PCT/US2019/032992 28.10.2019
`
`PATENT COOPERATION TREATY
`
`PCT
`
`INTERNATIONAL SEARCH REPORT
`
`(PCT Article 18 and Rules 43 and 44)
`
`Applicant’s or agent’s file reference
`44854-776601
`
`FOR FURTHER
`ACTION
`
`see Form PCT/ISA/220
`as well as, where applicable, item 5 below.
`
`International application No.
`PCTIUS 19/32992
`
`International filing date (day/month/year)
`17 May 2019 (17.05.2019)
`
`(Earliest) Priority Date (day/month/year)
`18 May 2018 (18.05.2018)
`
`Applicant
`
`TWIST BIOSCIENCE CORPORATION
`
`Certain claims were found unsearchable (see Box No. II).
`
`Unity of invention is lacking (see Box No. III).
`
`4. With regard to thetitle,
`
`
`This intemational search report has been prepared by this 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 of a total of
`sheets.
`[] It is also accompanied by a copy of each prior art documentcited in this report.
`
` 1. Basis of the report
`
`
`a. With regard to the language,the international search wascarried out onthe basisof:
`
`
`the international application in the language in which it was filed.
`whichis the language of
`C] a translation of the international application into
`a translation furnished for the purposes of international search (Rules 12.3(a) and 23.1(b)).
`
`
`b. [J 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 43.65/s(a)).
`
`With regard to any nucleotide and/or aminoacid sequencedisclosedin the international application, see Box No.I.
`
`
`
`
`
`
`
`
`
`
`
`the text is approved as submitted by the applicant.
`[_] the text has been established by this Authority to read as follows:
`
`
`
`
`
`5. 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 No. [V. The applicant
`
`
`may, within one month from the date of mailing ofthis international search report, submit comments to this Authority.
`
`
`6. With regard to the drawings,
`
`
`a.
`the figure of the drawings to be published with the abstract is Figure No. 1A
`[X]
`as suggested by the applicant.
`
`
`C] as selected by this Authority, because the applicant failed to suggest a figure.
`L| as selected by this Authority, because this figure better characterizes the invention.
`
`
`b. LJ noneofthe figures is to be published with the abstract.
`
`
`Form PCT/ISA/210 (first sheet) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/US 19/32992
`
`Box No. I
`
`Nucleotide and/or amino acid sequence(s) (Continuation ofitem 1.c of the first sheet)
`
`1. With regard to any nucleotide and/or amino acid sequence disclosed in the international application, the international search was
`carried out on the basis of a sequencelisting:
`
`formingpart of the international application asfiled:
`[| in the form of an Annex C/ST.25textfile.
`[} on paperor in the form ofan imagefile.
`furnished together with the international application under PCT Rule 13¢er. I(a) for the purposes of international search
`only in the form of an Annex C/ST.25 textfile.
`
`furnished subsequentto the international filing date for the purposes of international searchonly:
`in the form of an Annex C/ST.25 textfile (Rule 13¢er. 1(a)).
`[| onpaperorin the form ofan image file (Rule 13rer.1(b) and Administrative Instructions, Section 713).
`
`3. Additional comments:
`
`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 subsequentor additional copiesis identical to that forming part of the application as
`filed or does not go beyondthe application as filed, as appropriate, were furnished.
`
`Form PCT/ISA/210 (continuation of first sheet (1)) January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/US 19/32992
`
`Observations where certain claims were found unsearchable (Continuation of item 2 offirst sheet)
`
`
`
`This international search report has not been established in respect of certain claims under Article 17(2)(a) for the following reasons:
`1, [] Claims Nos.:
`because they relate to subject matter not required to be searched by this Authority, namely:
`
`Box No. II
`
`
`
`
`2. [] Claims Nos.:
`
`because they relate to parts of the international application that do not comply with the prescribed requirements to such an
`extent that no meaningful international search can be carried out, specifically:
`
`
`
`
`
`
`
`
`3.
`
`
`Claims Nos.: 5-23, 27-37, 41-58, 63, 65-75, 81-93, 97-107
`because they are dependent claims andare not drafted in accordance with the second and third sentences ofRule 6.4(a).
