www.uspto.gov
`
`UNITED STATES DEPARTMENT OF COMMERCE
`United States Patent and Trademark Office
`Address: COMMISSIONER FOR PATENTS
`PO. Box 1450
`Alexandria, Virginia 2231371450
`
`15/602,991
`
`05/23/2017
`
`William BANYAI
`
`44854-701308
`
`5477
`
`WILSON, SONSINI, GOODRICH & ROSATI
`650 PAGE MILL ROAD
`PALO ALTO, CA 94304-1050
`
`ZHANG KAUIANG
`
`ART UNIT
`
`1639
`
`PAPER NUMBER
`
`NOTIFICATION DATE
`
`DELIVERY MODE
`
`05/31/2019
`
`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):
`
`patentdoeket@ wsgroom
`
`PTOL-90A (Rev. 04/07)
`
`

`

`0/7709 A0170” Summary
`
`Application No.
`15/602,991
`Examiner
`KAIJIANG ZHANG
`
`Applicant(s)
`BANYAI et al.
`Art Unit
`1639
`
`AIA (FITF) Status
`Yes
`
`- The MAILING DA TE of this communication appears on the cover sheet wit/7 the correspondence address -
`Period for Reply
`
`A SHORTENED STATUTORY PERIOD FOR REPLY IS SET TO EXPIRE g MONTHS 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 (6) MONTHS from the mailing
`date of this communication.
`|f 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). Responsive to communication(s) filed on 19 December 2018.
`[:1 A declaration(s)/affidavit(s) under 37 CFR 1.130(b) was/were filed on
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`2a)D This action is FINAL.
`
`2b)
`
`This action is non-final.
`
`3)[:] An election was made by the applicant in response to a restriction requirement set forth during the interview on
`; the restriction requirement and election have been incorporated into this action.
`
`4)[:] 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 Expat/7e Quay/e, 1935 CD. 11, 453 O.G. 213.
`
`Disposition of Claims*
`5)
`Claim(s)
`
`1—10 and 12—38 is/are pending in the application.
`
`5a) Of the above claim(s) 23-38 is/are withdrawn from consideration.
`
`E] Claim(s)
`
`is/are allowed.
`
`Claim(s) 1—10 and 12—22 is/are rejected.
`
`C] Claim(s) _
`
`is/are objected to.
`
`) ) ) )
`
`6 7
`
`8
`
`
`
`are subject to restriction and/or election requirement
`[:1 Claim(s)
`9
`* If any claims have been determined allowable, you may be eligible to benefit from the Patent Prosecution Highway program at a
`
`participating intellectual property office for the corresponding application. For more information, please see
`
`http://www.uspto.gov/patents/init events/pph/index.'sp or send an inquiry to PPeredback@uspto.gov.
`
`Application Papers
`10):] The specification is objected to by the Examiner.
`
`11):] The drawing(s) filed on
`
`is/are: a)C] accepted or b)Ej 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).
`
`Priority under 35 U.S.C. § 119
`12)C] Acknowledgment is made of a claim for foreign priority under 35 U.S.C. § 119(a)-(d) or (f).
`Certified copies:
`
`a)C] All
`
`b)C] Some**
`
`c)C] None of the:
`
`1C] Certified copies of the priority documents have been received.
`
`2C] Certified copies of the priority documents have been received in Application No.
`
`3.[:] 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)
`
`Notice of References Cited (PTO-892)
`
`Information Disclosure Statement(s) (PTO/SB/08a and/or PTO/SB/08b)
`2)
`Paper No(s)/Mail Datew.
`U.S. Patent and Trademark Office
`
`3) C] Interview Summary (PTO-413)
`Paper No(s)/Mail Date
`4) CI Other-
`
`PTOL-326 (Rev. 11-13)
`
`Office Action Summary
`
`Part of Paper No./Mai| Date 20190528
`
`

