Ex parte Voordouw et al.

Board of Patent Appeals and Interferences

Sep 25, 2001

07719005 (B.P.A.I. Sep. 25, 2001)

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publication and is not binding precedent of the Board.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. 34

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte GERRIT VOORDOUW, DONALD W.S. WESTLAKE
and PHILLIP M. FEDORAK
__________

Appeal No. 1995-3965
Application No. 07/719,005
__________

ON BRIEF
__________

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

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on the appeal under 35 U.S.C. § 134 from the examiner’s
final rejection of claims 1, 3-5 and 7-13, which are all the claims pending in the
application.
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Claims 1 and 9 are illustrative of the subject matter on appeal and are
reproduced below:
1. A process for detecting the presence of different selected standard
microorganisms in a sample by reverse genome probing, wherein said
process comprises the steps of:
(A) preparing a master solid surface having affixed thereto isolated
spots of genomic deoxyribonucleic acid from each of said
different selected standard microorganisms by:
(i) obtaining an individual culture of each of said selected
standard microorganisms from an environment of
interest,
(ii) isolating a genomic deoxyribonucleic acid
preparation from each of said individual cultures, and
(iii) affixing each of said genomic deoxyribonucleic acid
preparation from step (Aii) to said master solid
surface,
(B) preparing a reverse genome probe from said sample by:
(i) isolating a total nucleic acid preparation from said
sample by:
(ii) labeling said total nucleic acid preparation,
(C) contacting said master solid surface from step (A) with said
reverse genome probe from step (B) under conditions permitting
hybridization,
(D) washing said master solid surface resulting from step (C) so as to
remove non-hybridized reverse genome probe, and
(E) detecting hybridized reverse genome probe.

9. A master solid surface for use in detecting the presence of different
selected standard microorganisms by reverse genome probing, said
master solid surface having affixed thereto isolated spots of genomic
deoxyribonucleic acid from each of said selected standard
microorganisms, wherein said different selected standard
microorganisms are isolated from an environment of interest.
The references relied upon by the examiner are:
Hitzman 4,540,052 Sep. 10, 1985

Kimmel, “Selection of Clones from Libraries: Overview,” Methods in Eznymology,
Vol. 152, pp. 393-399 (1987)
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Wang et al. (Wang), “Simultaneous Detection of Both DHBV DNA and DHBV DNA
Polymerase by Reverse Spot Hybridization,” Chinese J. Microbiol. Immunol., Vol. 9,
No. 4, pp. 261-264 (1989). BIOSIS Abstract only.
GROUNDS OF REJECTION1

Claims 1, 3-5 and 7-13 stand rejected under 35 U.S.C. § 103 as being
unpatentable over Wang in view of Hitzman and further in view of Kimmel.
We reverse.
DISCUSSION
In reaching our decision in this appeal, we considered appellants’
specification and claims, in addition to the respective positions articulated by the
appellants and the examiner. We make reference to the examiner’s Answer2, and
the examiner’s Supplemental Answer3 for the examiner’s reasoning in support of the
rejections. We further reference appellants’ Brief4, and appellants’ Reply Brief5 for
the appellants’ arguments in favor of patentability.
THE REJECTION UNDER 35 U.S.C. § 103:
Initially, we note that this appeal was remanded to the examiner, at the
request of the Office of the Group Director of Technology Center 1600, on April 15,
1998. See Paper No. 32½. However, after reconsideration of the issues on
appeal, the examiner returned the application to the Board, where it was returned

