PCT/US2016/052336 07.12.2016
`
`PATENT COOPERATION TREATY
`
`PCT
`
`INTERNATIONALSEARCH REPORT
`
`(PCT Article 18 and Rules 43 and 44)
`
`Applicant’s or agent’s file reference
`44854-7 18601
`
`FOR FURTHER
`ACTION
`
`see Form PCT/SA/220
`as well as, where applicable, item 5 below.
`
`| TWIST BIOSCIENCE CORPORATION
`
`{Earliest} Priority Date (day4month/year)
`
`18 September 2015 (18.09.2015}
`
`International application No.
`
`PCTMUS18/52336
`Applicant ——
`
`|
`
`b.t| none ofthe figures is to be published with the abstract.
`
`This international search report has been prepared bythis International Searching Authority and is transmitted to the applicant
`according to Article 18. A copy is being transmitted to the International Bureau.
`This international search report consists ofa total of a)a sheets.
`tj it is also accompanied by a copy of each prior art document cited in this report.
`
`Basis of the report
`
`a With regard to the language,the international search was carried out on the basis of
`<I the international application in the language in which it was filed,
`which is the language of
`[ a translation ofthe international application into
`a translation furnished for the purposes of international search (Rules 12.3(a) and 23.1(b)).
`b. i] This international search report has been established taking into account the
`rectification of an obvious mistake
`authorized by or notified to this Authority under Rule 91 (Rule 43.6 dis(a)).
`With regard to any nucleotide and/or amine acid sequence disclosed in the international application, see Box No. 1.
`CI Certain claims were found unsearchable (see Bax No. ID.
`
`c.
`
`7 Unity of invention is lacking (see Box No. 11D.
`
`. With regard to the title,
`
`the text is approved as submitted by the applicant.
`tt the text has been established by this Authority to read as follows:
`
`With regard to the abstract,
`
`the text is. approved as submitted by the applicant.
`[| the text has been established, according to Rule 38.2, by this Authority as it appears in Box NdV. The applicant may,
`within one month from the date of mailing of this international search report, submit comments to this Authority.
`
`‘With regard to the drawings,
`a.
`the figure of the drawings to be published with the abstract is Figure No.
`4 as suggested by the applicant.
`{| as selected by this Authority, because the applicant failed to suggest a figure.
`i|as selected by this Authority, because this figure betier characterizes the invention.
`
`14
`
`Form PCT/SA/2Z 10 (first sheet) (January 2015)
`
`

`

`PCT/US2016/052336 07.12.2016
`
`INTERNATIONAL SEARCH REPORT
`
`
`
`International application No.
`PCTAUS 18/$2336
`
`Box No. I
`
`Nucleotide and/or amine acid sequence(s} (Continuation of item 1.c of the first sheet}
`
`i. With regard to any nucleotide and/or amino acid sequence disclosed in the international application, the international searchwas
`carried out on the basis of a sequence listing:
`
`a
`
`b.
`
`forming part of the international application as filed:
`
`
`Px¢i
`inthe form of an Annex C/ST.25 text file.
`| on paper or in the form of an imagefile.
`
`furnished together with the international application under PCT Rule i3¢er.1(a) fer the purposes of international search
`only in the form of an Annex C/ST.25 text file.
`
`G.i| furnished subsequent to the international filing date for the purposes ofintemational search only:
`Py in the form of an Annex C/ST.25 text file (Rule Jer. 1{a)).
`[ on paper or in the form of an image file (Rule [¥er.1(o) and Administrative Instructions, Section 713).
`
`2. [I In addition,in the case that more than one version or copy of a sequencelisting has been filed or furnished, the required
`statements that the information in the subsequent or additional copies is identical to that forming part of the application as
`filed or does not go beyond the application as filed, as appropriate, were furnished.
`
`3. Additional comments:
`
`Form PCT/ISA/2 10 (continuation of first sheet (1)) January 2015)
`
`

