`
`UNITED STATES PATENT AND TRADEMARK OFFICE
`
`UNITED STATES DEPARTMENT OF COMMERCE
`United States Patent and Trademark Office
`Address: COMMISSIONER FOR PATENTS
`P.O. Box 1450
`Alexandria1 Virginia 22313- 1450
`www.uspto.gov
`
`APPLICATION NO.
`
`
`
`
`
` F ING DATE
`
`FIRST NAMED INVENTOR
`
`ATTORNEY DOCKET NO.
`
`
`
`
`
`CONF {MATION NO.
`
`12/507,022
`
`07/21/2009
`
`Arnold Oliphant
`
`067234—0229
`
`5169
`
`41552
`7590
`12/27/2010
`MCDERMOTT, WILL & EMERY LLP
`600 13th Street, NW
`Washington, DC 20005-3096
`
`EXAMINER
`TUNG, JOYCE
`PAPER NUMBER
`
`ART UNIT
`
`1637
`
`
`
`
`NOT *ICATION DATE
`
`DELIVERY MODE
`
`12/27/2010
`
`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):
`
`mweipdocket @ mwe.com
`SIP_Docket@mwe.com
`
`PTOL—90A (Rev. 04/07)
`
`
`
`
`Application No.
`Applicant(s)
`
`Office Action Summary
`
`12/507,022
`
`Examiner
`
`OLIPHANT ET AL.
`
`Art Unit
`
`Joyce Tung
`-- The MAILING DA TE of this communication appears on the cover sheet with the correspondence address --
`Period for Reply
`
`A SHORTENED STATUTORY PERIOD FOR REPLY IS SET TO EXPIRE 3 MONTH(S) OR THIRTY (30) DAYS,
`WHICHEVER IS LONGER, FROM THE MAILING DATE OF THIS COMMUNICATION.
`Extensions of time may be available under the provisions of 37 CFR 1. 136( a).
`In no event however may a reply be timely filed
`after SIX () MONTHS from the mailing date of this communication.
`If NO period for reply is specified above, the maximum statutory period will apply and will expire SIX (6) MONTHS from the mailing date of this communication.
`-
`- Failure to reply within the set or extended period for reply will, by statute, cause the application to become ABANDONED (35 U.S.C. § 133).
`Any reply received by the Office later than three months after the mailing date of this communication, even if timely filed, may reduce any
`earned patent term adjustment. See 37 CFR 1.704(b).
`
`Status
`
`1)I:I Responsive to communication(s) filed on
`
`
`
`.
`
`a)I:l This action is FINAL.
`
`2b)IZ| This action is non-final.
`
`3)|:l Since this application is in condition for allowance except for formal matters, prosecution as to the merits is
`
`closed in accordance with the practice under Exparte Quay/e, 1935 CD. 11, 453 O.G. 213.
`
`Disposition of Claims
`
`4)IXI Claim(s) M is/are pending in the application.
`
`4a) Of the above claim(s) _ is/are withdrawn from consideration.
`
`5)I:I Claim(s) _ is/are allowed.
`
`6)|Zl Claim(s Mus/are rejected.
`
`)
`
`)
`
`(
`
`(
`
`Application Papers
`
`is/are objected to.
`
`are subject to restriction and/or election requirement.
`
`9)I:I The specification is objected to by the Examiner.
`
`OH] The drawing(s) filed on _ is/are: a)|:l accepted or b)I:l objected to by the Examiner.
`
`Applicant may not request that any objection to the drawing(s) be held in abeyance. See 37 CFR 1.85(a).
`
`Replacement drawing sheet(s) including the correction is required if the drawing(s) is objected to. See 37 CFR 1.121 (d).
`
`11)|:l The oath or declaration is objected to by the Examiner. Note the attached Office Action or form PTO-152.
`
`Priority under 35 U.S.C. § 119
`
`12)I:I Acknowledgment is made of a claim for foreign priority under 35 U.S.C. § 119(a)-(d) or (f).
`
`a)|:l AII
`
`b)I:l Some * c)|:l None of:
`
`1.I:I Certified copies of the priority documents have been received.
`
`2.|:I Certified copies of the priority documents have been received in Application No. _
`
`3.|:I Copies of the certified copies of the priority documents have been received in this National Stage
`
`application from the International Bureau (PCT Rule 17.2(a)).
`
`* See the attached detailed Office action for a list of the certified copies not received.
