound transcription factor by digesting the transcription factor
bound to the chip with an appropriate protease such as trypsin,
analyzing the resulting peptide fragments by mass spectrometer
and comparing with a mass spectrum pattern (mass fingerprint)
of the protease-digested transcription factor. As the mass
spectrometer, MALDI-TOF is preferably exemplified.
Id. at 8.
Claim 1 is representative and reads as follows (App. Br. 20):
1. A transcription chip wherein at least one
polynucleotide comprising one or more element sequences to
which a transcription factor can be bound is immobilized on a
substrate,
wherein the transcription factor bound to one or more
element sequences of the polynucleotide is detected by a
peptide mass fingerprint method.
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The following rejections are before us for review:
(1) Claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation
by Remacle2 (Final Action 4-6);
(2) Claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation
by Smith3 (Final Action 6-7);
(3) Claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness
over Remade and Kido4 (Final Action 7-1 O); and
(4) Claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness
over Smith and Kido (Final Action 10-11 ).
ANTICIPATION
Appellants argue the merits of the two anticipation rejections together.
See App. Br. 11. Accordingly, we consider those two rejections together.
We select claim 1 as representative of the rejected claims. 37 C.F.R.
§ 41.37(c)(l)(iv).
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden ... of presenting a
primafacie case ofunpatentability ....
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.
2 WO 01/73115 Al (published Oct. 4, 2001 ).
3 Emily A. Smith et al., Surface Plasmon Resonance Imaging of
Transcription Factor Proteins: Interactions of Bacterial Response
Regulators with DNA Arrays on Gold Films, 19 Langmuir 1486-92 (2003)
("Smith").
4 Hiroshi Kido et al., Application of the "Gene-Dia®" Diamond DNA Chip
and Development of a Protein Chip, 85 J. Inst. Electronics Information and
Communication Engineers 725-27 (2002) (as translated) ("Kido").
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Appellants' arguments do not persuade us that a preponderance of the
evidence fails to support the Examiner's prima facie case of anticipation as
to claim 1.
Claim 1 recites a transcription chip that is composed of at least one
polynucleotide which is immobilized on a substrate. App. Br. 20. The
immobilized polynucleotide must include one or more element sequences to
which a transcription factor "can be bound." Id.
As the Examiner found (Final Action 5-7), both Remade and Smith
describe substrate-immobilized polynucleotides to which transcription
factors may be bound. See Remade, abstract ("[P]utting into contact the
transcriptional factor (1) with a double-stranded DNA sequence (2) bound to
an insoluble solid support (3), and detecting and/or quantifying said fixed
transcriptional factor (1 ), said double-stranded DNA sequence having a
specific sequence able to be fixed by the transcriptional factor."); see also
Smith 1486 (abstract) ("DNA arrays were fabricated from oligonucleotide
sequences of known DNA binding regions for two response regulators ....
The proteins exhibited specificity for the known binding sequences
compared to control sequences on the DNA array.").
As the Examiner found (Final Action 5), Remade, like Smith,
discloses that the transcription factors are proteins. Remade iJ 18 ("The
transcriptional factors ... can be part of a large protein complex .... ").
Thus, both Remade and Smith describe products that have the structural
elements expressly recited in claim 1, and which are capable of the intended
use of binding a transcription factor.
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Claim 1 also recites "wherein the transcription factor bound to one or
more element sequences of the polynucleotide is detected by a peptide mass
fingerprint method." App. Br. 20.
The Examiner concluded that this recitation is "at best either a
characteristic or an intended use limitation." Final Action 4, 6. The
Examiner found that the polypeptide transcription factors that bound the
immobilized polynucleotides in Smith and Remade met that intended use.
Id. at 5-7. The Examiner concluded that, because there was a reasonable
basis to find that the chips of Remade and Smith met this intended use, and
were therefore identical to the chip recited in claim 1, the burden had shifted
to Appellants to show that the chips of Remade and Smith did not meet all
of the claimed limitations. Id. at 4, 6 (citing In re Best, 562 F.2d 1252, 1255
(CCPA 1977); In re Fitzgerald, 619 F.2d 67 (CCPA 1980)).