`

`PCT/U32016/052336 07.12.2016
`
`INTERNATIONAL SEARCH REPORT
`
`International application Na.
`PCTAUS 16/52336
`
`A.
`
`IPCl8) - CI2N 5/071, 5/10, 15/10; C12Q 1/68; C408 30/06, 40/06, 50/06; AG1K 34/711, 31/7086 (2016.01)
`CPC
`+ C120 V6B, CIZN 15/10, 15/1034, 15/1083; C40B 40/06, 50/06; A61K 34/711, 34/7088
`
`
`
`IPC-C12M 1/00, CT2N 1/49, 5/071, 5/40, 15/10; C120 1/68; C408 30/06; C408 40/08, 50/06, 56/14: AGIK 31/711, 31/7088 (2018.1);
`jOPC:C12M 1/00; C12Q 1/00, 1/68; CIZN 9/00, 18/10, 15/1034, 15/1093; CO7K 16/00; C40B 40/08, 50/05: ABIK 34/711, 31/7088
`
`
`
`Electronic data base consulted during the international search (name of data base and, where practicable, search terms used)
`PatSear (US, EP, WO, JP, DE, GB, CN, FR, KR, ES, AU, IN, CA, INPADOC Data}; Goagle Scholar, EBSCO, PubMed
`Terms: protein, polypeptide, modulate, changes, adjust, array, plurality,library, collection, nucleotides, DNA, RNA, express, transcribe,
`translate, surface, area, extend, attach, cover, variant, antibody,
`
`C. DOCUMENTS CONSIDERED TO BE RELEVANT
`
`Category*
`
`x
`7
`¥
`¥
`
`¥
`
`Px
`
`PX
`
`
`Citation of document, with indication, where appropriate, ofthe relevant passages
`Relevant to claim No.
`
`WO 2015/021080 AZ (TWIST BIOSCIENCE CORPORATION} 12 February 2015; {0005},
`
`{0608}, [OO16]-[0017}, [0041], [0046], 00205), [60250], (00387), [o0406), [o0459}, f00507},
`{1-26
`{60504}
`14-26
`WO 2014/035683 A2 (THE SCRIPPS RESEARCH INSTITUTE) 06 March 2074: paragraphs
`{9004}-[0005}, [OG09}-{60 10}, [0035], [0044], [6073], (0077), [0084], [0083], jo086}, {OO1144,
`i
`{00162}
`
`US 2013/0045483 A1 (TREUSCH,S et ai.) 21 February 2013; paragraph [0172]
`
`US 2016/0220884 Ai (TWIST BIOSCIENCE CORPORATION) 11 August 2016; entire
`document
`
`US 2016/0264958 Al (TWIST BIOSCIENCE CORPORATION) 15 September 2046; entire
`document
`
`9, 24-26
`
`1-35
`
`1-35
`
`
`i P| Further documents are listed in the continuation of Box C.
` r| See patent family annex.
`wpe
`Special categories of cited documents.~
`later document published after the international filing date or prionty
`an
`document defining the general state of the art which is not considered
`date and not in conflict with the application but cited
`to understand
`to be of particular relevance
`the principle or theory underlying the invention
`earlier application or patent but published on or after the international «46°
`document of particular relevance: the claimed invention cannot be
`filing date
`considered novel or cannot be considered to involve an inventive
`step when the documentis taken alone
`document which may throw doubts on priority claim(s) or which is
`sited tc establish the publication date of another citation or other
`document of particular relevance; the claimed invention cannot be
`special reason (as specified}
`considered to involve an inventive step when the documentis
`document referring to an oral disclosure, use, exhibition or other
`combined with one or more other such documents, such combination
`means
`being obvious to a person skilled in the art
`document member of the same patent family
`
`document published prios to the international filing date but later than “ee
`the priority date claimed
`
`sy
`
`¥ “
`
`ape
`
`yp
`
`“cy”
`
`“pe
`
`Mail Stop PCT, Alin: ISA/JUS, Commissioner for Patents
`P.O. Box 1450, Alexandria, Virginia 22313-1450
`| Facsimile No. 574-273-8300
`
`Authorized officer
`
`PCT Helpdesk: §74-272-4300
`
`Date of mailing of the international search report
`
`O7 DEC 7016
`
`Shane Thomas
`
`POT OSP: 573-272-7774
`
`