`
`Box No. IH
`
` Observations where unity of invention is lacking (Continuation of item 3 of first sheet)
`
`This International Searching Authority found multiple inventionsin this international application, as follows:
`
`- see extra sheet for Box No. Ili Observations where unity of invention is lacking -
`
`
`
`
`
`
`
`
`
`
`
`.L] Asall required additional search fees were timely paid by the applicant, this international search report covers al! searchable
`claims.
`
`2. [| Asall searchable claims could be searched withouteffort justifying additional fees, this Authority did not invite payment of
`additional fees.
`
`3.[] Asonly someofthe required additional search fees were timely paid by the applicant, this international search report covers
`only those claims for which fees were paid, specifically claims Nos.:
`
`XI No required additional search fees were timely paid by the applicant. Consequently, this international search report is
`restricted to the invention first mentioned in the claims;
`it is covered by claims Nos.:
`
`Remarkon Protest
`
`
`
`The additional search fees were accompanied by the applicant’s protest and, where applicable, the
`paymentof a protest fee.
`
`
`
`
`The additional search fees were accompanied by the applicant’s protest but the applicable protest
`fee was not paid within the time limit specified in the invitation.
`
`Form PCT/ISA/210 (continuation offirst sheet (2)) (January 2015)
`
`OOU Noprotest accompanied the paymentof additional search fees.
`
`

`

`PCT/US2019/032992 28.10.2019
`
`INFERNATIONAL SEARCH REPORT
`
`
`Internationa! application No.
`PCT/US 19/32992
`
`
`CLASSIFICATION OF SUBJECT MATTER
` A.
`
`
`IPC(8) - C12N 15/10, C12Q 1/68 (2019.01)
`CPC - C12N 15/1093, C12Q 1/6874, C40B 40/06
`
`
` Accordin g to International Patent Classification (IPC) orto both national classification and IPC
`B.
`FIELDS SEARCHED
`
`
`Minimum documentation searched(classification system followed by classification symbols)
`
` See Search History Document
`Documentation searched other than minimum documentationto the extent that such documents are included in the fields searched
`
`See Search History Document
`
`
`Electronic data base consulted during the international search (name ofdata base and, where practicable, search terms used)
`See Search History Document
`
`
`C. DOCUMENTS CONSIDERED TO BE RELEVANT
`
`
`Category*
`Citation of document, with indication, where appropriate, of the relevant passages
`
`Y
`US 2017/0355984 A1 (COUNSYL, INC.) 14 December 2017 (14.12.2017) para [0117], [0187],
`
`
`{0190}, [0231}, [0232], [0235], [0236]
`
`
`US 2016/0019341 A1 (PERSONALIS, INC.) 21 January 2016 (21.01.2016) Claim 1, para
`[0025], Fig. 3
`
`Y
`
`Relevantto claim No.
`
`1-4
`
`
`
`“p”
`
`[| Further documents are listed in the continuation of Box C.
`[] See patent family annex.
`*
`Special categories of cited documents:
` Jater documentpublishedafterthe internationalfiling date or priority
`“a” document defining the generalstate ofthe 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
`“E”
`earlier application or patent but published onorafterthe international
`“Xx” document ofparticular relevance; the claimedinvention cannot be
`filing date
`considered nove! or cannot be considered to involve an inventive
`“L”
`document which may throw doubts on priority claim(s) or which is
`step when the documentis taken alone
`
`
`cited i establish the publication date of another citation or other
`«wy» document of particular relevance;the claimed invention cannotbe
`
`
`
`
`special reason (as specified)
`.
`considered to involve an inventive step when the documentis
`“O” 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 memberof the same patent family
`document published prior to the internationalfiling date but later than
`the priority date claimed
`
`
`Date of mailing of the international search report
`Date of the actual completion of the international search
`14 October 2019
`28 0CT 2019
`
`
`
`
`
`Authorized officer:
`
`Nameand mailing address of the ISA/US
`
`Lee W. Young
`
`Mail Stop PCT, Attn: ISA/US, Commissionerfor Patents
`
`
`P.O. Box 1450, Alexandria, Virginia 22313-1450
`
`
`Facsimile No.
`571-273-8300
`Form PCT/ISA/210 (second sheet) (January 2015)
`
`“T?
