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`_.
`V Postal Address: P. 0. Box as 07 57 B1634 Munchen Germany—|
`
`To
`.
`European Patent Office
`
`80298 Munich
`
`ATENTANWALTE
`ZUROPEAN PATENT ATTORNEYS
`Dr. VOLKER vossuus, Dipl.-Chem. (-6/1992)
`
`Dr. PAUL TAUCHNER. Dipl.—.Chem.
`Dr. DIETER HEUNEMANN, Dnpl.-Phys.
`DnPHERARAwtDmuC%m.
`Dr. GEHHARD HERMANN. Dipl.-Phys.
`JOSEF SCHMIDT. Dipl.-lng.
`Dr. HANS-RAINEFI JAENICHEN. Dipl.-Biol.
`Dr. ALEXA VON UEXKULL, M.Sc.
`DI’. RUDOLF VVEINBERGER, Dip|.~Chem.
`Dr. WOLFGANG BUELAK, Dipl.-Chem.
`EUROPEAN PATENT ATTORNEY
`Dr. RENATE EARTH, Dipl.-Chem.
`
`|_
`
`J
`
`RECHTSANWALTIN
`HELGA TREMMEL
`
`O 7?,
`L 479
`84 10 0836.0-21'G5/0117440
`Enzo Biochem Inc.
`our ref.: S 808 EP
`
`SIEBERTSTRASSE 4
`81675 MUNCHEN
`GERMANY
`TELEPHONE: (089) 4740 75
`CABLE: BENZOLPATENT MUNCHEN
`TELEX: 529 453 VOPAT D
`TELEFAX: (089) 4 70 60 53
`
`December 28, 1994
`Ba/Fr
`
`The
`
`following observations are made
`
`by
`
`the Patentee
`
`in
`
`response to the oppositions filed by Boehringer (Opponent I)
`
`on December 23,
`
`1993 and the opposition filed by Biotest
`
`(Opponent II) on January 3, 1994:
`
`1.
`
`The references cited during the opposition proceedings
`
`The following references were cited by Opponent I
`
`(O1 to
`
`012) and Opponent II (D1 to D6):
`
`U.S. Patent No. 4,358,535 (01)
`
`Clinica Chimica Acta 81: 1-40 (1977)
`
`(O2)
`
`Proc. Natl. Acad. Sci USA vol.
`November 1981 (03)
`
`78,
`
`pp.
`
`6633-6637,
`
`Proc. Natl. Acad. Sci. USA. vol.
`December 1982 (O4)
`
`79,
`
`pp.
`
`7331-7335,
`
`Proc. Natl. Acad. Sci. USA vol., 79, pp. 4381-4385, July
`1992 (05)
`
`BAYERISCHE VEREINSBANK NR. 32 920335, BLZ 7oo2o2 7o - DEUTSCHE BANK A.G. MUNCHEN. NF‘-55/57 342. BLZ 700 70010
`POSTGIROAMT MUNCHEN. NR. 129600-809. BLZ 7oo1ooao, V.A.T. NO. DE 130 751 524
`BD EXHIBIT 1029
`BD EXHIBIT 1029
`
`Page 1 of 22
`Page 1 of22
`
`

`
`CIOIOO
`
`I
`
`0
`
`O
`
`00O
`
`Proc. Natl. Acad. Sci. USA, vol. 80, pp. 4045-4049, July
`1983 (06)
`
`EP-A-0 063 879 (07)
`
`DE-A-29 15 082 (O8)
`
`DE-A-27 24 486 (09)
`
`US-A-4,271,140 (o1o)
`
`Journal of Histochemistry and Cytochemistry Vol. 27, 8,
`1131-1139 (1979)
`(011)
`
`Biochemie 1972, 54, 837-842 (012)
`
`.
`
`EPA-82301804.9 (D1)
`EPA-82303701.5 (D2)
`
`US—Patent No. 4,358,535 (D3)
`
`(1980), pp. 485-490, J. Bauman et
`128
`Exp. Cell Res.
`al.,
`"A
`new method
`for
`fluorescence microscopical
`localization of
`specific DNA
`sequences
`by
`in situ
`hybridization of fluorochrome-labeled RNA"
`(D4)
`
`GB-A-2,019,408 (D5)
`
`GB-A-2,026,690 (D6)
`
`01 is identical to D3 and O7 is identical to D1.
`
`O
`
`2.
`
`The subject matter of EP-B-117 440
`
`2.1. The technical problem underlying the present
`
`invention
`
`is to provide a method for detecting a polynucleotide
`
`sequence .
`
`The
`
`solution is
`
`achieved by
`
`a method whereby
`
`the
`
`sequence is fixed to a solid support
`
`in a non-porous,
`
`transparent or translucent system,
`
`a hybrid is formed
`
`between the sequence and a polynucleotide probe having
`
`a chemical
`
`label which comprises a signalling moiety
`
`capable of generating a soluble signal, directly or
`
`indirectly,
`
`and the soluble signal
`
`is generated and
`
`
`
`Page 2 of 22
`Page2of22
`
`