`
`Attachment(s)
`
`1) X Notice of References Cited (PTO-892)
`2) D Notice of Draftsperson‘s Patent Drawing Review (PTO-948)
`3) IZI Information Disclosure Statement(s) (PTO/SB/08)
`
`Paper No(s)/Mai| Date 9/2/10 12/1/10.
`US. Patent and Trademark Office
`
`4) D Interview Summary (PTO-413)
`Paper N°(5 )/Mai| Date. _
`5)I:I Notice of Informal Patent Application
`)6|:| Other:
`
`PTOL-326 (Rev. 08-06)
`
`Office Action Summary
`
`Part of Paper No./Mai| Date 20101204
`
`
`
`
`
`Application/Control Number: 12/507,022
`
`Page 2
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`Art Unit: 1637
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`DETAILED ACTION
`
`Double Patenting
`
`1.
`
`The nonstatutory double patenting rejection is based on a judicially created doctrine
`
`grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or
`
`improper timewise extension of the “right to exclude” granted by a patent and to prevent possible
`
`harassment by multiple assignees. A nonstatutory obviousness—type double patenting rejection
`
`is appropriate where the conflicting claims are not identical, but at least one examined
`
`application claim is not patentably distinct from the reference claim(s) because the examined
`
`application claim is either anticipated by, or would have been obvious over, the reference
`
`claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re
`
`Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225
`
`USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re
`
`Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163
`
`USPQ 644 (CCPA 1969).
`
`A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may
`
`be used to overcome an actual or provisional rejection based on a nonstatutory double patenting
`
`ground provided the conflicting application or patent either is shown to be commonly owned
`
`with this application, or claims an invention made as a result of activities undertaken within the
`
`scope of a joint research agreement.
`
`
`
`Application/Control Number: 12/507,022
`
`Page 3
`
`Art Unit: 1637
`
`Effective January 1, 1994, a registered attorney or agent of record may sign a terminal
`
`disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR
`
`3.73(b).
`
`2.
`
`Claims 15—43 are rejected on the ground of nonstatutory obviousness—type double
`
`patenting as being unpatentable over claims 1—29 of US. Patent No. 7582420. Although the
`
`conflicting claims are not identical, they are not patentably distinct from each other because the
`
`instant claims 15—43 are drawn to a method for detecting different target nucleic acid sequence of
`
`interest in a sample in which the method comprises steps similar to those used in the method of
`
`claims 1—29 of 7582420. The differences are that the instant method of claims 15—43 comprises
`
`step (b) of contacting the sample with dNTPs and primers to obtain first extension products, and
`
`after the first primer extension, the rest of the steps are the same as steps (b)—(g) as recited in
`
`claim 1 of US. Patent No. 7582420. The specification of US. Patent No. 7582420 discloses first
`
`extension from target without immobilization (see column 3, lines 50—54, fig. 2). Therefore, the
`
`instantly claimed invention and the invention of claims 1—29 of US. Patent No. 7582420 have
`
`overlapping subject matter.
`
`Claim Rejections - 35 USC § 103
`
`3.
`
`The following is a quotation of 35 USC. 103(a) which forms the basis for all
`
`obviousness rejections set forth in this Office action:
`
`(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in
`section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are
`such that the subject matter as a whole would have been obvious at the time the invention was made to a person
`having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the
`manner in which the invention was made.
`
`This application currently names joint inventors. In considering patentability of the
`
`claims under 35 USC. 103(a), the examiner presumes that the subject matter of the various
`
`
`
`Application/Control Number: 12/507,022
`
`Page 4
`
`Art Unit: 1637
`
`claims was commonly owned at the time any inventions covered therein were made absent any
`
`evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out
`
`the inventor and invention dates of each claim that was not commonly owned at the time a later
`
`invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c)
`
`and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
`
`4.
`
`Claims 15, 21—22, 25—35, and 38—43 are rejected under 35 U.S.C. 103(a) as being
`
`unpatentable over Bhatnagar et al. (5593840, issued Jan. 14, 1997) and in view of Barany et al.
`
`(6,027,889, issued Feb. 22, 2000) and Hartley et al. (5,043,272 issued Aug. 27, 1991).