`

`PCT/US2016/052336 07.12.2016
`
`PATENT COOPERATION TREATY
`
`Fromthe
`INTERNATIONALSEARCHING AUTHORITY
`
`To: David Harburger
`
`Wilson Sonsini Goodrich & Rosati
`650 Page Mill Road
`Palo Alto, California 94304
`United States of America
`
`PCT
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`(PCT Rule 43 bis.1)
`
`OF DEC 2016
`
`
`
`Date of mailing
`idaymonnivesr)
`
`Applicant’s or agent’s file reference
`44854-718601
`
`international application No.
`POTAIS 16/52336
`| international Patent Classification (IPC) or both national classification and [PC
`IPC(8) - C12N 5/074, 5/10, 15/10; C120: 1/68; C40B 30/06, 40/06, 50/06; AS1K 31/711, 34/7088 (2016.01)
`CPC -
`1/7O88
`Applicant ast BIOSCIENCE CORPORATION
`
`i,
`
`Box No.
`
`t
`
`Basis of the opinion
`
`Box No. tf
`
`Priority
`
`Box No, HI Non-establishment of opinion with regard to novelty, inventive step and industrial applicability
`
`Box No. TY
`
`Lack of unity of invention
`
`Box No. V
`
`Box No Vi
`
` Reasoned statement under Rule 43bis.1(a}{i} with regard to novelty, inventive step and industrial applicability;
`citations and explanations supporting such statement
`Certain documents cited
`
`Box No. VEE Certain defects in the international application
`
`Box No. VILE Certain observations on the international application
`
`FURTHER ACTION
`
`Ifa demand forinternational preliminary examination is made, this opinion will be considered to be a written opinionof the
`International Preliminary Examining Authority (IPEA”} except that this does not apply where the applicant chooses an Authority
`other than this one to be the IPEA and the chosen IPEA has notified the Intemational Bureau under Rule 66.1 Sis{b) that written
`opinions of this International Searching Authority will not be so considered,
`[fthis opinion is, as provided above, considered to be a written opinion of the IPEA,the applicant is invited to submit to ts IPEA
`a written reply together, where appropriate, with amendments, before the expiration of 3 months from the date of mailing of Fom
`PCT/IS4/228 or before the expiration of 22 months from the priority date, whichever expires later.
`For further options, see Form PCT/ISA/220,
`
`Mail Stop PCT, Attn: ISA/US
`Coriissioner for Patents
`>
`4
`P.O. Sox 1450. Alexandria, Virginia 22313-1450 Vf November 2016 a 7.474.201 $)
`Facsimile No, 571-273-8300
`
`Form PCTASA/237 (cover sheet} (January 2015}
`
`Authorized officer
`
`Shane Thomas
`POT Holpiesk: 874-272-4300
`POT OSP: 874-272-7774
`
`

`

`l. With regard to the language, this opinion has been established on the basis of:
`
`the international application in the language in which it was filed.
`Cy a translation of the international application into
`furnished for the purposes of international search (Rules 12.3(a) and 23.1(b).
`
`which is the language ofa translation
`
`2. ‘- This opinion has been established taking into account therectification of an obvious mistake authorized by or notified to
`this Authority under Rule 91 (Rule 43 bis. 1(a).
`
`3.
`
`|
`In addition, im the case that more than one version or copy of a sequence listing has been filed or furnished, the required
`Statements that the informationin the subsequent or additional copies is identical to that forming part ofthe application as |
`filed or does not go beyond the application as filed, as appropriate, were furnished.
`i
`
`PCTIUS2016/052336 07.12.2016
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`|
`
`international application No.
`PCTIUS 16/52336
`
`Box No. I
`
`Basis of this opinion
`
`[S<] Withregard to any aucleotide and/or amine acid sequence disclosed in the international application, this opinion has
`been established on the basis of a sequence listing:
`isé i forming part ofthe international application as filed:
`DY| in the form of an Annex C/ST.25 text file.
`i on paper or in the form of an image file.
`furnished together with the international application under PCT Rule 13 ser. i (a) for the purposes ofintemational
`search only in the form of an Annex C/ST.25 text file.
`c. | furnished subsequent to the international filing date for the purposes of international search only:
`[| in the form ofan Annex C/ST.25 text file (Rule 13¢er.1{a)).
`i on paper or in the form ofan image file (Rule 13ser.1(b) and Administrative Instructions, Section 713).
`
`Additional comments:
`
`