`
`000...
`
`0
`
`IO0
`
`detected. The essential features of the claimed process
`
`are outlined in claim 1 which reads as follows:
`
`"A method for detecting a polynucleotide sequence which
`
`comprises:
`
`- fixing said polynucleotide
`
`sequence
`
`to a
`
`solid
`
`support which comprises or
`
`is contained within a
`
`transparent or
`
`translucent
`
`system,
`
`such that
`
`the
`
`polynucleotide is in a
`
`single-strand form and is
`
`capable of hybridizing to complementary nucleic acid
`
`.
`
`sequences;
`- forming
`an entity comprising
`
`said polynucleotide
`
`sequence
`
`hybridized
`
`to
`
`a
`
`polynucleotide
`
`or
`
`oligonucleotide probe,
`
`said probe having attached
`
`thereto a
`
`chemical
`
`label
`
`comprising a
`
`signalling
`
`moiety capable of generating a signal; and
`
`— generating and detecting a signal, characterized in
`
`that the transparent or translucent system is a non-
`
`porous system and the generated signal
`
`is a soluble
`
`signal."
`
`Dependent claims 2 to 16 and 20 to 25 are directed to
`
`specific embodiments of features of claim 1.
`
`Claims 17
`
`to 19 are directed to a device and a kit,
`
`respectively,
`
`to be used in the method of claim 1.
`
`Claim 26 is directed to a transparent or
`
`translucent
`
`solid, non—porous substrate, and reads as follows:
`
`"A
`
`transparent
`
`or
`
`translucent
`
`solid,
`
`non—porous
`
`substrate
`
`having
`
`fixed
`
`thereto
`
`a
`
`double-stranded
`
`polynucleotide,
`
`one of
`
`the strands of
`
`said double-
`
`stranded
`
`polynucleotide
`
`being
`
`a
`
`non—radioactive
`
`chemically labelled polynucleotide or comprising a non-
`
`radioactive
`
`chemically—labe1led
`
`nucleotide
`
`as
`
`a
`
`nucleotide component of said one strand, wherein said
`
`
`
`Page 3 of 22
`Page3 of22
`
`

`
`chemically labelled polynucleotide
`attached
`label
`
`thereto
`
`a
`
`comprises or has
`
`chemical
`
`comprising
`
`a
`
`signalling moiety which generates
`
`a
`
`soluble
`
`signal
`
`which is detected spectrophotometrically."
`
`Claims 27 to 28 are specific embodiments of the subject
`
`matter of claim 26.
`
`Claim 29 is also directed to a method for detecting a
`
`polynucleotide sequence
`
`and
`
`comprises
`
`the
`
`following
`
`steps:
`
`- fixing a polynucleotide or oligonucleotide
`which
`has
`attached
`thereto
`a
`chemical
`
`probe
`label
`
`comprising a signalling moiety capable of generating
`
`a signal
`
`to a solid support which comprises or
`
`is
`
`contained within a transparent or translucent system
`
`such that said probe is in single-stranded form and
`
`is capable of hybridizing" to complementary nucleic
`
`acid sequences;
`
`- forming an entity comprising said probe hybridized to
`
`said polynucleotide sequence, and,
`
`- generating and detecting a signal, characterized in
`
`that
`
`the transparent or
`
`translucent
`
`system is non-
`
`porous and the generated signal is a soluble signal.
`
`The patentability of the subject matter of the patent
`
`in suit
`
`The Opponents,
`
`Boehringer
`
`(Opponent
`
`I)
`
`and Biotest
`
`(Opponent
`
`II),
`
`maintain that
`
`the present patent
`
`is
`
`unpatentable over
`
`the prior art
`
`for the same
`
`reasons
`
`that
`
`were
`
`considered
`
`and
`
`dismissed
`
`during
`
`the
`
`prosecution of the present patent and its corresponding
`
`US Patent. The references cited by the Opponents are
`
`either
`
`identical
`
`to
`
`or
`
`less
`
`relevant
`
`than
`
`the
`
`
`
`Page 4 of 22
`Page4of22
`
`

`
`IIOIOO
`
`UOOIII
`
`I
`
`IO0
`
`'5\
`
`references
`
`cited and
`
`considered
`
`by
`
`the Examining
`
`Division during substantive examination. The references
`
`were overcome by Patentee's arguments and amendments to
`
`the claims and found not
`
`to stand in the way of
`
`the
`
`patentability of the invention. Essentially, Opponents
`
`are re-raising and re-arguing prior art work that was
`
`distinguished to the satisfaction of
`
`the European and
`
`US Patent Examiners.
`
`Specifically, both opponents cited the work of David
`
`Ward and rely heavily on articles published by him and
`his colleagues
`to support
`their arguments
`that
`the
`claimed
`invention is unpatentable.
`In
`fact, Oppo-
`
`nent's I entire argument is based on David Ward's work
`
`since all the primary references cited by this Opponent
`
`for both lack of novelty and
`
`inventive
`
`step were
`
`authored or co—authored by David Ward. See opponent's I
`
`opposition papers and cited references 03, O4, O5, O6
`
`and 07. Likewise, Opponent II cites the European patent
`
`application wherein David Ward is named as an inventor,
`
`see D1 of opponent's II enclosures, as does Opponent I
`
`(see reference 07);
`
`a
`
`reference that was considered
`
`repeatedly during prosecution of the contested patent.
`
`"
`
`.
`
`David Ward's work led to the discovery that nucleic
`
`acids
`
`could be
`
`labelled in positions
`
`that
`
`do not
`
`interfere with the hybridization ability of the acids.
`
`The inventive aspects of this work are best described
`V/and U.S. Patent No.
`
`
`by European patent
`
`EP 63,879
`
`5,328,824, of which patentee is the exclusive licensee.
`
`Patentee's licensee status as to the Ward patents give
`
`it a thorough and unique understanding of the work and
`
`the cited Ward, et al., publications.
`
`The Ward articles teach nucleic acid probes labelled in
`
`non-destructive
`
`positions which
`
`can
`
`be
`
`used
`
`to
`
`hybridize
`
`to specific
`
`target
`
`sequences
`
`of nucleic
`
`
`
`Page 5 of 22
`Page5 of22
`
`