`
`Bhatnagar et al. disclose a process for amplifying nucleic acid sequence from a DNA or
`
`RNA template. The process allows efficiently detecting a particular point mutation (See the
`
`abstract). The process provides primers comprising a first primer which is substantially
`
`complementary to first segment at a first end of the target nucleic acid sequence and a second
`
`primer, which is substantially complementary to a second segment at a second end of the target
`
`nucleic acid sequence and whose 3’ end is adjacent to the 5’ end of the first primer (see column
`
`3, lines 11—18). The second primer (oligo 2) is extended and then ligated to the first primer (See
`
`fig. 3) to produce fused amplification products (See column 3, lines 31—34). The fused
`
`amplification products are amplified by a third primer (See column 3, lines 35—44). The allele is
`
`determined by detecting labeled oligonucleotide (see column 3, lines 64—65). The process also
`
`provides four different nucleotide bases (See column 3, lines 27). The amplified fused
`
`amplification products are detected by a detectable signal (See column7, lines 8—22).
`
`Regarding claims 25—26, Bhatnagar et al. disclose that one of the primers is comprised of
`
`a number of similar oligonucleotide sequences, one of which is exactly complementary to the
`
`
`
`Application/Control Number: 12/507,022
`
`Page 5
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`Art Unit: 1637
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`possible allele or point mutations and each of which oligonucleotide is labeled with a different
`
`label. The allele is determined by detecting which labeled oligonucleotide is contained within the
`
`resulting amplification products (See column 3, lines 59—65). Therefore the detection position of
`
`the target nucleic acid sequence would be one or two nucleotides.
`
`Regarding claims 27—28, Bhatnagar et al. do not disclose the length of the second target
`
`domain as required in claims 27—28. Bhatagar et al. disclose that nucleotide sequence, content
`
`and length will vary depending on the sequence to be amplified (See column 6, lines 18—30). This
`
`inherently teaches that the second target domain will vary from one nucleotide in length to 5
`
`nucleotides in length as recited in the claims 27 —28.
`
`Regarding claim 29, Bhatnagar et al. disclose a third primer which is similar to the first
`
`end of the target nucleic acid sequence and which is substantially complementary to at least a
`
`portion of said first primer, said portion including the 5' end of the first primer such that when
`
`the third primer is hybridized to the first primer, the position of the third primer complementary
`
`to the base at the 5' end of the first primer contains a modification which substantially avoids
`
`strand displacement under polymerizing conditions (see column 3, lines 18—25).
`
`Bhatnagar et al. do not explicitly disclose a first probe comprising a first universal
`
`priming sequence and a second probe comprising a second universal priming sequence as recited
`
`in claim 15, a third probe comprising a third universal priming sequence in claim 29 and each
`
`probe set comprising universal priming sequence as recited in claim 30.
`
`
`
`Application/Control Number: 12/507,022
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`Page 6
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`Art Unit: 1637
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`Hardy et al. disclose random priming amplification. The method uses random
`
`oligonucleotide primer to prime single—stranded template nucleic acid (see column 2, lines 45—
`
`67).
`
`One of ordinary skill in the art would have been motivated to apply a probe which
`
`comprises a universal priming sequence because Hardy et al. disclose that amplification is
`
`performed without prior knowledge of specific sequence (see the Abstract). It would have been
`
`
`prima facie obvious to use probes comprising universal sequence.
`
`Regarding claims 31—32, Bhantnagar et al. disclose that the primer may be labeled with a
`
`detectable marker (See column 15, lines 17—18).
`
`Regarding claim 35, Bhatnagar et al. disclose extending a third primer (See column 3,
`
`lines 40—44).
`
`Regarding claim 38, Bhatnagar et al. disclose a second primer which is complementary to
`
`a second segment at a second end of the target nucleic acid sequence (See column 3, lines 15—17)
`
`and a third primer is similar to the first end of the target and is substantially complementary to at
`
`least a portion of the first primer (see column 3, lines 18—26). Bhatnagar et al disclose that a
`
`second primer is substantially complementary to a second segment at a second end of the target
`
`nucleic acid sequence and whose 3’ end is adjacent to the 5’ end of the first primer (see column
`
`3, lines 11—18). Claim 38 does not recite the limitations for a third target domain of a target
`
`
`
`Application/Control Number: 12/507,022
`
`Page 7
`
`Art Unit: 1637
`
`nucleic acid sequence. Any nucleotides within the segment is interpreted a third target domain.
`
`Bhatanagar et al. inherently disclose the limitation of claim 38.
`
`Regarding claims 39 and 42, Bhatnagar et al. disclose that the adjacent 5’ end of the first
`
`primer and the 3 ’ end of the second primer will ligate to form a fiased amplification product
`
`substantially complementary to the target nucleic acid sequence (See column 3, lines 31—35).
