`
`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
`
`12/13/2018
`
`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
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`following e—mail address(es):
`
`patentdoeket@ wsgroom
`
`PTOL-90A (Rev. 04/07)
`
`
`
`Off/09 A0170” Summary
`
`Application No.
`15/602,991
`Examiner
`KAIJIANG ZHANG
`
`Applicant(s)
`BANYAI et al.
`Art Unit
`1639
`
`AIA 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 24 August 2018.
`[:1 A declaration(s)/affidavit(s) under 37 CFR 1.130(b) was/were filed on
`
`2a). This action is FINAL.
`
`2b) C] 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—22 is/are pending in the application.
`
`5a) Of the above claim(s)
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`is/are withdrawn from consideration.
`
`E] Claim(s)
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`is/are allowed.
`
`Claim(s) 1—10 and 12—22 is/are rejected.
`
`[:1 Claim(s) _
`
`is/are objected to.
`
`) ) ) )
`
`6 7
`
`8
`
`
`
`are subject to restriction and/or election requirement
`[j Claim(s)
`9
`* If any claims have been determined aflowabie. 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.jsp 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
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`is/are: a)D accepted or b)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).
`
`Priority under 35 U.S.C. § 119
`12):] Acknowledgment is made of a claim for foreign priority under 35 U.S.C. § 119(a)-(d) or (f).
`Certified copies:
`
`a)D All
`
`b)I:J Some”
`
`c)C] None of the:
`
`1.[:] Certified copies of the priority documents have been received.
`
`2.[:] 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) C] Notice of References Cited (PTO-892)
`
`Information Disclosure Statement(s) (PTO/SB/08a and/or PTO/SB/08b)
`2)
`Paper NoIS)/Mai| 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 20181206
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 2
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`DETAILED ACTION
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`1.
`
`This action is written in response to applicant’s correspondence filed 8/24/2018.
`
`Applicant has amended claims 1-2, 7-10 and 17-18, and added new claims 21 -22.
`
`Claims 1-10 and 12-22 are currently pending for examination. All the amendments and
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`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, the rejection under 35 USC 102 has been withdrawn. In view of applicant’s
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`persuasive argument that “to modify the cDNA microarray of Lewin to add members
`
`from the gene [per the teaching of Carr] runs counter to Lewin’s explicit efforts to screen
`
`out redundant members of the library” (see pages 9-10 of applicant’s response filed
`
`8/24/2018), the 103 rejection over Lewin in view of Carr has been withdrawn. However,
`
`the 103 rejection based on the Tian reference has been maintained.
`
`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 3
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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
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`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 13-22 are rejected under 35 U.S.C. 103 as being unpatentable
`
`over Tian et al. (Nature 2004, 432:1050-1054).
`
`Regarding claims 1, 2, 4-10, 13 and 21 -22
`
`Tian et al. disclose a polynucleotide cDNA library, comprising thousands of
`
`polynucleotides that collectively encode cDNA sequences for 21 E. coli genes (see
`
`Abstract; page 1052, paragraph bridging columns 1-2), wherein at least 89% 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 page 1052, column 1, paragraph 2; Table 1. The error rate of “1 in 1,394
`
`bp”, for the 70-mer polynucleotides in the library of Tian et al., means that about 95%
`
`(Le, 1 — 70/1394 2 95%) of the polynucleotides have no errors. Furthermore, since the
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`recited “sequences received in the instructions provided in the computer readable non-
`
`transient medium” are neither disclosed nor defined in any way, the recited comparison
`
`is completely arbitrary and is thus meaningless. For example, when the actual
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`sequences of the polynucleotides in library of Tian et al. are the sequences received in
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 4
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`the instructions provided in a computer readable non-transient medium, 100% of the
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`polynucleotides in the library of Tian et al. would have no errors compared to the
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`sequences received in the instructions provided in the computer readable non-transient
`
`medium.), and wherein each of the polynucleotides comprises a first overlap region
`
`which is complementary to a second overlap region of another polynucleotide of the
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`polynucleotides (see page 1052, paragraph bridging columns 12 “Our computer-aided
`
`design software (CAD-PAM) designed overlapping 50-bp oligonucleotide sequences
`
`(embedded in 70-mers) for the 21 ribosomal genes and synthesized them all on a 4K
`
`Xeochip.”), such that a plurality of genes (e.g., the 21 E. coli ribosomal genes, g any
`
`combination of genes selected from the 21 E. col/ribosomal genes) are formed when a
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`subset of the polynucleotides are assembled (Abstract; page 1052, paragraph bridging
`
`columns 1-2). Tian et al. do not specifically disclose the particular numbers regarding
`
`the polynucleotides or the particular numbers regarding the encoded genes as recited in
`
`the claims. Tian et al. also do not specifically disclose that the first overlap region
`
`comprises at least 10 bases in length or 10 to 50 bases in length as recited in the
`
`claims.