`
`..
`
`..
`
`7>7«
`
`0
`
`‘
`
`acids.
`
`The
`
`articles
`
`also disclose
`
`a
`
`process
`
`for
`
`enzymatically incorporating a label
`
`into nucleic acids.
`
`The detection systems of the Ward articles are based on
`
`the generation of
`
`a
`
`signal which is localized and
`
`precipitated.
`
`In fact,
`
`these are the only systems which
`
`would be feasible for the objectives of the articles,
`
`which is to label
`
`and
`
`localize specific sequences.
`
`Transparent or
`
`translucent,
`
`non-porous
`
`systems
`
`that
`
`produce soluble signals certainly are Q9; taught by the
`
`Ward articles since such systems would not perform the
`
`nucleic
`acid
`sequences.
`of
`localizing
`objective
`the articles may
`although some of
`Moreover,
`suggest
`using a transparent, non-porous system (e.g.
`a slide)
`
`these characteristics are not taught to be requirements
`
`of the disclosed systems;
`
`some have them,
`
`some don't.
`
`And nowhere is it suggested that such systems be used
`
`with labels that generate soluble signals. Thus,
`
`the
`
`cited references teach away from the instant invention.
`
`3.2. Arguments for patentability to counter opposition I
`
`3.2.1. Novelty
`
`I argues lack of novelty of claim 26 based
`Opponent
`on 03, O4, O5 and 06. As previously noted in 3.1, all
`
`of
`
`these
`
`cited references were
`
`authored or
`
`co-
`
`authored by David Ward.
`
`Claim 26 is directed to a transparent or translucent,
`
`solid,
`
`non-porous
`
`substrate having fixed to it
`
`a
`
`double-stranded polynucleotide,
`
`in which one of
`
`the
`
`strands comprises a chemical
`
`label
`
`that comprises a
`
`signalling" moiety which generates a soluble signal
`
`which is detected spectrophotometrically.
`
`Opponent
`
`I
`
`argues
`
`that
`
`reference 03 discloses
`
`a
`
`method of gene mapping by in-situ hybridization of
`
`
`
`Page 6 of 22
`Page6of22
`
`

`
`I
`
`OUIIO.
`
`IIIIIC
`
`biotin-labelled
`
`probes wherein
`
`detection
`
`is
`
`by
`
`antibiotin antibody—alkaline phosphatase. Opponent
`
`I
`
`assumes and asserts that the signals generated in the
`
`methods of 03 are soluble by referencing 02, a review
`
`article of
`
`enzyme-immunoassays
`
`for proteins which
`
`states
`
`that
`
`alkaline
`
`phosphatase
`
`is
`
`capable
`
`of
`
`generating a soluble signal.
`
`Reference 03 discloses a process
`
`for enzymatically
`
`incorporating a label
`
`into nucleic acid probes
`
`for
`
`0
`
`in-situ hybridization with
`target
`sequences,
`and
`detection of the labelled, bound probes by detection
`
`systems that require a signal which is localized and
`
`a precipitate -- e.g. dot or blot systems. 03 teaches
`
`away
`
`from the
`
`instant
`
`case
`
`since
`
`the
`
`signals
`
`generated in the methods
`
`and
`
`systems of
`
`03
`
`are
`
`required to be a localized signal or a precipitate.
`
`03 does not disclose or suggest,
`
`in any manner,
`
`the
`
`generation
`
`of
`
`a
`
`soluble
`
`signal,
`
`or
`
`a
`
`system,
`
`substrate or method in which a
`
`soluble signal
`
`generated
`
`and
`
`detected
`
`in
`
`a
`
`transparent
`
`is
`
`or
`
`translucent, non—porous system.
`
`"
`
`lines 12-14, specifically states
`The abstract of 03,
`that
`the described biotin-labelled polynucleotides
`
`can be selectively immunoprecipitated in the presence
`
`of antibiotin antibody and Staphylococcus
`
`aureus
`
`Protein A. Additionally,
`
`in the passage emphasized by
`
`page 6637,
`I,
`Opponent
`reference states:
`
`column 2,
`
`lines 1-11,
`
`the
`
`"Our studies have led to the development
`of a rapid method of gene mapping by in
`situ hybridization
`that
`uses
`rabbit
`antibiotin
`antibody
`and
`f1uorescein-
`labeled goat anti-rabbit IgG to identify
`the loci of hybridized Bio—DNA probes
`and
`a
`histochemical
`procedure
`for
`detecting biotin-labeled sequences
`on
`nitrocellulose filters that uses anti-
`
`
`
`Page 7 of 22
`Page 7 of 22
`
`