`

`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 2
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`DETAILED ACTION
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`Continued Examination Under 37 CFR 1. 1 14
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`1.
`
`A request for continued examination under 37 CFR 1.114, including the fee set
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`forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this
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`application is eligible for continued examination under 37 CFR 1.114, and the fee set
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`forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action
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`has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission filed on
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`12/19/2018 has been entered.
`
`Applicant has amended claims 1 and 14-15, and added new claims 23-38.
`
`Newly submitted claims 23-38 are directed to an invention that is independent or distinct
`
`from the invention originally claimed for the following reasons: claims 23-38 are drawn
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`to a process of making the product of claims 1-10 and 12-22, however the product as
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`claimed (i.e., the product of claims 1-10 and 12-22) can be made by another and
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`materially different process (e.g., a process that involves making double-stranded
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`cDNAs from total RNA, fragmenting the double-stranded cDNAs and then size-selecting
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`double-stranded cDNA fragments that are greater than 75 base pairs in length (in this
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`case, each single-stranded cDNA fragment comprises an overlap region which is
`
`complementary to the entire region of its complementary single-stranded cDNA
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`fragment, wherein the overlap region comprises at least 75 bases in length); g a
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`process of fragmenting prokaryotic genomic DNA (which is the same as the
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`corresponding cDNA) followed by size-selecting the double-stranded fragments that are
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`at least 75 base pairs in length (in this case, each single-stranded DNA fragment
`
`comprises an overlap region which is complementary to the entire region of its
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`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 3
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`complementary single-stranded DNA fragment, wherein the overlap region comprises at
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`least 75 bases in length).
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`Since applicant has received an action on the merits for the originally presented
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`invention, this invention has been constructively elected by original presentation for
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`prosecution on the merits. Accordingly, claims 23-38 are withdrawn from consideration
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`as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP §
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`821.03.
`
`Claims 1-10 and 12-22 are currently under examination. All the amendments
`
`and arguments have been thoroughly reviewed but are found insufficient to place the
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`instantly examined claims in condition for allowance. In view of applicant’s amendment
`
`to claim 1, all the rejections from the previous Office action have been withdrawn.
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`However, new grounds of rejection are presented as set forth below.
`
`Claim Rejections - 35 USC § 103
`
`2.
`
`In the event the determination of the status of the application as subject to AIA 35
`
`U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any
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`correction of the statutory basis for the rejection will not be considered a new ground of
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`rejection if the prior art relied upon, and the rationale supporting the rejection, would be
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`the same under either status.
`
`3.
`
`The following is a quotation of 35 U.S.C. 103 which forms the basis for all
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`obviousness rejections set forth in this Office action:
`
`A patent for a claimed invention may not be obtained, notwithstanding that the claimed
`invention is not identically disclosed as set forth in section 102 of this title, if the differences
`between the claimed invention and the prior art are such that the claimed invention as a whole
`would have been obvious before the effective filing date of the claimed invention to a person
`having ordinary skill in the art to which the claimed invention pertains. Patentability shall not
`be negated by the manner in which the invention was made.
`
`