`

`PCT/US2016/052336 07.12.2016
`
`INTERNATIONAL SEARCHING AUTHORITY
`
`PCTAIS 16/52336
`
`Box No. ¥
`
`Statement
`
`Novelty (N)
`
`faventive step CS}
`
`industrial applicability CLA}
`
`Citations and explanations:
`
`Claims
`Claims
`
`Claims
`Claims
`
`Claims
`Claims
`
`Claims 27-35 lack novelty under PCTArticle 33(2)} as being anticipated by WO 2015/021080 A2 (TWIST BIOSCIENCE CORPORATION)
`(hereinafter “Twist’).
`
`Intemational application No. WRITTEN OPINION OF THE
`
`As perclaim 27, Twist discloses a method for nucleic acid synthesis (synthesized nucieic acids: paragraph [0005}}, the method
`comprising: a} providing predetermined sequences (predetermined sequences; paragraph (60051) encoding for a plurality of non-identical
`aligonucieic acids (thousands to hundreds of thousands of unique oligonucleotides; paragraph [06406}), wherein each of the non-identical
`aligonucieic acids is at least 20 bases in length {at least S00 bp; paragraph [0008}), and wherein the plurality of non-identical oligonucteic
`acids encodes for up ta 19 variants for each of at least 3 codonsfor at least one sequence (ihe inkjet assembly can comprise at least
`1-100 or more inkjet heads. The inkjats heads may each depssit a different codonbuilding blocks, comprising an adenine, guanine,
`i
`thyming, cytosine, or uridine group, or a modified nucleotide; paragraphs [0046], (60556)}, and wherein the plurality of non-identical
`oligonucleic acids collectively encodes for at least one gene and variants thereof (at least one of the synthetic genes differs from any other |
`synthetic gene by atleast 0.1 %; paragraph [0005)); b} providing a structure having a surface (microstructures fabricated into a support
`j
`surface; paragraph [0016}); c} synthesizing the pluratity of non-identical oligonucieic acids (synthesizing thousands to hundreds of
`thousands of unique oligonuclestides; paragraphs [0005], [00406}}, wherein each of the non-identical aligonucleic acids extends from the
`surface (ihe coating of reagents comprises oligonucleotides; paragraph {6017]}}; and d} assembling a library of variant nucleic acids from
`the plurality of non-identical cligonucleic acids (gene library comprises a collection of genes; paragraph [G005)).
`
`{As per claim 28, Twist discloses the method of claim 27, and Twist further discloses wherein the plurality of non-identical cligonucieic
`acids comprises at least 75,000 non-identical oligenucleic acids (ihousands to hundreds of thousands of unique oligonucleotides:
`paragraph {O0406}).
`
`As per claim 29, Twist discloses the method of claim 27, and Twist further discloses wherein a subset of the plurality of non-identical
`oligonucisic acide collectively encodes for a single gene and variants thereof (at least one of the synthetic genes differs from any other
`synthetic gane by atleast 0.1%) paragraph (0065) is located within a single cluster on the surface of the structure (the resalved loci can
`be clustered in close proximity to form one or more circular region: paragraph (00205).
`
`As per claim 30, Twist discloses the method of claim 29, and Twist further discloses wherein the surface of the structure comprises at least
`6006 of the single clusters (ihe surface has a density of resolved loci of about 1 to about 00006 sites per 1 mm2; paragraph (00256).
`
`As per claim 31, Twist discloses the method of claim 30, and Twist further discloses wherein each clusteris jacated within a channel about
`6.5 to 2 mm in diameter (channels is wider than 50 micrometers in diameter, paragraph [GO16]).
`
`As per claim 32, Twist discloses the method of claim 29, and Twist further discloses wherein the singie cluster comprises SO to 500 foci
`(the surface has a density of resolved loci of about 1 to about 500000 sites per 1 mm*2; paragraph [00250)) for nucleic acid extension.
`
`As per claim 33, Twist discloses the method of claim 27, and Twist further discloses wherein the plurality of non-identical oligonucteic
`acids collectively encode for variants of more than cone gene (cornprises at isasi 100 different preselected synthetic genes; paragraph
`{G005}}).
`
`As per cairn 34, Twist discloses the method of claim 27, and Twist further discloses wherein the plurality of non-identical oliganucleic
`acids collectively encode for variants of at least 5,000 genes (ihe collection comprises at least 5000 genes: paragraph [0605)).
`
`As per claim 35, Twist discloses the method of clair 27, and Twist further discloses wherein the library of variant nucieic acids encodes
`j for at least a portion of an enzyme, peptide (genes encodes for components ofa first metabolic pathway; paragraph [OO0Sh, or antibody.
`Continued Within the Next Supplemental Box-***-
`
`Form PCT/SA/237 (Box No. V) January 2015)
`
`