`
`
`
`PCT Helpdesk: 571-272-4300
`PCT OSP: 571-272-7774
`
`

`

`PCT/US2019/032992 28.10.2019
`
`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/US 19/32992
`
`Continuation of:
`Box No.Ill. Observations whereunity of invention is lacking
`
`----continued on next sheet----
`
`Counsyl teaches(instant claim 1) a method for sequencing genomic DNA(para [0117], methods of sequencing a nucleic acid molecule,
`methods of sequencing a nucleic acidlibrary.), comprising:
`(a) contacting a composition comprising a first polynucleotidelibrary comprising at least 30,000 polynucleotides, wherein eachof the at
`least 30,000 polynucleotides (para [0187], A set of capture probes(also referred to as a capture probelibrary) can be usedto enrich a
`pluratity of nucteic acid molecules (for example, in a sequencing library which may or may not be amplified, for example using PCR). The
`capture probes comprise a nucleic acid sequence complementary to various portions within the regionofinterest. In some
`embodiments, a set of capture probesincludes, for example, between about 2 and about 20,000 capture probe.... A sequencing library
`can include nucleic acid molecules comprising a portion of the region ofinterest (for example, genomic DNAcontainingthe region of
`interest can be fragmentedinto a plurality of nucleic acid molecules, with each nucleic acid molecule originating from the region of
`interest comprising a portion of the regionof interest) is present in an amountsuch that, following hybridization with genomic fragments
`and sequencing ofthe hybridized genomic fragments (para [0190], An equal numberof each capture probe in the set of capture probes
`can result in sequencing depth variation because some capture probes may moreefficiently bind a particular fragment of a sequence of
`interest than another capture probe. This may be due, for example, to a variance in the concentration of the capture probe,....Large
`variance in sequencing depth can decreaseoverall sequence quality by limiting sensitivity and specificity in low sequencing depth sub-
`regionsof a region of interest.), the polynucleotidelibrary provides:
`a read depth of of the genomic fragments corresponding to the polynucleotides (para [0235], Sequencing depth variation (for example,
`after sequencing a nucleic acid sequencing library described herein) can be improve by balancingthe different capture probesin the set
`of capture probes. Balanced capture probesare a set of capture probes for a sequence of interest, wherein the amount of each capture
`probein the set is predetermined to account for varying efficiency of capture for each probe.).
`
`This application contains the following inventions or groups of inventions which are not solinked as to form a single generalinventive
`concept under PCT Rule 13.1. In orderfor all inventions to be searched, the appropriate additional search fees must be paid.
`
`Groups |: Claims 1-4, drawn to a method for sequencing genomic DNA comprising a polynucleotide library which providesa specific
`ratio of the read depth of the bases of the genomic fragments.
`
`GroupsII: Claims 24-26, 38-40, drawn to a composition comprising a polynucleotide library.
`
`GroupsIll: Claims 59-62, 64, 76-80, 94-96, drawn to a composition for nucleic acid hybridization, and a methodof use for nucleic acid
`hybridization or genomic sequencing.
`
`Theinventionslisted as Groups | throughIli do notrelate to a single generalinventive concept under PCT Rule 13.1 because, under
`PCT Rule 13.2, they lack the same or corresponding special technical features for the following reasons:
`
`Special Technical Features
`
`Group | includesthe special technical feature of adding a second polynucleotide library comprising at least one polynucleotide that binds
`to genomic fragments comprising the one or morepositions having less than average read depth, not required by GroupsII andIll.
`
`GroupII includes the special technical feature of a composition comprising a polynucleotidelibrary, wherein less than alt polynucleotides
`comprises a molecular tag, an index sequence, an adapteror a blocker, not required by Groups | andIll.
`
`Group Ill includes the special technical feature of a composition for nucleic acid hybridization or genomic sequencing comprising an
`additive, wherein the additive reducesoff-target hybridization of the at least one polynucleotide or reduce the local concentration of
`nucleic acid at the air-liquid interface, not required by Groups| andII.
`
`CommonTechnica! Features
`
`The inventions of GroupsI-III share the technical feature of a polynucleotide library, nucleic acid hybridization and genomic sequencing.