`
`..
`
`..
`
`.
`
`..
`
`..
`
`%‘*
`
`conjugates
`phosphatase
`body-alkaline
`the ability
`(unpublished data). Second,
`to synthesize immunogenic DNAs
`(and to a
`lesser extent RNAs) enzymatically, both
`in purified in vitro systems
`and
`in
`crude cell lysates, may allow the use of
`immunoprecipitation techniques".
`(empha-
`sis added)
`
`It is well known in the art
`
`that
`
`the histochemical
`
`procedure referred to in the article results in a
`
`precipitated signal within the cellular morphology.
`
`Likewise,
`
`the
`
`reference
`
`to
`
`gene mapping
`
`and
`
`determining the loci of hybridized Bio-DNA probes
`
`indicates a precipitated,
`
`localized signal. Thus,
`
`03
`
`0
`
`"
`
`is limited to the generation of an insoluble product.
`
`Opponent
`
`I
`
`also emphasizes
`
`the portion of
`
`the
`
`reference which explains that biotin-labeled polymers
`
`can
`
`be
`
`used
`
`in
`
`conjunction with
`
`appropriate
`
`immunofluorescent,
`
`immunohistochemical,
`
`or affinity
`
`reagents
`
`for
`
`detecting
`
`or
`
`localizing
`
`specific
`
`sequences in chromosomes, cells,
`
`tissue sections and
`
`blots. Again the passage actually supports the fact
`
`that 03 generates an insoluble signal. Quite clearly,
`
`the
`in-situ hybridization methods
`of
`03, while
`capable
`of being performed
`on non-porous,
`solid
`supports that may be (but need not be)
`transparent or
`
`translucent, has to be limited to the generation of a
`
`localized signal.
`lines 14-17 that:
`
`In fact,
`
`03 states on page 6633,
`
`the
`tenacity of
`specificity and
`"The
`biotin-avidin complex has been exploited
`to
`develop methods
`for
`the
`visual
`localization
`of
`specific
`proteins,
`lipids and carbohydrates on or within
`cells." [emphasis added].
`
`By contrast,
`
`the signal of the contested patent
`
`(and
`
`specifically of claim 26)
`
`is not localized, nor is it
`
`
`
`Page 8 of 22
`Page8of22
`
`

`
`I
`
`O
`
`I
`
`CIIUIO
`
`CUIIOI
`
`a precipitate, but it is required to be soluble and
`
`detected in a liquid media visually or spectrophoto-
`
`metrically. The signal of 03 is only capable of being
`
`detected through precipitation or localization within
`the
`confinement
`of
`a
`cellular
`or
`chromosomal
`
`structure. This
`
`is
`
`completely different
`
`from the
`
`present invention.
`
`opponent's I reliance on reference 02 to assert that
`
`the enzymes used in the procedure of 03 are capable
`
`of
`
`generating
`
`soluble
`
`signals
`
`is
`
`inappropriate.
`
`"
`
`the
`of whether
`Regardless
`generating a soluble signal,
`
`of
`capable
`is
`enzyme
`the detection procedures
`
`disclosed in 03 are not suitable for the generation
`
`and
`
`detection
`
`of
`
`a
`
`soluble
`
`signal.
`
`Combining
`
`reference 03
`
`and 02
`
`(which is inadmissible in the
`
`assessment of novelty anyway)
`
`does not
`
`teach or
`
`suggest
`
`a
`
`system,
`
`substrate or method wherein a
`
`soluble signal can be generated and detected.
`
`Opponent I also asserts that the disclosed procedures
`
`of reference 04 and reference 05 destroy the novelty
`
`of
`
`claim 26.
`
`O4 discloses
`
`the hybridization of
`
`0
`
`biotinated nucleic acid probes with nucleic acids in
`tissue samples; 05 discloses a method of detecting
`
`Drosophila polytene
`
`chromosomes
`
`on glass
`
`supports
`
`using biotin-labeled probes. The detection methods of
`
`O4 and 05 use peroxidase. Again, Opponent I relies on
`
`reference 02 to assert
`
`that the signal generated by
`
`the techniques of O4 and 05 may be a soluble signal.
`
`As pointed out with respect to 03, whether the enzyme
`
`employed is capable of generating a soluble signal
`
`does not mean that the detection procedure disclosed
`
`in 04
`
`and 05 are suitable for
`
`the generation and
`
`detection of a soluble signal. They are not.
`
`
`
`Page 9 of 22
`Page9of22
`
`

`
`Throughout
`
`the references,
`
`04 and 05 indicate that
`
`the disclosed procedures are for localizing specific
`
`sequences; see for instance:
`
`the last
`
`sentence of 04's abstract
`
`-
`
`“The
`
`procedure described preserved morphological
`
`detail yet
`
`is compatible with hybridization
`
`conditions
`
`and
`
`reveals
`
`the disposition of
`
`actin mRNA during gene expression" (emphasis
`
`added);
`
`page
`
`7334 of 04, 1st col.,
`
`lines 14-17
`
`-
`
`"Similar results have been obtained by using
`
`avidin complexed to biotinated peroxidase;
`
`in
`
`this variation of
`
`the method the sites of
`
`hybridization
`
`are
`
`localized
`
`through
`
`the
`
`deposition
`
`of
`
`insoluble
`
`enzyme
`
`products"
`
`(emphasis added);
`
`the first
`
`sentence of 05's abstract
`
`-
`
`"A
`
`method
`
`is
`
`described
`
`for
`
`localizing
`
`DNA
`
`sequences hybridized in situ to Drosophila
`
`polytene chromosomes" (emphasis added)
`
`Lines
`
`12-16
`
`of
`
`05's
`
`abstract
`
`-
`
`"This
`
`immunological approach offers four advantages
`
`...
`
`the time required to determine the sites
`
`of hybridization is decreased ..." (emphasis
`
`added);
`
`Page
`
`4382
`
`of
`
`05,
`
`under Detection
`
`of
`
`Hybridized Probe,
`
`third paragraph - "Histo-
`
`chemical detection was done by ..." (emphasis
`
`added);
`
`Page
`
`4383
`
`of
`
`05,
`
`second
`
`col.,
`
`second
`
`paragraph - "It was our
`
`intention to use
`
`
`
`Page 10 of 22
`Page1()of22
`
`