`
`However, Tian et al. teach that, for the polynucleotide cDNA library discussed
`
`above, only a small fraction of a microchip’s synthetic capacity was used (see page
`
`1053, column 1, paragraph 2). Tian et al. further teach that “[t]he next stage in testing
`
`the limits to simultaneous synthesis and assembly will employ 95,000—382,000
`
`oligonucleotides per $700 microchip from Nimblegen (yielding 2—18 Mbp)” and that
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`“[t]he first such assembly has been successful (see http://arep.med.harvard.edu/SBP/)”
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`(see page 1053, column 1, paragraph 2). Furthermore, Tian et al. teach that the needs
`
`
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`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 5
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`to make sufficient supply of custom genes and genomes for the emerging field of
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`synthetic biology can be met by “performing massively parallel custom syntheses on
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`microchips” (see page 1050, the first two paragraphs after the Abstract). In addition,
`
`Tian et al. teach that the technology as demonstrated in synthesizing the polynucleotide
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`cDNA library as discussed above “is currently enabling us to improve and test
`
`components needed for the synthesis of ribosomes in vitro”, and that “[o]ur ability to
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`remap a whole set of genes from the Mycoplasma18 codons to those of E. coli (for
`
`example, by eliminating the UGA ‘stop’ codon and changing G + C content from 25% to
`
`51%) will help us to calibrate proteomics experiments, test de novo protein designs and
`
`identify new biochemical activities, including those that are missing from our list of the
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`core components of novel self-replicating systems” (page 1053, column 1, paragraph 3).
`
`Thus, 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 utilize a single microchip’s full
`
`
`synthetic capacity and/or to perform massively parallel custom syntheses on multiple
`
`microchips, as taught by Tian et al., for purposes of making sufficient supply of custom
`
`genes and genomes for the emerging field of synthetic biology thus arriving at the
`
`particular numbers regarding the polynucleotides and the particular numbers regarding
`
`the encoded genes as recited in the claims, because the combined teachings of Tian et
`
`al. suggested so.
`
`In addition, changes in size/proportion (e.g., scaling up by using
`
`larger size/proportion of the microchip as used by Tian et al.) are considered to be
`
`prima facie obvious (see MPEP 2144.04(IV)(A)), and mere duplication of parts (e.g.,
`
`using many of the same microchips for massively parallel syntheses of multiple sets or
`
`subsets of polynucleotides) is deemed prima facie obvious (see MPEP 2144.04(Vl)(B)).
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 6
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`Regard the preferred or optimal length range of the first overlap region 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 length range in the
`
`polynucleotide cDNA library as taught or rendered obvious by Tian et al. via routine
`
`experimentation thus arriving at the preferred or optimal length 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 214405.”).
`
`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
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`claimed polynucleotide cDNA library over the polynucleotide cDNA library as taught or
`
`rendered obvious by Tian et al. (see MPEP 2113).
`
`Regarding claim 3
`
`The polynucleotide cDNA library as taught or rendered obvious by Tian et al.,
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`wherein each of the polynucleotides is isolated (e.g., isolated in a separate chamber or
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`feature of the microchip (see page 1051, column 1, paragraph 3; Figure 2), g isolated
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`
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`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 7
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`during the hybridization selection step (see page 1052, column 1, paragraph 2; Figure
`
`1)).
`
`Regarding claims 14 and 15
`
`The polynucleotide cDNA library as taught or rendered obvious by Tian et al.,
`
`wherein each polynucleotide is 70 bases in length (see page 1052, paragraph bridging
`
`columns 1-2).
`
`Regarding claim 16
`
`Although Tian et al. do not specifically teach the length 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 length range in the polynucleotide cDNA library as taught or rendered obvious by
`
`Tian et al. via routine experimentation thus arriving at the working or optimal length
`
`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 214405.”).
`
`Regarding claims 17 and 18
`
`The polynucleotide cDNA library as taught or rendered obvious by Tian et al.,
`
`wherein each of the genes (obtained via sequential PAM reactions) can be at least 3 kb
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 8
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`in length or as long as 14.6 kb in length (page 1052, paragraph bridging columns 1-2;
`
`page 1053, column 2, paragraph 3).
`
`Regarding claims 19 and 20
`
`The polynucleotide cDNA library as taught or rendered obvious by Tian et al.,
`
`wherein the polynucleotides are attached to a structure which is a solid support (e.g.,
`
`microchip) (see Abstract; page 1052, paragraph bridging columns 1-2).
`
`6.
`
`Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Tian et al.
`
`(Nature 2004, 432:1050-1054) as applied to claim 1 above, and further in view of
`
`Hodgson (US 2002/0025561 A1) and Kini et al. (US 2009/0285825 A1).