`
`The inventions of Groups | and II share the technical feature of a polynucleotide library that provides
`a read depth of at least 80 percentof the bases of the genomic fragments corresponding to the polynucleotides; and a total number of
`sequencing reads, wherein the total number of sequencing reads are capable of covering 100 percent of each of the bases of the
`genomic fragments corresponding to the polynucleotides at a theoretical read depth, wherein the ratio of the read depth of at least 80
`percentof the bases of the genomic fragments corresponding to the polynucleotides to the theoretical read depth is at least 0.5 witha
`plurality of genomic fragments.
`
`However, these shared technical features do not represent a contribution over prior art in view of US 2017/0355984 A1 to Counsyl, Inc.
`(hereinafter “Counsyl") and US 2016/0019341 A1 to Personalis, Inc. (hereinafter “Personalis")
`
`Form PCT/ISA/210 (extra sheet) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/US 19/32992
`
`Continuation of:
`Box No.III. Observations where unity of invention is lacking
`
`Counsyl does not specifically teach wherein said read depth coversat least 80 percent of the bases of the genomic fragment anda total
`numberof sequencing reads, wherein the total number of sequencing reads are capable of covering 100 percent of each of the bases of
`the genomic fragments corresponding to the polynucleotides at a theoretical read depth, wherein the ratio of the read depth ofat least
`80 percentof the basesof the genomic fragments correspondingto the polynucleotides to the theoretical read depth is at least 0.5 with a
`plurality of genomic fragments. However, Counsyl teachesthat a balanced capture probes provides improved sequencing efficiency by
`providing the ratio of a predicted sequencing depth profile and a desired sequencing depthprofile as an objective function of the
`balanced capture probes (para [0236]. a balanced set of capture probesis constructed to enrich a nucleic acid library (or nucleic acid
`sequencinglibrary) to minimize the difference between a predicted sequencing depthprofile and a desired sequencing depth profile. The
`desired sequencing depthprofile can be uniform or non-uniform, and the desired sequencing depth profile can be implied by an
`objective function used to minimize the difference between the predicted and desired sequencing depth profiles. In some embodiments,
`construction of the balanced set of capture probes is constrained by a minimum amountor a maximum amount of the capture probesin
`the balanced set of capture probes. The desired sequencing depth profile is made in reference to a reference sequencinglibrary, which
`is a nucleic acid library used to prepare the balanced set of capture probes. Thus, when a set of capture probesis balanced using a
`reference sequencinglibrary, the sequencing depth profile obtained after sequencing a test sequencing library maybe different from the
`desired sequencing depth profile due to differences between the reference sequencing library and the test sequencinglibrary.). Thus,it
`would have been obvious to one ofordinary skill in the art to have provided a balanced capture probes to achieve the claimed
`limitations: “wherein the ratio of the read depth of at least 80 percentof the bases of the genomic fragments corresponding to the
`polynucleotidesto the theoretical read depthis at least 0.5 with a plurality of genomic fragments.”.
`
`feature.
`
`Counsyl further teaches:
`(b) enriching at least one genomic fragmentthat bindsto thefirst polynucleotide library to generate at least one enriched target
`polynucleotide (para [0232], hybrid capture methodsare usedto enrich the region of interest by combining capture probesthat are
`substantially complementary to a portion of the regionof interest with the nucleic acid library (or nucleic acid sequencinglibrary), thereby
`hybridizing the capture probes to nucleic acid molecules comprising the portion of the region of interest.);
`(c) sequencingtheat least one enriched target polynucleotide (para [0232], the enriched nucleic acid molecules from the nucleic acid
`library (or nucteic acid sequencinglibrary) can be sequenced.);
`(e) repeating steps a-c, wherein a second polynucleotidelibrary comprising capture probesis added to the composition, wherein the
`second polynucleotide library comprisesat least one polynucleotide that binds to genomic fragments (para [0231], the enriched nucleic
`acid molecules are re-enriched in a second (or more) round of hybridization to the capture probes. ).
`
`Counsyl does not specifically teach (d) identifying one or more positions of the at least one enriched polynucleotide having less than
`average read depth; adding at least 1500 polynucleotides to the composition; wherein the presence of the second polynucleotide library
`increases the read depth at the one or more positions having less than average read depth. Personalis teaches (b) enriching at least
`one genomic fragmentthat bindsto thefirst polynucleotidelibrary to generate at least one enriched target polynucleotide (Claim 1,A
`method for genetic analysis of a subject, comprising: b. subjecting a second nucleic acid sample of said subject to target-specific
`sequencing to generate target-specific sequencing data;), and (d) identifying one or more positionsof the at least one enriched
`polynucleotide having less than average read depth (para [0025], FIG. 3 illustrates a statistical model on sensitivity vs. coverage of
`genomic regions with single run whole genome sequencing data.).It would have been obvious to one of ordinary skill in the art to have
`adding a second balanced capture probes, such asat least 1500 polynucleotides, to the genomic region having less than average read,
`to improve the read depth of said region.