`
`O
`
`O
`
`O
`
`IOOOIO
`
`UCOIOI
`
`avidin
`
`conjugated
`
`to
`
`various
`
`indicator
`
`molecules in order to localize biotin-labeled
`
`hybridization probes" (emphasis added).
`
`In addition,
`
`the
`
`figures
`
`of
`
`04
`
`and
`
`05
`
`clearly
`
`indicate that
`
`the procedures of
`
`these references
`
`result in the deposition of precipitates, and not the
`
`generation of a soluble signal.
`
`Lastly, with respect
`
`to novelty, Opponent
`
`I argues
`
`0
`
`that reference 06 destroys the novelty of claim 26
`even
`though,
`as Opponent
`I
`acknowledges,
`the
`
`reference was published after the priority date of
`
`the present patent. Opponent
`
`I
`
`argues
`
`that
`
`the
`
`contested patent is not entitled to the priority date
`
`(and hence the reference is prior art) because the
`
`claimed feature "generating a soluble ;:'Lgnal" is not
`disclosed in U.S. Serial No. 461,469,
`the priority
`document.
`¢"’”’M”
`
`Contrary to opponent's
`
`I position,
`
`throughout
`
`the
`
`priority document it is indicated that the preferred
`
`methods
`
`of
`
`detection
`
`involve
`
`spectrophotometric
`
`.
`
`techniques which permit quantitative determination of
`the bound probes. See for instance page 22,
`lines 12-
`
`21 of
`
`the priority document. The originally filed
`
`claims
`
`also
`
`clearly
`
`indicate
`
`a
`
`preference
`
`for
`
`embodiments wherein the substrate or method permits
`
`the transmission of
`
`light
`
`through the substrate and
`
`solution containing
`
`the
`
`bound
`
`probes
`
`for
`
`color
`
`observation or colorimetric determination. See
`
`for
`
`instance, originally filed claims 34, 36, 38, 56,
`
`62
`
`and 69 of
`
`the priority’ document. Such descriptions
`
`can only convey to one
`
`skilled in the art
`
`the
`
`generation
`
`and
`
`detection
`
`of
`
`a
`
`soluble
`
`signal.
`
`Accordingly,
`
`the priority document explicitly and
`
`inherently discloses to one skilled in the art all
`
`
`
`Page 11 of 22
`Page1J.of22
`
`

`
`I
`
`I
`
`Q
`
`000000
`
`OOIOIU
`
`I
`
`I
`
`I
`
`O
`
`ICIIII
`
`O
`
`I
`
`I I
`
`the limitations of
`
`the claimed invention,
`
`including
`
`the limitation of "generating a soluble signal". Thus
`
`reference 06
`
`is not proper prior art against
`
`the
`
`subject Patent.
`
`Besides not being a proper prior art reference, 06 is
`
`distinguishable
`
`from the
`
`claimed
`
`invention.
`
`The
`
`reference discloses
`
`the hybridization of nucleic
`
`acids
`
`with
`
`biotin-labelled
`
`DNA
`
`probes
`
`nitrocellulose wherein
`
`the
`
`signalling moiety
`
`on
`
`is
`
`horseradish peroxidase or alkaline phosphatase. As
`
`"
`
`is
`reference
`the
`abstract,
`its
`in
`out
`pointed
`directed to the generation of an unsoluble product;
`
`see lines 7-10, "... which results in the deposition
`
`of a purple precipitate at
`
`the sites of hybridiza-
`
`tion" (emphasis added). As with the other references,
`
`the
`
`insolubility of
`
`the
`
`generated
`
`signal
`
`is
`
`a
`
`requirement of
`
`the disclosed system ,and needed to
`
`fulfill the localization objective.
`
`3.2.2. Inventive step
`
`Opponent
`
`I also alleges that claims 1-29 lack an
`
`"
`
`inventive step when examined in light of references
`01 through 012. With respect to references 02-06,
`the
`
`remarks presented hereinabove are equally applicable
`
`to opponent's
`
`I
`
`lack of
`
`inventive step argument.
`
`opponent's
`
`I
`
`argument
`
`is
`
`primarily
`
`based
`
`on
`
`references 01 and. O7
`
`taken together‘ with reference
`
`02, which as mentioned above
`
`is
`
`simply a
`
`review
`
`article indicating that certain enzymes are capable
`
`of producing soluble or
`
`insoluble signals when used
`
`in immunoassays for proteins and antibodies.
`
`Reference 07,
`
`like reference 03-06,
`
`is a publication
`
`EP Patent No.
`and his colleagues:
`by David Ward
`63,879,
`to which patentee is an exclusive licensee.
`
`
`
`Page 12 of 22
`Page 12 of 22
`
`