`

`Box No. Vi
`
`Certain documents cited
`
`Certain published documents (Rules 43 bis.1 and 70.10)
`
`Application No.
`Patent No.
`US 2016/0229884 At
`US 2016/0264958 Ai
`
`Publication date
`{day/month/vear)
`1/08/2016
`15/09/20 16
`
`Filing date
`(day/month/vear}
`O3/G2/2016
`13/05/2016
`
`Kind of non-wriiten disclosure
`
`Date of non-written disclosure
`(day/monti'year}
`
`Date of written disclosure
`referring to non-written disclosure
`
`PCTIUS2016/052336 oy. 2.2016
`
`WRITTEN OPINION OF THE
`“INTERNATIONAL SEARCHING AUTHORITY
`
`International application No.
`PCTIUS 16152336
`
`j
`
`Priority date (valid claim)
`(day/month/year)
`OAMO2/2015
`04/02/2015
`
`(day/month/vear}
`
`Form PCTASA/237 (Box No. VD Ganuary 2015)
`
`

`

`PCT/US2016/052336 07.12.2016
`
`WRITTEN OPINION OF THE
`.
`ae
`“
`-.
`~
`:
`INTERNATIONALSEARCHING AUTHORITY
`
`international application No.
`POTIUS16/82336
`
`Box No. VE Certain defects in the international application
`
`The following defects in the form or contents of the international application have been noted:
`
`Ciaim 11 is objected to under PCT Rule 66.2(a\iii} as containing the folowing defect in the form or contents thereof: in line 17 of claim 11,
`i
`the term “ireated at least’ is believed to be a typagraphical error and for the purposesof this opinion will be interpreted as the tern “treated!
`i with atleast”,
`
`Form PCT/ISA/237 (Box No. VID Ganuary 2015)
`
`