`
`Assaid technical features were knownin the art at the time of the invention, these cannot be considered special technicalfeatures that
`would otherwise unify the groups.
`
`Groups| throughIII therefore lack unity under PCT Rule 13 because they do not share a sameor corresponding special technical
`
`Form PCT/ISA/210 (extra sheet) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`PATENT COOPERATION TREATY
`
`From the
`INTERNATIONAL SEARCHING AUTHORITY
`
`To: SEAN A. REED
`WILSON SONSINI GOODRICH & ROSATI
`650 PAGE MILL ROAD
`PALO ALTO, CA 94304
`
`
`
`
`
`
`
`
`
`
`PCT
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`(PCT Rule 43is.1)
`
`| Vashaonah/yaer)
`
`
`
`| FOR FURTHER ACTION
`
`
`Applicant’s or agent’s file reference
`
`
`See paragraph 2 below
`44854-776601
`
`
`
`Priority date (day/monthyear)
`International filing date (day/month/year)
`International application No.
`
`18 May 2018 (18.05.2018)
`
`17 May 2019 (17.05.2019)
`PCT/US 19/32992
`
`
`International Patent Classification (IPC) or both national classification and IPC
`IPC(8) - C12N 15/10, C12Q 1/68 (2019.01)
`
`CPG.
`C12N 15/1093, C12Q 1/6874, C40B 40/06
`
`2 8 0 CT 2019
`
`
`
`
`
`Applicant TWIST BIOSCIENCE CORPORATION
`
`
` !
`
`1. This opinion contains indications relating to the following items:
`
`OOOKKKOX Box No. VIII Certain observations on the international application
`
`Box No.
`
`|
`
`Basis of the opinion
`
`Box No. Il
`
`Priority
`
`Box No. III Non-establishment of opinion with regard to novelty, inventive step and industrial applicability
`
`Box No. IV
`Box No. V__
`
`Lack of unity of invention
`Reasoned statement under Rule 43b/s.1(a)(i) with regard to novelty, inventive step and industrial applicability;
`citations and explanations supporting such statement
`
`Box No. VI
`
`Certain documents cited
`
`Box No. VII Certain defects in the international application
`
`| 2. FURTHER ACTION
`If a demand for international preliminary examination is made, this opinion will be considered to be a written opinion of the
`International Preliminary Examining Authority (‘IPEA”) exceptthat this does not apply where the applicant chooses an Authority
`:
`other than this one to be the [PEA and the chosen IPEA hasnotified the International Bureau under Rule 66.1 4/s(b) that written
`!
`:
`opinions ofthis International Searching Authority will not be so considered.
`If this opinion is, as provided above, considered to be a written opinion ofthe !PEA,the applicantis invited to submitto the IPEA
`a written reply together, where appropriate, with amendments, before the expiration of 3 monthsfrom the date of mailing of Form
`PCT/ISA/220 or before the expiration of 22 months from thepriority date, whichever expireslater.
`For further options, see Form PCT/ISA/220.
`
`
`
`Nameand mailing address of the ISA/US|Date of completion of this opinion Authorized officer
`
`Mail Stop PCT,Attn: ISA/US
`
`
`Lee W. Young
`
`
`Commissionerfor Patents
`14 October 2019
`PCT Helpdesk: 571-272-4300
`
`
`P.O. Box 1450, Alexandria, Virginia 22313-1450
`
`PCT OSP: $71-272-7774
`
`Facsimile No. 571-273-8300
`
`
`Form PCT/ISA/237 (cover sheet) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International application No.
`PCT/US 19/32992
`
`Box No. |
`
`Basis of this opinion
`
`1. With regard to the language, this opinion has been established on the basis of:
`[x] the international application in the language in whichit wasfiled.
`[] a translation of the international! application into
`furnished for the purposes of international search (Rules 12.3(a) and 23.!(b)).