`

`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 4
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`4.
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`This application currently names joint inventors. In considering patentability of the
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`claims the examiner presumes that the subject matter of the various claims was
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`commonly owned as of the effective filing date of the claimed invention(s) absent any
`
`evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to
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`point out the inventor and effective filing dates of each claim that was not commonly
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`owned as of the effective filing date of the later invention in order for the examiner to
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`consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2)
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`prior art against the later invention.
`
`5.
`
`Claims 1-10 and 12-22 are rejected under 35 U.S.C. 103 as being unpatentable
`
`over Church et al. (WO 2012/154201 A1).
`
`Regarding claims 1-2, 4-5 and 21
`
`Church et al. teach, throughout the whole document, a polynucleotide cDNA
`
`library comprising a large number of polynucleotides (see paragraphs [029], [033],
`
`[096], [099] and [0106]; Figure 1), wherein each of the polynucleotides is at least 75
`
`bases in length (e.g., 130-mer or 200-mer. See paragraphs [034] and [096]), wherein at
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`least 80% (e.g., more than 87%, g 100%) of the polynucleotides have no errors
`
`compared to preselected sequences received in the instructions provided in the
`
`computer readable non-transient medium without error correction (see paragraph
`
`
`[0106]. When the polynucleotides are 130-mers, the overall error rate, which reflect
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`errors introduced in both the synthesis step and the subsequent amplification and
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`assembly steps, is approximately “1/1000 bp”. Thus, the aggregate error rate for the
`
`synthesized polynucleotides, prior to their use in the subsequent amplification and
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`assembly steps (which also introduce errors), is less than 1/1000 bp. This means that
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`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 5
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`more than 87% (Le, 1 — 130/1000 = 87%) of the polynucleotides have no errors.
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`Furthermore, since the recited “sequences received in the instructions provided in the
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`computer readable non-transient medium” are neither disclosed nor defined in any way,
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`the recited comparison is completely arbitrary and is thus meaningless. For example,
`
`when the actual sequences of the polynucleotides in library of Church et al. are the
`
`sequences received in the instructions provided in a computer readable non-transient
`
`medium, 100% of the polynucleotides in the library of Church et al. would have no
`
`errors compared to the sequences received in the instructions provided in the computer
`
`readable non-transient medium.), wherein each of the polynucleotides comprises a first
`
`overlap region which is complementary to a second overlap region of another
`
`polynucleotide of the polynucleotides (see paragraph [099]: “...OLS Pool 1 were
`
`designed such that the processed ssDNA pools fully overlapped to form a complete
`
`dsDNA sequence. In OLS Pool 2, the processed dsDNA fragments partially overlapped
`
`by approximately 20 bp...”), such that a plurality of genes are formed when a subset of
`
`the polynucleotides are assembled (see paragraphs [011] and [029]; Figure 1), and
`
`wherein the first overlap region comprises at least 10 bases in length (see paragraph
`
`[099]: “...OLS Pool 1 were designed such that the processed ssDNA pools fu||y
`
`overlapped to form a complete dsDNA sequence. In OLS Pool 2, the processed dsDNA
`
`fragments partially overlapped by approximately 20 bp...”). Regarding the number of
`
`polynucleotides in the polynucleotide cDNA library, Church et al. teach that the number
`
`of polynucleotides may be at least 20,000, 60,000, 100,000 or more (see paragraph
`
`[033]). Although Church et al. didn’t actually produce a polynucleotide cDNA library (i.e.,
`
`each of the OLS Pools 1 and 2 as disclosed in “EXAMPLE I” contains approximately
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`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 6
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`13,000 polynucleotides) comprising at least 20,000, 60,000 or 100,000 polynucleotides,
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`it would have been prima facie obvious to one of ordinary skill in the art at the time the
`
`invention was made to do so because Church et al. expressly suggested so (see
`
`paragraph [033]). In addition, Church et al. teach that the synthesis platform is
`
`“scalable” (see EXAMPLE I), and further teach that high-fidelity DNA microchips can be
`
`used to develop a “highly parallel” nucleic acid sequence synthesis platform (see
`
`paragraph [029]). Thus, one of ordinary skill in the art could produce a polynucleotide
`
`cDNA library comprising at least 20,000, 60,000, 100,000 or more polynucleotides in
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`any one or more of the following ways: 1) scaling-up of the synthesis platform as used
`
`by Church et al. in EXAMPLE I; 2) simultaneously using multiple microchips on multiple
`
`instruments for synthesizing the polynucleotides (i.e., parallel synthesis using multiple
`
`instruments); 3) successively synthesizing the polynucleotides on a single instrument
`
`(which would involve using one microchip after another).
`
`The recitation “synthesized based on instructions provided in a computer
`
`readable non-transient medium” is (or is similar to) non-structurallimitation (i.e.,
`
`limitation about how the claimed product or the component(s) of the claimed product is
`
`made) as those recited in product-by-process claims, thus does not distinguish the
`
`claimed polynucleotide cDNA library over the polynucleotide cDNA library as taught or
`
`rendered obvious by Church et al. (see MPEP 2113).
`
`Regarding claim 3
`
`The polynucleotide cDNA library according to Church et al., wherein each of the
`
`polynucleotides is isolated (e.g., isolated in a separate feature of the microchip) (see
`
`Figure 1).
`
`