`
`S4
`
`The
`
`remarks presented above
`
`for
`
`references O3-O5
`
`(especially those presented
`
`for
`
`03)
`
`are
`
`equally
`
`applicable to 07. Additionally,
`
`reference 07 was
`
`repeatedly considered. during both the European and
`
`U.S. prosecutions
`
`and
`
`found not
`
`to be
`
`a bar
`
`to
`
`patentability. Nowhere does 07 disclose a method or
`
`substrate wherein a soluble signal
`
`is generated and
`
`detected in a transparent or translucent, non-porous
`
`system. Combining the reference with 02, which only
`
`indicates
`
`that
`
`certain
`
`enzymes
`
`are
`
`capable
`
`of
`
`"
`
`producing a soluble signal, does not provide a method
`or system which meet the claim limitations.
`
`Similarly,
`
`reference 01 was
`
`raised during both the
`
`European and U.S. prosecutions and determined not to
`
`be
`
`a
`
`bar
`
`to
`
`patentability.
`
`01
`
`describes
`
`a
`
`hybridization. method in which clinical
`
`samples are
`
`spotted
`
`onto
`
`an
`
`inert
`
`support,
`
`such
`
`as
`
`a
`
`nitrocellulose filter. It is especially suitable for
`
`screening
`
`bacterial
`
`colonies
`
`for
`
`a
`
`specific
`
`polynucleotide
`
`sequence.
`
`The cell
`
`number may
`
`be
`
`increased by placing the
`
`support
`
`on
`
`a nutrient
`
`medium. In order to allow diffusion of nutrients,
`
`the
`
`.
`
`support has
`
`labeling is with radionuclides
`
`to be porous. The preferred method of
`
`(column 3,
`
`lines 25-
`
`27). This would allow for
`
`fast
`
`screening of many
`
`samples, as the authors point out
`
`in column 9,
`
`lines
`
`1-5:
`
`"Numerous
`
`samples may be spotted on the same
`
`filter
`
`and
`
`processed
`
`simultaneously,
`
`greatly
`
`increasing
`
`clinical
`
`efficiency.
`
`The
`
`technique
`
`therefore offers significant opportunities for large
`
`scale epidemiological
`
`and surveillance studies".
`
`such
`
`a method,
`
`the
`
`detectable
`
`signal must
`
`In
`
`be
`
`insoluble.
`
`The
`
`use
`
`of
`
`labels
`
`other
`
`than
`
`radionuclides,
`
`such
`
`as
`
`enzymes
`
`and
`
`fluorescent
`
`compounds, would also generate an insoluble signal,
`
`
`
`Page 13 of 22
`Page 13 of 22
`
`

`
`v
`
`e.g., deposition of colored precipitates, according
`to this method.
`
`Additionally, 01 does not disclose a transparent or
`
`translucent,
`
`non-porous
`
`system in which a
`
`soluble
`
`signal may be generated. Accordingly,
`
`the claimed
`
`method, by utilizing a solid support and a soluble
`
`signal
`
`in
`
`a
`
`transparent,
`
`non-porous
`
`system,
`
`is
`
`unobvious from the disclosure of 07, either alone or
`
`in combination with 02. The invention of the present
`
`patent allows for accurate quantitation of the target
`sequence by visual or spectrophotometric techniques.
`
`There
`
`is
`
`no
`
`suggestion or disclosure
`
`in 01
`
`of
`
`accurately quantitating the target polynucleotide by
`
`means of
`
`a
`
`soluble signal
`
`in a
`
`transparent,
`
`non-
`
`porous system.
`
`Moreover,
`
`the combining of references 01 and O2
`
`is
`
`improper. Opponent
`
`I
`
`is using hindsight more than 10
`
`years after the invention to say that it would have
`
`been obvious to combine immunoassays for proteins and
`
`antibodies, which can use a soluble signal, with DNA
`
`sequence—specific probes.
`
`Such
`
`use was
`
`far
`
`from
`
`‘I
`
`the assays for sequence-
`obvious since, at the time,
`specific nucleic acid probes were
`concerned with
`
`localization. This argument of combining immunoassays
`
`for proteins with nucleic acid probes was raised and
`
`dismissed in the past and lacks merit
`
`in the present
`
`oppositions.
`
`The
`
`remaining references cited by Opponent
`
`I
`
`are
`
`secondary references, cited for specific propositions
`
`such as the use of
`
`ligand/receptor
`
`interactions in
`
`the
`
`detection
`
`of
`
`nucleic
`
`acids.
`
`None
`
`of
`
`the
`
`references, either alone or
`
`in combination with the
`
`cited primary
`
`references,
`
`disclose
`
`or
`
`suggest
`
`a
`
`detection system wherein a probe is hybridized to the
`
`Page 14 of 22
`Page1¢lof22
`
`