`

`PCT/US2016/052336 07.12.2016
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`international application No.
`PCTIUS 16/82336
`
`Supplemental Box
`
`
`in casé the space in any of the preceding boxes is not sufficient.
`Continuation of:
`
`"Continued from Box V: Citations and Explanations-***-
`
`Ciaims 1-8, 10-23 jack an inventive step under PCT Article 33(3) as being obvious over WO 2014/035683 A2 (THE SCRIPPS RESEARCH
`INSTITUTE} (hereinafter "Scripps”) in view of Twist.
`
`As per ciaim 7, Soripps discloses a method for modulating protein activity (methedsforidentifying modulatory protein agents, 3.9.,
`antibodies or other polypeptides; paragraph [0004]}, the methad comprising: e) transferring the library of variant nucleic acids to cells and
`expressing a plurality of variant proteins (methods entail first expressing in a population of cells of a eukaryotic ceil type a library of
`candidate agents; paragraph [G004]}; and 4} identifying an activity associated with a variant protein of the plurality of variant proteins,
`wherein the activity is modulated relative io a protein encoded by ihe single reference sequence (the modulated phenotypes can be
`initiation of or alteration in a process or activity linked ta signal transduction cascades; paragraph [0081}). Scripps does not disclose the
`method comprising: a) providing pradetermined sequences encoding for at least about 30,000 non-identical oligonucteic acids, wherein
`{ eachof the al least about 30,000 non-identical ofigonucteic encodes for a variant codon sequence compared to a single reference
`} sequence; b) providing a structure having a surface, c} synthesizing the al least about 30,000 non-identical oligonucieic acids, wherein
`each of the at iaast about 30,000 non-identical cligenucleic acids extends from the surface; d} mixing the feast about 30,000 non-identical
`dligonucteic acids with a DNA polymerase and the single reference sequence to form a library of variant nucleic acids. However, Twist
`does disclose the method comprising: a} providing predetermined sequences encoding for at least about 30,600 non-identical oligonuclaic
`acids, whersin each of the at least about 30,000 non-identical oligonucieic encodes for a variant codon sequence compared to a single
`reference sequence (predetermined sequences for thousands to hundreds of thousarics of unique/ variant oligonucleotides compared to
`the witd-lype/desired sequences; paragraphs {0005}, [00387], [06406], [G0504))}; b} providing a siructure having a surface (microstructures
`fabricated inte a support surface: paragraph [0016})c) synihesizing the ai teast about 30,000 non-identical cligonucleic acids, wherein
`each of the at least about 30,000 non-identical oliganucleic acids extends from the surface (thousands to hundreds of thousands of unique
`dligonucleotides are the coating of reagents of the surface; paragraph [0917], [00406}}: d) mixing the least about 30,000 non-identical
`oligonucieic acids with a DNA polymerase and the single reference to form a library sequence of variant nucteic acids (mixing thousands td
`hundrads of thousands of unique cligonucleotides with a suitable polymerase along with the wild-type/desired sequences to form a gane
`i
`library of gene variants; paragraph [0005], [0041], [00406}, {00459}, [00501], (60504}}.
`It would have been obvious to one af ordinary skill
`|
`in the art at the time of the invention to modify the Scripps invention to provide a gene library of a plurality of gene. variants, as taught by
`Twist, in order to provide a large format. screening mathad to identify proteins that modulate cellular furctions.
`
`As par claim 2, Scripps and Twist, in combination, disclose the method of claim 1, and Scripps further discloses wherein the activity
`comprises cellular reproduction, growth, adhesion, death, migration, energy production, oxygen utilization, metabolic activity, cell signaling
`(ihe modulated phenotypes can beinitiation of or alteration in a process or activity linked to signal transduction cascades; paragraph
`JOO84)}, aging, response te free radical damage, or any combination thereof.
`
`As per claim 3, Scripps and Twist, in combination, disctose the method of claim 1, and Scripps further discloses wherein the cells are
`eukaryotic calls (of eukaryotic cells; paragraph {0004} or prokaryotic cells.
`
`j As per claim 4, Scripps and Twist, in combination, disclose the method of claim 1, wherein the cells are bacterial, plant, mouse (study of
`|
`the activity of our agonist antibodies in the mouse feasible; paragraph [00162)), or primate cells.
`
`As per claim 5, Scripps and Twist, in combination, disclose the method of claim 1, Scripps does nat disclose wherein the library of variant
`nucleic acics encodes sequences for variant genes or fragments thereat. However, Twist doas disclose wherein the library of variant
`nucleic acids encodes sequences for variant genes (gene variants; paragraph [00501}) or fragmants thereof.
`it wauld have been obvious
`io one of ordinary skill in the art ai the time of the invention to modify the Scripps invention te provide sequences for variant genes, as
`taught by Twist, in orcer to provide a plurality of novel polypeptides to screen for modulatory behavior.
`
`As perclair 6, Scripps and Twist, in combination, disclose the method of claim 1, and Scripps further discloses wherein the variant protein
`is an antibody (antibodies; paragraph [00162}), enzyme or peptide.
`
`AS per claim 7, Scripps and Twist, in combination, disclose the method of claim 1, and Scripps further discloses wherein the variant proteirg
`has enhanced or reduced binding affinity for another molecule (differant binding specificities; paragraph [0035)).
`
`As per claim 8, Scripps and Twist, in combination, disclose the methed of claim 1, and Scripps further discloses wherein the variant proteir i
`has enhanced or reduced (agonist activity was lost; paragraph [00197}} enzyrnalic activity.
`i
`
`As per claim 10, Scripps and Twist, in combination, disclose the method of claim 1, but Scripps does not disclose wherein the atleast
`about 30,000 nor-identical oligonucieic acids have an aggregate error rate of less than 1 in 1000 bases compared to predetermined
`sequences for the plurality of nan-identical oligonucieic acids. However, Twist does disclose wherein the atleast about 30,000
`non-identical otigonucieic acids (thousands to hundreds of thousands of unique oligonucleotides; paragraph [00406)} have an aggregate
`error rate of less than 1 in 1000. bases compared to predetermined sequences for the plurality of non-identical oligonucisic acids (error rate
`of less than 1 in 3000 bp compared to predetermined sequences comprising the genes; paragraph [0005)).
`kh would have been obvious te
`one of ordinary skillin the art af the ime of the invention to modify the Scripps invention to provide an aggregate error rate of less than 1 in
`1000 bases, as taught by Twist, in order to provide known sequences that have not mutated during the amplification and/or cloning
`process.
`
`;
`
`-"*-Continued Within the Next Supplemental Box-***-
`
`