Appellants contend that, to show that a prior art reference inherently
meets a claimed feature, and to shift the burden under Best or Fitzgerald, it
is imperative that the Examiner provide a basis in fact or technical reasoning
to show that the allegedly inherent property is necessarily present in the
cited prior art, as opposed to merely being a possibility. App. Br. 12-15.
Appellants contend that the Examiner did not adequately establish, through
such reasoning, that the polypeptide transcription factors of Remade and
Smith inherently meet the requirements of the final "wherein" clause of
claim 1. Id. at 13; see also Reply Br. 5-6 (arguing that the Examiner did not
show that one or more of the polypeptide transcription factors of Remade
and Smith "is detected by a peptide mass fingerprint method")( emphasis in
original); Reply Br. 7 (arguing that claim 1 recites that the transcription
factor is bound to the polynucleotide ). Appellants contend that
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"[a ]tlinnance of rejections such as this would overburden and or
incapacitate every Appellant facing a conclusory allegation of inherent
anticipation and is contrary to law because, as courts have held, proof that
the alleged inherent characteristic necessarily flows from the teachings of
the applied prior art is unequivocally required." App. Br. 14-15.
Appellants' arguments do not persuade us that the Examiner erred in
maintaining these rejections. As an initial matter, as to claim interpretation,
we conclude that the Examiner's interpretation of claim 1 is consistent with
the broadest reasonable interpretation in light of the Specification. Adopting
Appellants' interpretation, that claim 1 actually requires a step of detecting
the transcription factor by a peptide mass fingerprint method, would place
claim 1 in violation of the prohibition against claims simultaneously directed
to both an apparatus and a process. See MPEP § 2173.05(p)(II) ("A single
claim which claims both an apparatus and the method steps of using the
apparatus is indefinite under 35 U.S.C. 112 ... , second paragraph."). As
the Examiner pointed out, moreover, claim 1 does not require the
transcription factor to be actually bound to the immobilized polynucleotide,
only that the factor "can be bound." App. Br. 20.
As to the issue of whether the Examiner provided a reasonable basis
for finding that the chips of Remade and Smith meet the intended use that a
bound transcription factor be detectable by a peptide mass fingerprint
method, as noted above, and as the Examiner found (Final Action 5, 7), both
references disclose that their immobilized polynucleotides can bind protein,
i.e., polypeptide, transcription factors. See Remade ,-i 18; Smith 1486
(abstract). Thus, while the Examiner might not have been as articulate as he
could have been, the Examiner's evident position is that, because the
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transcription factors that may become bound to the substrate-immobilized
polynucleotides of Remade and Smith are polypeptides, they would be
detectable by a peptide mass fingerprint method. We detect no error in this
reasonmg.
As noted above, the Specification discloses that bound transcription
factors may be quantified by a "publicly known method such as ... using
mass spectrometer." Spec. 8. As a preferred example of such methods, the
Specification discloses "digesting the transcription factor bound to the chip
with an appropriate protease such as trypsin, analyzing the resulting peptide
fragments by mass spectrometer and comparing with a mass spectrum
pattern (mass fingerprint) of the protease-digested transcription factor." Id.
We agree with the Examiner that, because the transcription factors of
Remade and Smith are polypeptides, it was reasonable to find that those
transcription factors would be detectable by known polypeptide analytical
methods, including the peptide mass fingerprint method described in the
Specification. Accordingly, in addition to establishing that Remade and
Smith describe products having all of the structural elements required by
claim 1, the Examiner had a reasonable basis for finding that those products
would be capable of the intended uses recited in claim 1.
We, therefore, find also that the Examiner had a reasonable basis for
shifting to Appellants, under In re Best, the burden of explaining why the
products in Remade and Smith would not meet the intended uses recited in
claim 1. As our reviewing court's predecessor explained in In re Best, 562
F.2d at 1254-1255 (quoting In re Swinehart, 439 F.2d 210, 212-13 (CCPA
1971)):
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[W]here the Patent Office has reason to believe that a functional
limitation asserted to be critical for establishing novelty in the
claimed subject matter may, in fact, be an inherent
characteristic of the prior art, it possesses the authority to
require the applicant to prove that the subject matter shown to
be in the prior art does not possess the characteristic relied on.