`
`which is the languageofa translation
`
`This opinion has been established taking into accountthe rectification of an obvious mistake authorized byor notified to
`this Authority under Rule 9} (Rule 43 is. 1(a)).
`
`
`
`
`
`
`
`With regard to any nucleotide and/or amino acid sequence disclosed in the international application,this opinion has
`been established on the basis of a sequencelisting:
`
`
`a. [] formingpart of the international application asfiled:
`[| in the form of an Annex C/ST.25 textfile.
`{_] on paperor in the form ofan imagefile.
`
`
`b. E furnished together with the international application under PCT Rule 13¢er.1(a) for the purposes of international
`search only in the form of an Annex C/ST.25 text file.
`c. >< furnished subsequentto the international filing date for the purposes of international search only:
`Xl
`in the form of an Annex C/ST.25textfile (Rule 13¢er.1(a)).
`
`
`C] on paperor in the form ofan image file (Rule 13/er.1(b) and Administrative Instructions, Section 713).
`
`
`
`[XxX 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.
`
` 4.
`
`Additional comments:
`
`Form PCT/ISA/237 (Box No. 1) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`
`WRITTEN OPINION OF THE
`International application No.
`INTERNATIONAL SEARCHING AUTHORITY
`PCT/US 19/32992
`
`
`
`Box No. Il}—Non-establishment of opinion with regard to novelty, inventive step and industrial applicability
`
`The questions whether the claimed invention appears to be novel, to involve an inventive step (to be non obvious), or to be industrially
`applicable have not been examined in respectof:
`
`
`[] the entire intemational application.
`BZ]_claims Nos. 5:23, 27-37, 41°88, 63, 65-75, 81-93, 97-107
`
`
`because:
`relate to the following
`the said international application, or the said claims Nos.
`subject matter which does not require an international search (specify):
`
`
`
`the description, claims or drawings (indicate particular elements below} or said claims Nos. §-23, 27-37, 41-58, 63, 65-75, 8
`Xx]
`are so unclear that no meaningful opinion could be formed (specify):
`
`Claims 5-23, 27-37, 41-58, 63, 65-75, 81-93, 97-107 are held unsearchable because they are dependentclaims and are notdrafted in
`accordancewith the second andthird sentences of Rule 6.4(a).
`
`[] the claims, or said claims Nos. are so inadequately supported
`
`
`by the description that no meaningful opinion could be formed (specify):
`
`
`
`
`
`
`<]
`no international search report has been established for said claims Nos. 5-23, 27-37, 41-58, 63, 65-75, 81-93, 97-107
`
`
`[|
`a meaningful opinion could notbe formed without the sequence listing; the applicant did not, within the prescribed time limit:
`[] furnish a sequence listing in the form of an Annex C/ST.25 text file, and such listing was not available to the
`International Searching Authority in the form and manneracceptableto it, or the sequence listing furnished did not
`
`
`comply with the standard provided for in Annex C of the Administrative Instructions.
`
`
`[| furnish a sequencelisting on paperor in the form ofan image file complying with the standard provided for in Annex
`C ofthe Administrative Instructions, and such listing was not available to the International Searching Authority in the
`form and manneracceptableto it; or the sequencelisting furnished did not comply with the standard provided for in
`Annex C of the Administrative Instructions.
`
`[] pay the required late furnishing fee for the furnishing of a sequence listing in response to an invitation under
`Rule 13¢er.1(a) or (b).
`
`
`[|
`See Supplemental Box for further details.
`
`
`Form PCT/SA/237 (Box No. II) January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`Box No.1V
`
`Lack of unity of invention
`
`
`
`
`WRITTEN OPINION OF THE
`International application No.
`
`INTERNATIONAL SEARCHING AUTHORITY
`PCT/US 19/32992
`
`
`
`I. i] In response to the invitation (Form PCT/ISA/206) to pay additional fees the applicant has, within the applicable time limit:
`
`
`paid additional fees under protest and, where applicable, the protest fee.
`
`paid additional fees under protest but the applicable protest fee was not paid.
`
`
`not paid additionalfees.
`
`
`2. [| This Authority found that the requirementof unity of invention is not complied with and chose not to invite the applicant to
`pay additional fees.