`

`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Regarding claim 6
`
`Page 7
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`According to Church et al., the polynucleotide cDNA library may comprises at
`
`least 100,000 or more polynucleotides (see paragraph [033]). Although Church et al. do
`
`not specifically disclose the number range for the polynucleotide as recited in the instant
`
`claim, it would have been prima facie obvious to one of ordinary skill in the art at the
`
`time the invention was made to vary or optimize such number range in the
`
`polynucleotide cDNA library of Church et al. via routine experimentation thus arriving at
`
`the working or optimal number range as instantly claimed. The MPEP states that
`
`“Where the general conditions of a claim are disclosed in the prior art, it is not inventive
`
`to discover the optimum or working ranges by routine experimentation” In re Aller, 220
`
`F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955); see also Peterson, 315 F.3d at 1330,
`
`65 USPQZd at 1382 (“The normal desire of scientists or artisans to improve upon what
`
`is already generally known provides the motivation to determine where in a disclosed
`
`set of percentage ranges is the optimum combination of percentages”) (see MPEP
`
`2144.05.ll). Furthermore, in the case where the claimed ranges “overlap or lie inside
`
`ranges disclosed by the prior art” a prima facie case of obviousness exists (see MPEP
`
`2144.05.l).
`
`Regarding claim 7
`
`The polynucleotide cDNA library according to Church et al., wherein at least
`
`1000 genes are formed when a subset of the polynucleotides are assembled (see
`
`paragraphs [011]: “...the nucleic acid seguence of interest is a DNA seguence, e.g., a
`
`regulatory element, a gene, a pathway and/or a genome. In yet other aspects, 50, 100,
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`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 8
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`500, 750, 1,000 or more oligonucleotide sets are provided, wherein each set is specific
`
`for a unique nucleic acid sequence of interest”).
`
`Regarding claims 8- 10
`
`Church et al. teach or expressly suggest that “750, 1,000 or more” genes
`
`(assembled as “nucleic acid sequence of interest”, each of which comprises sequence
`
`encoded by the cDNA sequence encoding for one of the “750, 1,000 or more” genes,
`
`and each of which is assembled using one of the “750, 1,000 or more” oligonucleotide
`
`sets) may be synthesized/assembled (see paragraphs [011]: “...the nucleic acid
`
`sequence of interest is a DNA sequence, e.g., a regulatory element, a gene, a pathway
`
`and/or a genome. In yet other aspects, 50, 100, 500, 750, 1,000 or more oligonucleotide
`
`sets are provided, wherein each set is specific for a unique nucleic acid sequence of
`
`
`interest”). Although Church et al. do not specifically disclose the number range(s) for
`
`the genes as recited in the instant claims, it would have been prima facie obvious to one
`
`of ordinary skill in the art at the time the invention was made to vary or optimize such
`
`number range(s) in the polynucleotide cDNA library of Church et al. via routine
`
`experimentation thus arriving at the working or optimal number range(s) as instantly
`
`claimed. The MPEP states that “Where the general conditions of a claim are disclosed
`
`in the prior art, it is not inventive to discover the optimum or working ranges by routine
`
`experimentation” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955); see
`
`also Peterson, 315 F.3d at 1330, 65 USPQZd at 1382 (“The normal desire of scientists
`
`or artisans to improve upon what is already generally known provides the motivation to
`
`determine where in a disclosed set of percentage ranges is the optimum combination of
`
`percentages”) (see MPEP 2144.05.ll). Furthermore, in the case where the claimed
`
`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 9
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`ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of
`
`obviousness exists (see MPEP 2144.05.l).
`
`Regarding claim 12
`
`For the platform used for the synthesis of OLS Pool 1, each of the
`
`polynucleotides in the library overlaps with (or is complementary to) the entire region of
`
`its complementary polynucleotide in the library (see paragraph [099]: “...OLS Pool 1
`
`were designed such that the processed ssDNA pools fully overlapped to form a
`
`complete dsDNA sequence”). The polynucleotide cDNA library of Church et al. is
`
`limited to any particular type of sequences, it applies to all types of polynucleotide
`
`sequences, including sequences comprising a GC content of 35% to 65% (in which
`
`case, the first overlap region would comprise a GC content of 35% to 65%).
`
`Regarding claim 13
`
`The polynucleotide cDNA library according to Church et al., wherein the first
`
`overlap region comprises 10 to 100 bases in length (see paragraph [099]: “...OLS Pool
`
`1 were designed such that the processed ssDNA pools fully overlapped to form a
`
`complete dsDNA sequence. In OLS Pool 2, the processed dsDNA fragments partially
`
`overlapped by approximately 20 bp...”).
`
`Regarding claims 14-16
`
`The polynucleotide cDNA library according to Church et al., wherein each
`
`polynucleotide is 130 or 200 bases in length (see paragraph [096]).
`
`Regarding claims 17- 18
`
`