`
`Bhatnagar et al. define “substantially complementary” that generally, the primer must hybridize
`
`to the target nucleic acid sequence at the end to be ligated or extended to allow target dependent
`
`ligation or extension (see column 6,
`
`lines 14—17). The teachings of Bhatnagar et al. satisfy the
`
`limitations of the claim.
`
`Regarding claims 40—41, Bhatnagar et al. do not disclose that a second probe has an
`
`interrogation position at 5 ’ end.
`
`Barany et al. disclose that the products may be detected in two different formats. One of
`
`the formats is oligonucleotide address sequences for detecting specific DNA sequence by
`
`hybridization (See column 19, lines 8—13). The address sequence is located at 5’ end of each
`
`allele—specific probe. The sequences are unique addressable sequences which specifically
`
`hybridize to their complementary address sequences on an addressable array (See column 19,
`
`lines 10—13).
`
`Regarding claim 43, Bhatnagar et al. do not disclose first extension product which is
`
`obtained by contacting a sample with dNTPs and primers which hybridizes to a first target
`
`domain and then extending the primers.
`
`
`
`Application/Control Number: 12/507,022
`
`Page 8
`
`Art Unit: 1637
`
`Barany et al. disclose a method for detecting a plurality of sequences differing by one or
`
`more single base changes in a plurality of target nucleotide sequences (see column 5, lines 52—
`
`55). The method involves a first polymerase chain reaction phase using a first oligonucleotide
`
`primer which is specific to a target portion (see column 5, lines 62—65). The first polymerase
`
`chain reaction involves a denaturation treatment, a hybridization treatment, and an extension
`
`treatment (see column 6, lines 20—24). The method can be used in multiplex detection in which a
`
`differential PCR process is required (see column 13, lines 10—12).
`
`Regarding steps (g)—(h) of claim 15 and claims 33—34, Bhatnagar et al. do not disclose
`
`immobilizing an amplicon on a solid capture probe that are specific for individual adapter
`
`sequence.
`
`Barany et al. disclose that when using arrays, the oligonucleotide primers or probes used
`
`in the above—described coupled PCR and LDR phases, respectively, have an addressable array-
`
`specific portion, after the LDR or PCR phases are completed, the addressable array—specific
`
`portions for the products of such processes remain single stranded and are caused to hybridize to
`
`the capture oligonucleotides during a capture phase (see column 26,
`
`lines 65—67, column 28,
`
`lines 51—56, column 29, 48—53, column 36, lines 11—18, 38—46). The addressable portion on the
`
`primer or probe is interpreted as an adapter sequence. Where an array is utilized, the detection
`
`phase of the process involves scanning and identifying if LDR or PCR products have been
`
`produced and correlating the presence of such products to a presence or absence of the target
`
`nucleotide sequence in the test sample (see column 36, lines 57—62). The LDR probe set
`
`comprises a first probe having a target—specific portion and a 5 ’ upstream primer— specific portion
`
`
`
`Application/Control Number: 12/507,022
`
`Page 9
`
`Art Unit: 1637
`
`and a second probe having a target—specific portion and a 3 ’ downstream primer—specific portion
`
`(see column 25, lines 31-36).
`
`One of ordinary skill in the art would have been motivated to combine the teachings of
`
`Barany et al. and Bhatnagar et al. to carry out the invention as claimed because the method of
`
`Barany et al. uses a primary PCR and Barany et al. disclose that the primary PCR cannot
`
`distinguish amplifications from deletions, so when making distinctions, the process must be used
`
`in conjunction with LDR/PCR or a differential PCR process (see column 13, lines 1—12), and
`
`Bhatnagar et al. disclose that the method is used in detecting multiple alleles in which the fidelity
`
`is increased (see column 2,
`
`
`lines 63—67). It would have been prima facie obvious to carry out the
`
`method as claimed.
`
`5.
`
`Claims 23—24 and 36—37 are rejected under 35 U.S.C. 103(a) as being unpatentable over
`
`Bhatnagar et al. (5593840, issued Jan. 14, 1997) and in view of Barany et al. (6,027,889, issued
`
`Feb. 22, 2000) as applied to claims 15, 21—22, 25—35 and 38—43 above, and further in view of
`
`Shuber et al. (Human Molecular Genetics, 1997, Vol. 6(3), pg. 337—347).
`
`The teachings of Bhatnagar et al. and Barany et al. are set forth in section 4 above. None
`
`of the references discloses the limitations of claims 23—24 and 36—37.