`
`The polynucleotide cDNA library of claim 1
`
`is taught or rendered obvious by Tian
`
`et al. as discussed above. Tian et al. do not specifically disclose the use of the particular
`
`GC content range in the first overlap region as recited 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
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 9
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`overlap region, based on the teachings of Hodgson and Kini et al., used in the
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`polynucleotide cDNA library of Tian 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 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”). 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 amendments and arguments filed on 8/24/2018 have been fully
`
`considered.
`
`In view of applicant’s amendment to claim 1, the rejection under 35 USC
`
`102 has been withdrawn. In view of applicant’s persuasive argument that “to modify the
`
`cDNA microarray of Lewin to add members from the gene [per the teaching of Carr]
`
`runs counter to Lewin’s explicit efforts to screen out redundant members of the library”
`
`(see pages 9-10 of applicant’s response filed 8/24/2018), the 103 rejection over Lewin
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 10
`
`in view of Carr has been withdrawn. However, the 103 rejection based on the Tian
`
`reference has been maintained, and applicant’s argument directed at the maintained
`
`rejection is found unpersuasive.
`
`In response to applicant’s first argument (see pages 6-7 of applicant’s response
`
`filed 8/24/2018), the primary structure of each polynucleotide in the claimed library is
`
`just the nucleotide sequence of said polynucleotide, and has nothing to do with how it’s
`
`made. Since the nucleotide sequences of the “preselected cDNA sequences” as recited
`
`in the claim are not specified or defined in any way, the recitation “wherein at least 80%
`
`of the at least 20,000 polynucleotides have no errors compared to the preselected
`
`cDNA sequences received in the instructions provided in the computer readable non-
`
`transient medium” does NOT impose any structural limitation on the polynucleotides in
`
`the claimed library because the structure of each polynucleotide is ONLY defined by its
`
`specific nucleotide sequence but NOT how it’s made. As a simple example, George
`
`made a polynucleotide having the nucleotide sequence “AACCGGTT”, with no error
`
`occurred during the synthesis (i.e., the polynucleotide made has no error compared to
`
`preselected sequence); whereas Thomas intended to make a polynucleotide having the
`
`nucleotide sequence “TACCGGTT” (which differs from the polynucleotide made by
`
`George by the 5’-terminal nucleotide), but had an error during the synthesis and actually
`
`got the same polynucleotide as the polynucleotide made by George. Clearly, the
`
`polynucleotide made by George is structurally indistinguishable from the polynucleotide
`
`made by Thomas, even though they were made in different ways (i.e., one was made
`
`with no sequence error compared to preselected sequence, whereas the other was
`
`made with a sequence error compared to preselected sequence).
`
`
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`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 11
`
`Applicant’s second argument is as follows:
`
`miscas:*ah‘tsafex having at \amaimeamm.1331?» mar:
`
`§.aaaaa-a1zaa§3¥a< mam armraaaii as: aaf’alaa: :aaaaamiaied away.
`
`This is not found persuasive. First, as discussed in the rejection w as
`
`discussed in the response to applicant’s first argument above, the recitation regarding
`
`errors compared to preselected sequences does NOT distinguish the claimed library
`
`over the Tian reference.
`
`Furthermore, even if the recitation regarding errors compared to preselected
`
`sequences is considered, the scaled-up library as taught or rendered obvious by Tian et
`
`al. still meets the claim when the scale-up is performed using iLallel syntheses on
`
`multiple microchips followed by hybridization selection on the multiple pools generated
`
`from the multiple microchips separately (which would not lead to lower error rate).
`
`Conclusion
`
`8.
`
`THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time
`
`policy as set forth in 37 CFR 1.136(a).
`
`
`
`Application/Control Number: 15/602,991
`Art Unit: 1639
`
`Page 12
`
`A shortened statutory period for reply to this final action is set to expire THREE
`
`MONTHS from the mailing date of this action.
`
`In the event a first reply is filed within
`
`TWO MONTHS of the mailing date of this final action and the advisory action is not
`
`mailed until after the end of the THREE-MONTH shortened statutory period, then the
`
`shortened statutory period will expire on the date the advisory action is mailed, and any
`
`extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of
`
`the advisory action.
`
`In no event, however, will the statutory period for reply expire later
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`than SIX MONTHS from the mailing date of this final action.
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`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
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`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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`published applications may be obtained from either Private PAIR or Public PAIR.
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`Status information for unpublished applications is available through Private PAIR only.
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`Application/Control Number: 15/602,991
`Art Unit: 1639
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`Page 13
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`For more information about the PAIR system, see http://pair-direct.uspto.gov. Should
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`you have questions on access to the Private PAIR system, contact the Electronic
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`Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a
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`USPTO Customer Service Representative or access to the automated information
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`system, call 800-786-9199 (IN USA OR CANADA) or 571 -272-1 000.
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`/KAIJIANG ZHANG/
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`Primary Examiner, Art Unit 1639
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