`

`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 10
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`The polynucleotide cDNA library according to Church et al., wherein each of the
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`genes is at least 0.5 kb in length (see paragraph [011]), or at least 3 kb in length (see
`
`paragraph [011]).
`
`Regarding claims 19-20
`
`The polynucleotide cDNA library according to Church et al., wherein the
`
`polynucleotides are attached to a structure which is a solid support (e.g., microchip)
`
`(see Figure 1; paragraphs [014], [029] and [096]).
`
`Regarding claim 22
`
`The polynucleotide cDNA library according to Church et al., wherein the first
`
`overlap region comprises 10 to 50 bases in length (see paragraph [099]: “...OLS Pool 1
`
`were designed such that the processed ssDNA pools fully overlapped to form a
`
`complete dsDNA sequence. In OLS Pool 2, the processed dsDNA fragments partially
`
`overlapped by approximately 20 bp...”).
`
`6.
`
`Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Church et
`
`al. (WO 2012/154201 A1) as applied to claim 1 above, and further in view of Hodgson
`
`(US 2002/0025561 A1, cited previously) and Kini et al. (US 2009/0285825 A1, cited
`
`previously).
`
`Church et al. teach or render obvious the polynucleotide cDNA library of claim 1
`
`as discussed above. For the platform used for the synthesis of OLS Pool 2, Church et
`
`al. teach that the first overlap region comprises 20 bases in length (see paragraph [099]:
`
`“In OLS Pool 2, the processed dsDNA fragments partially overlapped by approximately
`
`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 11
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`20 bp...”), but do not specifically disclose the use of the particular GC content range in
`
`the first overlap region as specified in instant claim 12.
`
`However, Hodgson teaches that, for such assembling using overlapping
`
`polynucleotides, it is desirable to have a higher GC content in the overlap sequences,
`
`because a higher GC content would lead to a higher melting temperature and thus allow
`
`the overlapping polynucleotides to be annealed and ligated at a higher temperature
`
`which favors more specific interaction and greater enzyme activity (see paragraph
`
`[0048]). Likewise, Kini et al. also taught the use of overlapping region with more than
`
`50% GC content for such assembling using overlapping polynucleotides (see paragraph
`
`[0217D.
`
`It would have been prima facie obvious to one of ordinary skill in the art before
`
`the effective filling date of the claimed invention to optimize the GC content in the first
`
`overlap region, based on the teachings of Hodgson and Kini et al., used in the
`
`polynucleotide cDNA library of Church et al. thus arriving at the instantly claimed
`
`invention, because: 1) Hodgson taught that a higher GC content would lead to a higher
`
`melting temperature and thus allow the overlapping polynucleotides to be annealed and
`
`ligated at a higher temperature which favors more specific interaction and greater
`
`enzyme activity (see paragraph [0048]); 2) the MPEP states that “Where the general
`
`conditions of a claim are disclosed in the prior art, it is not inventive to discover the
`
`optimum or working ranges by routine experimentation” In re Aller, 220 F.2d 454, 456,
`
`105 USPQ 233, 235 (CCPA 1955); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at
`
`1382 (“The normal desire of scientists or artisans to improve upon what is already
`
`generally known provides the motivation to determine where in a disclosed set of
`
`

`

`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 12
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`percentage ranges is the optimum combination of percentages”) (see MPEP
`
`2144.05.|I). Given the teachings of the prior art and the level of the ordinary skilled
`
`artisan at the time of the applicant’s invention, it must be considered, absent evidence
`
`to the contrary, that said skilled artisan would have had a reasonable expectation of
`
`success in practicing the claimed invention.
`
`Response to Arguments
`
`7.
`
`Applicant’s arguments filed 12/19/2018 have been considered but are moot
`
`because the arguments do not apply to any of the currently presented rejections.
`
`8.
`
`No claims are allowed.
`
`Conclusion
`
`Any inquiry concerning this communication or earlier communications from the
`
`examiner should be directed to KAIJIANG ZHANG whose telephone number is
`
`(571)272-5207. The examiner can normally be reached on Monday - Friday, 8:30 am -
`
`5 pm.
`
`Examiner interviews are available via telephone, in-person, and video
`
`conferencing using a USPTO supplied web-based collaboration tool. To schedule an
`
`interview, applicant is encouraged to use the USPTO Automated Interview Request
`
`(AIR) at http://www.uspto.gov/interviewpractice.
`
`If attempts to reach the examiner by telephone are unsuccessful, the examiner’s
`
`supervisor, Heather Calamita can be reached on 571-272-2876. The fax phone number
`
`for the organization where this application or proceeding is assigned is 571-273-8300.
`
`Information regarding the status of an application may be obtained from the
`
`Patent Application Information Retrieval (PAIR) system. Status information for
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`

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`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 13
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`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 -272-1 000.
`
`/KAIJIANG ZHANG/
`
`Primary Examiner, Art Unit 1639
`
`