`

`PCT/US2016/052336 07.42.2016
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`P International application No.
`
`POCTAIS16/52336
`
`Supplemental Box
`
`
`Tn case the space in any of the preceding boxes is not sufficient,
`Continuation of
`
`~**Continued from Previous Supplemental Box-***-
`
`As perclaim 11, Scripps discloses. a method for modulating cellular activity (the invention provides methods for identifying protein or
`polypeptide agents (antibodies, polypeptides or peptides) which are capable of reprograming or trans-differentiating a target cell;
`paragraph {0010)), the method comprising: 9) transferring the library of variant nucleic acids to a first set of ceils (methods antail first
`| expressing in a population of calls of a eukaryotic cell type a library of candidate agents; paragraph [O004]); and f} measuring a changein 4
`| cellular activity (cells are analyzed using anoptical system that can measure spatial; paragraph {(0086)}}, wherein the cellular activity is
`measured for the first set of cells or a second set of cells, wherein the second sat of calls are treated at least one expression product
`isolated from the first set of celis (antibodies expressed in and secreted fram a second cell are selected for modulators that Kill or inhibit
`{slow or stop) the growth of an indicatorcell; paragraph [0077}). Scripps does not disclose the method camprising: a) providing
`predetermined sequences encoding for at least about 30,000 non-identical oligonucleic acids, wherein each of the at least about 36,000
`non-identical oligonucleic encodes for a predetermined variant sequence compared to a single reference sequence: b) providing a
`structure having 4 surface: c) synthesizing the at least about 36,000 non-identical oligonucleic acids, wherein each of the at least about
`30,000 non-identical oliganucteic acids extends from the surface, and wherein the at least about 30,000 non-identical aligonucieic acids
`have an aggregate error rate of less than 1 in 1000 bases comparedto predetermined sequences for the plurality of non-identical
`oligonuclaic; d) mixing the feast about 30,000 non-identical oligonucteic acids with a DNA polymerase and the single reference sequence
`to form a library of variant nucleic acids. However, Twist does disclose the method cornprising: a} providing predetermined sequences
`{predetermined sequences; paragraph [0005]) encoding for at least about 30,000 non-identical oligonucleic acids (thousands to hundreds
`of thousands of unique oligonucieotides; paragraph [00406}}, wherein each of the at least about 30,006 non-identical oligonucicic encodes
`for a predetermined variant sequence (synthetic variants; paragraph [00387)]) compared to a single reference sequence (wild-type/desired
`sequences; paragraph [00504)}, 0} providing a structure having a surface (microstructures fabricated into a suppor surface; paragraph
`{0016)}, &} synthesizing the at least about 30,000 non-identical oligonucleic acids (Ghousands to hundreds of thousands of unique
`oligonucleotides; paragraph (00406), wherain aach of the at least about 30,000 non-identical oligonucteic acids (thousands to hundreds of
`thousands of unique oligonucisotides; paragraph [00406] extends fram the surface (the coating of reagents comprises otigonucieatides;
`paragraph (00177), and wherein the at least about 30,000 non-identical oligonucteic acids Ghousands to hundreds of thousands of unique |
`oligonucleotides; paragraph [004065)}) have an aggregate errar rate of less than 1 in 1000 bases compared to predetermined sequences forf
`the plurality of non-identical ollgonuciaic acids (error rate of less than 1 in 3000 bp compared to predetermined sequences comprising the i
`; genes; paragraph [GO0S}}; d)} mixing (mixing; paragraph [G044]) the least about 30,006 non-identical oligonucieic acids (thousands to
`i
`hundreds of thousands of unique oligonucleotides; paragraph [00406)) with a DNA polymerase (suitable polymerases; paragraph (00459) |