`
`target sequence and generates a soluble signal
`
`in a
`
`transparent, non—porous system.
`
`3.3. Arguments for patentability to counter opposition II
`
`3.3.1. Objections under Article 100(c) EPC
`
`3.3.1.1. Opponent
`
`system"
`
`II
`
`or
`
`argues
`
`that
`
`the terms
`
`"non-porous
`
`"non—porous
`
`substrate"
`
`are
`
`not
`
`D
`
`literally disclosed
`
`and
`
`that
`
`there
`
`is
`
`no
`
`explanation in the papers as originally filed or
`
`specification what
`patent
`the
`in
`understood by these terms.
`
`is
`
`to
`
`be
`
`First of all, with respect
`
`to this definition
`
`there appears to be a misunderstanding. The terms
`
`g:
`"system"
`
`and
`
`"substrate"
`
`H
`are not
`
`the same or
`
`is true for the terms
`same
`interchangeable. The
`"system" and “supporém. As set forth in claim 1,3
`the support comprises or
`is contained within a
`
`system. The disclosure indicates that the support
`
`may be porous
`
`(such as nitrocellulose) or non-
`
`porous
`
`(such as glass), but
`
`the systeni must be
`
`non-gorg .
`
`Furthermore, it is not necessary for a term to be
`
`literally disclosed :hi
`
`the application as filed,
`
`rather
`
`an
`
`amendment
`
`should
`
`be
`
`regarded
`
`as
`
`introducing new matter only "if the overall change
`
`in the content of the application .... results in
`
`the
`
`skilled
`
`person
`
`being
`
`presented
`
`with
`
`information
`
`which
`
`is
`
`not
`
`directly
`
`and
`
`unambiguously
`
`derivable
`
`from that
`
`previously
`
`presented by the application, even when account is
`
`taken of matter which is implicit
`
`to a person
`
`skilled in the art
`
`in what has been expressly
`
`mentioned." (Guidelines C VI. 5.4.). However,
`
`the
`
`
`
`Page 15 of 22
`Page 15 of 22
`
`

`
`I
`
`I
`
`C
`
`O
`
`COI
`
`O I 0000
`
`COCO
`
`non—porous property of the system is self-evident
`
`from the disclosure and clearly derivable for a
`
`person skilled in the art. The
`
`claimed method
`
`requires
`
`the generation of
`
`a
`
`soluble
`
`signal.
`
`Accordingly,
`
`by necessity,
`
`this
`
`requires
`
`the
`
`presence of a solution which,
`
`in turn, requires a
`
`container or system that
`
`is non—porous.
`
`In some
`
`embodiments of
`
`the
`
`invention,
`
`the
`
`support
`
`is
`
`porous, such as nitrocellulose, and must therefore
`
`be contained in a non-porous
`
`system.
`
`In other
`
`embodiments
`the support may be
`the system,
`in
`which case the support is non-porous and contains
`the
`solution in which
`the
`soluble
`signal
`is
`
`generated.
`
`3.3.1.2. Opponent
`
`II
`
`furthermore
`
`argues
`
`that
`
`the claim
`
`limitation of "soluble signal" is not sufficiently
`
`disclosed
`
`in
`
`the
`
`original
`
`application.
`
`This
`
`objection has
`
`already been
`
`raised during the
`
`examination proceedings and has been successfully
`
`overcome by applicants line of argument and has
`
`been resolved to the Examiner's satisfaction.
`
`In
`
`the
`
`following the
`
`arguments
`
`set
`
`forth during
`
`substantive examination and found persuasive by
`
`the Examiner are repeated. The
`
`feature "solub1e
`
`"
`
`0
`
`signal" can be derived, e.g.
`
`from the disclosure
`
`on page 21,
`
`lines 9 to 26 where spectrophotometric
`
`and ELISA.
`
`techniques are discussed as preferred
`
`practices of the invention. It is known in the art
`
`that techniques,
`
`such as spectrophotometric-based
`
`and ELISA techniques are premised upon the use of
`
`a solution. It
`
`is further disclosed on page 53,
`
`lines 1 to 3 where it is stated that "the enzyme
`
`terminated by adding 1.0 ml of 0.5%
`reaction was
`sodium. bicarbonate and absorbance was determined
`
`at A300." Absorbance of a substrate can only be
`
`measured in solution. This
`
`line of argument
`
`is
`
`
`
`Page 16 of 22
`Page16of22
`
`

`
`U65
`
`still valid and has not been refuted by Opponent
`
`II. We also refer to our earlier remarks regarding
`
`opponent's I challenge of priority.
`
`3.3.1.3.
`
`Opponent II further alleges that claim 1 violates
`
`Article 100(c)
`
`EPC by omitting steps which are
`
`originally disclosed. We do not
`
`think ‘that
`
`this
`
`objection is justified.
`
`According to the EPC and
`
`the jurisdiction of the EPO,
`
`a claim must clearly
`
`define the object of the invention,
`
`i.e.
`
`indicate
`
`all the essential
`
`features of it. This, however,
`
`does not mean
`
`that
`
`a
`
`reference _to
`
`a
`
`specific
`
`passage of
`
`the original disclosure necessitates
`
`the incorporation of all features mentioned there
`
`into the claims as long as the above requirement
`
`is
`
`fulfilled,
`
`which
`
`is the case here,
`
`as all
`
`essential features of the invention are set forth
`
`in claim 1.
`
`3.3.3.
`
`objection under Article 1oo(b) EPC
`
`Opponent II alleges that the contested patent does
`
`not
`
`disclose
`
`the
`
`invention
`
`in
`
`a
`
`manner
`
`sufficiently clear and complete for those skilled
`
`in the art
`
`to carry it out,
`
`and refers to the
`
`decision T 409191 which allegedly states that the
`
`requirements of Article 83 EPC will be satisfied
`
`only if the skilled person is able to carry out
`
`the invention within the entire scope claimed.
`
`However,
`
`this decision is not
`
`relevant
`
`to the
`
`present case. It concerns a completely different
`
`field and the question discussed therein does not
`
`apply to the present case, although Opponent II
`
`has tried to fabricate a relationship. He points
`
`out
`
`that
`
`the
`
`application
`
`contains
`
`hardly
`
`any
`
`example or no examples at all with respect
`
`to
`
`eukaryotic cells.
`
`First of all,
`
`examples are not
`
`
`
`Page 17 of 22
`Page 17 of 22
`
`