1 We note the examiner withdrew (Supplemental Answer, page 1) the rejection of
claims 1, 7, 8, 9 and 13 under 35 U.S.C. 102(b) as being unpatentable over the
abstract of Wang in view of appellants’ amendment received October 7, 1994
(Paper No. 28).
2 Paper No. 27, mailed August 9, 1994.
3 Paper No. 30, mailed November 14, 1994.
4 Paper No. 26, received May 31, 1994.
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“to its existing place in the order in which appeals are decided.” See Paper No. 33,
mailed May 22, 2000.
According to the examiner (Answer, page 5) Wang “teach the detection of
hepatitis B virus (HBV) using the ‘reverse spot hybridization’ which inherently makes
use of a ‘reverse genome probe.’” The examiner further explains (id.) that Wang
uses Southern blot methodology that includes:
a solid surface such as a nitrocellulose filter or nylon membrane to
which DNA is immobilized; a hybridization solution containing a
radioactive probe which is incubated with the solid surface under
conditions in which the probe hybridizes to the complementary DNA
on the solid surface; a wash step in which the unbound probe is
washed away; and a detection step in which the position and amount
of hybridized probe is measured.

According to the examiner (Answer, page 6) Wang differs from the claimed
invention in that Wang does not teach “the use of a plurality of genomic
deoxyribonucleic acid spots, [or] the use of a selected standard which is a plurality
of microorganisms. In addition, with regard to claims 3, 5 and 11, the examiner
finds (id.) that Wang does not teach “an oil field environment … [or] the use of a
sulfate reducing bacterium.”
To overcome these deficiencies the examiner relies on Hitzman and Kimmel.
According to the examiner (Answer, page 6) “Hitzman discloses an oil field
environment … and the use of sulfate reducing bacterium.” Thus, the examiner finds
(id.) that it “would have been prima facie obvious to one of ordinary skill in the art at
the time the invention was made to use the oil field and bacterium of Hitzman in the