`and the single reference sequence (wild-type/desired sequences; paragraph (00504)to forrn a library of variant nucleic acids (a gene
`p
`library; paragraph [0005]).
`it would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Scripps
`invention to provide a gene library of a plurality of gene variants, as taught by Twist, in order to provide a large format screening method to
`identify proteins that modulate cellular functions.
`
`48 per claim 12, Scripps and Twist, in combination, disclose the method of claim 14, and Scripps further discloses wherein the cellular
`activity comprises reproduction, growth, adhesion, death, migration, energy production, oxygen ulilization, matabolic activity, cell signating
`{the modulated phenotypes car be initiation of or alteration in a process or activity linked to signal transduction cascades: paragraph
`[0081}), response to free radical damage, or any cormbination thereof.
`
`As per claim 13, Scripps and Twist, in combination, disclose the method of claim 44, and Scripps further discloses wherein the first set of
`catis or the second sel of calls are eukaryotic cells (of eukaryotic oalis; paragraph [0004)}) or prokaryotic cells.
`
`As per claim 14, Scrinps and Twist, in combination, disclose the method of claim 11, and Scripps further discloses wherein the first set of
`ceils or the second set of cells are bacterial, plant, mouse (study of the activity of aur agonist antibodies in the mouse feasible: paragraph
`{00162)), or primate cells.
`
`As per claim 15, Scripps and Twist, in combination, disclose the method of claim 11, Scripps does not disclose wherein the library of
`variant nuciaic acids encodes sequences for variant genes or fragments thereof. Howevar, Twist does disclose wherein the library of
`|
`variant nucleic acids encodes sequences for variant genes (gens variants; paragraph [60501}) or fragments thereof.
`It would have been
`obvious to one of ordinary skill in the art at the time of the inventionto modify the Scripps invention te provide sequences for variant genes!
`as taught by Twist, in order to pravide a plurality of novel polypeptides to screen for modulatory behavior.
`
`| As per claim 16, Scripps and Twist, in combination, disclose the method of claim 15, and Scripps discloses further comprising translation of
`| each of the variant genes to form a@ protein (expressing a library of candidate polypeptide agents; paragraph [0010)}.
`
`As per claim 17, Scripps and Twist, in combination, disclose the method of clair 16, and Scripps discloses wherein the protein is an
`antibody (antibodies; paragraph [00162]}, enzyme, or paptide.
`
`4S par claim 18, Scripps and Twist, in combination, disclose the mathod of claim 17, and Scripps discloses wherein ihe library of variant
`nucieic acids encodes for al least a portion of a variable region (light chain variable regions; paragraph {0605}) or constant ragion of the
`antibody.
`
`As per claim 19, Scripps and Twist, in combination, disclose the methad of claim 16, and Scripps discloses wherein thelibrary of variant
`nucteic acids encodes for at least one CDR ragion (complementarity determining regions (CORs); paragraph [0044)}) of the aniibodly.
`
`As per claim 20, Scripps and Twist, in cornbination, disclose the method of claim 16, and Scripps discloses wherein the protein has
`enhanced or reduced binding affinity for another molecule, or wherein the protein has enhanced or reduced enzymatic activity (agonist
`activity was lost; paragraph [00197}).
`
`"Continued Within the Next Supplerngnial Box-***-
`
`Form PCTASA/237 Gupplemental Box} Ganuary 2015)
`
`

`

`PCT/US2016/052336 07.12.2016
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International application No.
`PCTIUS 16/52336
`
`Supplemental Box
`
`
`
`in case the space in any of the preceding boxes is not sufficient,
`Continuation of:
`
`e.Coniinued from Previous Supplemental Box-***-
`
`As per claim 21, Scripps and Twist, in combination, disclose the methad of claim 11, and Scripps discloses wherein the library of variant
`nucleic acids encodes for a transcription regulatory