`
`Shuber et al. disclose a method for mutation detection in which multiplex DNA samples
`
`are immobilized on a solid support and a single hybridization is performed with a pool of allele—
`
`specific oligonucleotide probes. The samples can be over hundreds in number (See pg. 337, the
`
`Abstract). It is inherent that there would be over hundreds of allele specific oligonucleotide
`
`probes used in the identification of large numbers of samples.
`
`
`
`Application/Control Number: 12/507,022
`
`Page 10
`
`Art Unit: 1637
`
`Shuber et al. also disclose washing away of unhybridized probes (page 345, paragraph
`
`11).
`
`One of ordinary skill in the art would have been motivated to apply a solid support as a
`
`first solid support for immobilizing over hundreds of samples as taught by Shuber et al. into the
`
`method of Bhatnagar et al. because by doing so, Shuber et al. state the mutation detection can be
`
`
`done rapidly and accurately (See pt. 337, the Abstract). It would have been prima facie obvious
`
`to apply a solid support as a first solid support for immobilizing at least 100 different target
`
`nucleic acid sequences for detecting different target nucleic acid sequences.
`
`6.
`
`Claims 16—20 are rejected under 35 U.S.C. 103(a) as being unpatentable over Bhatnagar
`
`et al. (5593840, issued Jan. 14, 1997) and in view of Barany et al. (6,027,889, issued Feb. 22,
`
`2000) as applied to claims 15, 21—22, 25—35 and 38—43 above, and further in view of Shuber (US
`
`5888778, issued Mar. 30, 1999).
`
`The teachings of Bhatnagar et al. and Barany et al. are set forth in section 4 above. None
`
`of the references discloses the limitations of claims 16—20.
`
`Shuber discloses a screening method for detecting and identifying genetic mutations (see
`
`column 4, lines 12—16). Nucleic acids are bound to a solid support allowing the simultaneous
`
`processing and screening a large number of samples (see column 4, lines 25—27, column 9, lines
`
`14—15). The first probes extended with a labeled dNTP are isolated (see column 9, lines 18—22).
`
`A “separation moiety” can be biotin for the isolation of extended first probe (see column 9, lines
`
`51—53). The affinity for the separation moiety is streptavidin (see column 9, lines 53—57). A
`
`“separation moiety” is incorporated in labeled dNTP (see column 9, lines 62—67). In one
`
`embodiment, a target nucleic acid is bound to a solid support with or without prior amplification
`
`
`
`Application/Control Number: 12/507,022
`
`Page ll
`
`Art Unit: 1637
`
`(see column ll, lines 6—8). The target nucleic acid is bound Via biotin—conjugated PCR primer
`
`(see column ll, lines 28—29).
`
`One of ordinary skill in the art would have been motivated to apply purification of
`
`extended probe Via labeled dNTP as taught by Shuber because by doing so, it allows the
`
`simultaneous determination of a large number of samples and then facilitates the analysis (see
`
`
`column ll, lines l6—18). It would have been prima facie obVious to carry out the steps as recited
`
`in claims l6-20.
`
`Summary
`
`No claims are free of the prior art.
`
`Any inquiry concerning this communication or earlier communications from the
`
`7.
`
`8.
`
`examiner should be directed to Joyce Tung whose telephone number is (571) 272—0790. The
`
`examiner can normally be reached on Monday — Friday, 8:30-5:00.
`
`If attempts to reach the examiner by telephone are unsuccessful, the examiner’s
`
`supervisor, Gary Benzion can be reached on 571 272—0782. The fax phone number for the
`
`organization where this application or proceeding is assigned is 571—273—8300.
`
`
`
`Application/Control Number: 12/507,022
`
`Page 12
`
`Art Unit: 1637
`
`Information regarding the status of an application may be obtained from the Patent
`
`Application Information Retrieval (PAIR) system. Status information for published applications
`
`may be obtained from either Private PAIR or Public PAIR. Status information for unpublished
`
`applications is available through Private PAIR only. For more information about the PAIR
`
`system, see http://pair—direct.uspto.gov. Should you have questions on access to the Private PAIR
`
`system, contact the Electronic Business Center (EBC) at 866—217—9197 (toll—free). If you would
`
`like assistance from a USPTO Customer Service Representative or access to the automated
`
`information system, call 800—786—9199 (IN USA OR CANADA) or 571—272—1000.
`
`/Kenneth R Horlick/
`
`Primary Examiner, Art Unit 1637
`
`/Joyce Tung/
`Examiner, Art Unit 1637
`
`December 09, 2010
`
`
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