`
`Lthk
`
`an absolute requirement as Rule 27 EPC states that
`
`the description should contain examples
`
`"where
`
`appropriate".
`
`Furthermore,
`
`according
`
`to
`
`established case law an invention is considered to
`
`be sufficiently disclosed if at
`
`least one way is
`
`clearly indicated enabling the person skilled in
`
`the art to carry it out (see, e.g., T 292/85,
`
`this
`
`View has been confirmed by similar statements in
`
`later decisions). Based
`reference
`to‘ the
`lambda
`
`on
`
`a
`
`calculation with
`
`genome, Opponent
`
`II
`
`alleges that it is not possible to detect specific
`
`polynucleotide
`
`sequences
`
`in
`
`eukaryotic
`
`cells
`
`according to the claimed method.
`
`The argument
`
`apparently
`
`arguing
`
`is besides the point. Opponent II is
`that
`detect
`a
`
`one
`
`cannot
`
`specific sequence
`
`in a eukaryotic cell
`
`by the
`
`claimed method because the sequence is in too low
`
`of a concentration and too much of the target DNA
`
`would have to be bound to the support.
`
`opponent's II underlying assumptions,
`
`however, are
`
`fatally flawed.
`
`In his calculations, Opponent II
`
`assumes there is one probe per sequence and one
`
`enzyme
`
`(signalling
`
`moiety)
`
`per
`
`probe.
`
`Conveniently,
`
`Opponent
`
`II
`
`ignores the fact
`
`that
`
`one can easily use more than one enzyme per probe
`
`and/or more than one probe per sequence.
`
`In other
`
`words,
`
`if
`
`concentration,
`
`low
`target
`the
`sequence
`is
`in
`the measure to be taken would be to
`
`increase the number of probes directed at
`
`the
`
`target sequence in order to detect it,
`
`instead of
`
`increasing the amount of
`
`target. Alternatively,
`
`one can also increase the number of enzymes or
`
`signalling moieties per probe
`
`to
`
`increase the
`
`signal.
`
`Moreover,
`
`Opponent II uses a full genome
`
`in its calculations when in actuality one would
`
`
`
`Page 18 of 22
`Page18of22
`
`

`
`IOIOIO
`
`O
`
`COCO.‘
`
`not search an entire genome, but rather fragments
`
`thereof. The patent discloses the use of sandwich
`
`assays, which when used with fragments of the DNA,
`
`can
`
`concentrate
`
`the
`
`sequence
`
`of
`
`interest
`
`by
`
`extracting and
`
`separating
`
`out
`
`those
`
`fragments
`
`containing the sequence of
`
`interest.
`
`Using this
`
`procedure or the one outlined above,
`
`the claimed
`
`method can easily be used on nucleic acids from
`
`eukaryotic cells.
`
`303.4O
`
`objections under Article 100 (3) EPC
`
`Opponent II alleges that the subject matter of the
`
`contested patent
`
`is not patentable in view of the
`
`cited prior art, and additionally argues that the
`
`features "soluble signal" and "non-porous system"
`
`cannot
`
`be
`
`used
`
`to
`
`substantiate
`
`the
`
`required
`
`novelty
`
`or
`
`to
`
`substantiate
`
`inventive
`
`step.
`
`However,
`
`as explained herein,
`
`these limitations
`
`are properly supported by the disclosure and,
`
`thus
`
`are proper claim limitations which are available
`
`to distinguish the prior art.
`
`Reference D1 cited by Opponent II is David Ward's
`European Patent EP Patent No.
`63,8797’ discussed
`
`hereinabove as opponent's
`
`I
`
`reference 07. Refe-
`
`rence D3
`
`is opponent's
`
`I
`
`hereinabove.
`
`Reference
`
`D2
`
`reference 01 discussed
`and
`
`was
`
`raised
`
`thoroughly considered,
`
`together with references D1
`
`and
`
`D3,
`
`during
`
`prosecution
`
`of
`
`the
`
`present
`
`application.
`
`Opponent
`
`II
`
`is
`
`simply
`
`requesting
`
`reconsideration of
`
`the same prior art and argu-
`
`ments considered by the Examiner during prose-
`
`cution. We therefore refer to the line of argument
`
`presented during the examination proceedings with
`
`
`
`Page 19 of 22
`Page19of22
`
`

`
`O
`
`ICCOUI
`
`IIICCO
`
`M44
`
`respect to D2, when it was expressly stated that,
`
`in contrast to the subject matter of the contested
`
`patent, D2 teaches the use of two different probes
`
`complementary to different portions of
`
`a
`
`gene
`
`sequence with each probe being labelled at the end
`
`which
`
`will
`
`abut
`
`the
`
`other
`
`probe
`
`upon
`
`hybridization. The first probe is labelled with a
`
`chemiluminescent
`
`complex that emits
`
`light of
`
`a
`
`specific wavelength measurable
`
`by
`
`spectrophoto-
`
`metry when excited by the proximity of the first
`
`signalling moiety. Further,
`
`according to D2 each
`
`probe
`
`by
`
`itsel

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