5 Paper No. 28, received October 7, 1994.
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method of Wang et al. to develop a test for the presence of these bacteria in the oil
field.” The examiner further finds (Answer, bridging sentence, pages 6-7) that a
person of ordinary skill in the art would have been motivated to combine Hitzman
with Wang since Hitzman discloses “the presence of microorganisms, particularly
sulfate-reducing bacterial, in the flood water causes serious problems of plugging of
the oil bearing formation and corrosion of injection and downhole equipment….”
The examiner relies (Answer, page 7) on Kimmel to teach that “‘[i]ndividual
recombinants within libraries can be screened for homology with a nucleic acid
sequence … [i]n addition, populations can be screened as mixtures of
recombinants….’”
Therefore the examiner concludes (id.) that it “would have been prima facie
obvious to one of ordinary skill in the art at the time the invention was made to use
the multiple nucleic acid screening of Kimmel with the method of Wang and Hitzman
for the expected benefit of constructing a method of detecting multiple nucleic acid
sequences in a single experiment.”
With regard to Wang and Hitzman, appellants argue (Brief, page 14) that the
references are “fundamentally different from the present invention because” neither
reference alone or in combination teach or suggest “the use of a reverse gene
probe for the detection of more than one microorganism with a single hybridization.”
Furthermore, while appellants agree (Brief, page 15) that “Kimmel clearly teaches
that populations can be screened as mixtures of recombinants”, appellants find that
“Kimmel does not teach that such screening can be done with a single
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hybridization.” Therefore, appellants conclude (Answer, page 17) that “[w]hen
considering the above-described fundamental difference as a whole, it is crucial to
note that Kimmel provides absolutely no suggestion of any technique which would
enable the detection of more than one microorganism using a single
incubation/hybridization.”
In response the examiner argues (Answer, pages 8 and 9) that appellants
admit, “in Paper 16, filed May 10, 1993 ‘that the laboratory procedures required to
carry out the reverse hybridization technique are well known and are fully disclosed
in Wang et al.’” We are not persuaded by this argument. While “laboratory
procedures” (e.g., Southern Blot procedures) may be well known, it is the claimed
invention as a whole that must be considered in an obviousness determination.
See In re Antonie, 559 F.2d 618, 625, 195 USPQ 6, 8 (CCPA 1977). Furthermore,
as set forth in In re Nomiya, 509 F.2d 566, 571, 184 USPQ 607, 612 (CCPA 1975)
“[t]he court must be ever alert not to read obviousness into an invention on the basis
of the applicant’s own statements; that is, we must view the prior art without reading
into that art appellant’s teachings.”
The examiner also argues (Answer, pages 9-10) that “Kimmel explicitly
teaches the same principle as found in this application, namely, that one could mix
probes of different DNA species and use this probe mixture to simultaneously
detect complementary DNA of several different species by hybridizing to multiple
spots … with a single hybridization….” Thus the examiner concludes (Answer,
bridging sentence, pages 10-11), “[t]aken together with the Wang et al. procedure,
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using reverse probes to identify a single organism, these references suggest
identifying a plurality of microorganisms using a plurality of probes.”
Appellants, however, outline (Reply Brief, pages 5-6) three “differences
between the differential scanning technique of the Kimmel review and the process
of the present invention….” First, the “dots” of Kimmel’s method “are prepared for
[sic] the single cDNA, clones or mixture of cDNA clones, and thus represents [sic]
only a small portion … of the genomic DNA of a[n] eukaryotic organism…. In direct
contrast [to Kimmel’s method] the dots of different selected standards of the present
invention are prepared from genomic DNA….” Second, in Kimmel’s method “[t]he
reverse probe … is the mRNA of a given eukaryotic organism or the mRNA of a
given cell type of a given eukaryotic organism… In direct contrast, the reverse
probe of the present invention is prepared from … all genomic DNA in the
sample….” Finally, appellants’ argue (Reply Brief, page 6) “the present invention
teaches a convenient process for the quick, convenient, initial characterization of
different microorganisms in a complex microbial community using a single
hybridization. The Kimmel review makes absolutely no such a [sic] teaching.”
To this, the examiner finds (Supplemental Answer, page 1) “[t]hese
arguments are not persuasive for the reasons of record.” We cannot agree. The
initial burden of presenting a prima facie case of obviousness rests on the
examiner. In re Oetiker, 977 F.2d 1443, 1445, 24 USPQ2d 1443, 1444 (Fed. Cir.
1992). On this record, appellants identify three differences between the claimed
invention and the prior art relied upon. These differences highlight Kimmel’s failure
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to suggest screening a genomic DNA blot with genomic DNA probes. In contrast,
the claimed invention requires that a genomic DNA dot blot be probed with genomic
DNA. As set forth in Antonie “[j]ust as we look to a chemical and its properties when
we examine the obviousness of a composition of matter claim, it is this invention as
a whole, and not some part of it, which must be obvious under 35 USC 103. Cf. In
re Papesch, 50 CCPA 1276, 315 F.2d 381, 137 USPQ 43 (1963).”
On these facts, we are constrained to reach the conclusion that the examiner
failed to provide the evidence necessary to support a prima facie case of
obviousness for the invention as a whole. While a person of ordinary skill in the art
may possess the requisite knowledge and ability to modify the protocol taught by
the combination of Wang, Kimmel, and Hitzman, the modification is not obvious
unless the prior art suggested the desirability of the modification. In re Gordon, 733
F.2d 900, 902, 211 USPQ 1125, 1127 (Fed. Cir. 1984). Here, the examiner
identifies no such reason to modify the references as applied.
Accordingly, we reverse the rejection of claims 1, 3-5 and 7-13 under
35 U.S.C. § 103 as obvious over Wang in view of Hitzman and further in view of
Kimmel.
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OTHER ISSUES
Prior to any further action, the examiner and appellants should consider
whether dependent claims 3, 10 and 12 further limit claims 1, 9 and 10 respectively
from which they ultimately depend.
REVERSED

William F. Smith )
Administrative Patent Judge )
)
) BOARD OF PATENT
Donald E. Adams )
Administrative Patent Judge ) APPEALS AND
)
) INTERFERENCES
Toni R. Scheiner )
Administrative Patent Judge )

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DA/dym

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