In the instant case, Appellants do not identify any clear or specific
evidence showing, nor do Appellants explain specifically why, the Examiner
erred in finding that the polypeptide transcription factors disclosed in
Remade and Smith would be incapable of the intended use recited in the
final "wherein" clause recited in claim 1. As to Appellants' argument that
the Examiner improperly examined the Specification rather than the
appealed claims (Reply Br. 7), we are not persuaded that it was unreasonable
for the Examiner to consult the Specification (see Ans. 2) to determine
whether the Specification disclosed any features that might be critical to the
intended use recitation at issue.
In sum, for the reasons discussed, Appellants' arguments do not
persuade us that the Examiner erred in finding that Remade and Smith
describe products that have all of the features required by claim 1.
Accordingly, we affirm the Examiner's rejections of claim 1 as anticipated
by those references. Because they were not argued separately, claims 2, 3,
and 10-20 fall with claim 1. 37 C.F.R. § 41.37(c)(l)(iv).
As to Appellants' argument that the Examiner's Answer failed to
include a number of required sections (Reply Br. 8-10), MPEP § 1201
explains that, in relation to appeals in which the notice of appeal was filed
after January 23, 2012, the appeal rules are significantly different than they
were previously. Current MPEP § 1207.02, applicable here, does not require
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the content Appellants assert is mandatory in the Examiner's Answer. As to
Appellants' argument that the Examiner's Answer included an unreviewed
new interpretation of law (Reply Br. 10), as evidenced by the discussion
above, we are not persuaded that that Examiner's interpretation is
inconsistent with precedent.
OBVIOUSNESS
In rejecting claims 1-5 and 10-20 for obviousness over Remade and
Kido, the Examiner relied on the teachings of Remade discussed above, and
cited Kido as evidence that an ordinary artisan would have considered it
obvious to use the diamond thin film support and spacer recited in claims 4
and 5 on Remacle's transcription factor-analyzing chip. Final Action 9-10.
Appellants argue that Kido fails to "remedy the deficiencies of
Remade, et al. therefore, it is impossible to combine the information in
Remade, et al. and Kido, et al. and arrive at Appellant's invention. One
having ordinary skill in the art could not possibly have been motivated to
combine information that is missing from references." App. Br. 16.
As discussed above, Appellants do not persuade us that Remade is
deficient as to any of the limitations of claim 1. Accordingly, because
Appellants' arguments do not identify any deficiency in the Examiner's
obviousness rejection of claims 1-5 and 10-20 over Remade and Kido, we
affirm that rejection.
In rejecting claims 1-5 and 10-20 for obviousness over Smith and
Kido, the Examiner relied on the teachings of Smith discussed above, and
cited Kido as evidence that an ordinary artisan would have considered it
obvious to use the diamond thin film support and spacer recited in claims 4
and 5 on Smith's transcription factor-analyzing chip. Final Action 10-11.
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Appellants argue that Kido fails to "remedy the deficiencies of Smith,
et al. therefore, it is impossible to combine the information in Smith, et al.
and Kido, et al. and arrive at Appellant's invention. One having ordinary
skill in the art could not possibly have been motivated to combine
information that is missing from references." App. Br. 16.
As discussed above, Appellants do not persuade us that Smith is
deficient as to any of the limitations of claim 1. Accordingly, because
Appellants' arguments do not identify any deficiency in the Examiner's
obviousness rejection of claims 1-5 and 10-20 over Smith and Kido, we
affirm that rejection.
SUMMARY
For the reasons discussed, we affirm the Examiner's rejection of
claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by
Remade.
For the reasons discussed, we affirm the Examiner's rejection of
claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by Smith.
For the reasons discussed, we affirm the Examiner's rejection of
claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over
Remade and Kido.
For the reasons discussed, we affirm the Examiner's rejection of
claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over
Smith and Kido.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § l.136(a).
AFFIRMED
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