`
`
`
`
`3. This Authority considers that the requirementof unity of invention in accordance with Rule 13.1, 13.2 and 13.3 is
`[] complied with.
`
`
`[Xx]
`not complied with for the following reasons:
`This application contains the following inventions or groups of inventions which are not solinked as to form a single generalinventive
`concept under PCT Rule 13.1. In orderforall inventions to be searched, the appropriate additional search fees must be paid.
`
`
`Groups |: Claims 1-4, drawn to a method for sequencing genomic DNA comprising a polynucleotidelibrary which provides a specific ratio
`of the read depth of the bases of the genomic fragments.
`
`
`GroupsII: Claims 24-26, 38-40, drawn to a composition comprising a polynucleotide library.
`GroupsII: Claims 59-62, 64, 76-80, 94-96, drawn to a composition for nucleic acid hybridization, and a method of use for nucleic acid
`hybridization or genomic sequencing.
`
`
`The inventions listed as Groups| throughIlt do not relate to a single general inventive concept under PCT Rule 13.1 because, under
`PCT Rule 13.2, they lack the same or corresponding special technical features for the following reasons:
`
`
`Special Technical Features
`
`
`Group| includes the special technicalfeature of adding a second polynucleotide library comprising at least one polynucleotide that binds
`to genomic fragments comprising the one or more positions having less than average read depth,not required by Groups|| andIII.
`
`
`GroupII includes the special technical feature of a composition comprising a polynucleotidelibrary, wherein less than all polynucleotides
`comprises a moleculartag, an index sequence, an adapteror a blocker, not required by Groups {and II.
`
`
`GroupIll includes the special technical feature of a composition for nucleic acid hybridization or genomic sequencing comprising an
`additive, wherein the additive reducesoff-target hybridization of the at least one polynucleotide or reducethe local concentration of
`
`
`nucleic acid at the air-liquid interface, not required by Groups| andII.
`
`
`
`
`
`
`
`
`
`
` Consequently, this opinion has been established in respect of the following parts of the international application:
`[] all parts.
`
`XI the parts relating to claims Nos. 1-4
`
`The inventions of GroupsI-I!t share the technical feature of a polynucleotidelibrary, nucleic acid hybridization and genomic sequencing.
`The inventions of Groups | and II share the technical feature of a polynucteotide library that provides
`a read depth ofat least 80 percentof the basesof the genomic fragments correspondingto the polynucleotides; and a total numberof
`sequencing reads, wherein the total numberof sequencing reads are capable of covering 100 percent of eachof the bases of the
`genomic fragments corresponding to the polynucleotides at a theoretical read depth, wherein the ratio of the read depth of at least 80
`percent of the bases of the genomic fragments corresponding to the polynucleotides to the theoretical read depth is at least 0.5 with a
`plurality of genomic fragments.
`However, these shared technical features do not represent a contribution overprior art in view of US 2017/0355984 A1 to Counsyl, Inc.
`(hereinafter “Counsyl") and US 2016/0019341 A1 to Personalis, Inc. (hereinafter "Personalis")
`werecontinued in Supplemental Box--------
`
`paid additionalfees.
`
`Common Technical Features
`
`
`
`Form PCT/ISA/237 (Box No. IV) (January 2015)
`
`

`

`PCT/US2019/032992 28.10.2019
`
`Box No. V
`
`Statement
`
`
`WRITTEN OPINION OF THE
`International application No.
`T
`s
`
`INTERNATIONAL SEARCHING AUTHORITY
`PCT/US 19/32992
`
`
`Reasoned statement under Rule 43éis.1(a)(i) with regard to novelty, inventive step or industrial applicability;
`citations and explanations supporting such statement
`
`
`
`Novelty (N)
`Claims
`1-4
`YES
`Claims
`
`
`Claims
`
`Inventive step (1S)
`
`Claims
`1-4
`NO
`
`Industrial applicability (IA)
`Claims
`1-4
`YES
`Claims
`
`
`
`
`
`Citations and explanations:
`2.
`Claims 1-4 lack an inventive step under PCT Article 33(3) as being obvious over US 2017/0355984 A1 to Counsyl, Inc. (hereinafter
`"Counsyl") and US 2016/0019341 A1 to Personalis, inc. (hereinafter "Personalis").
`
`
`Regarding claim 1, Counsyl teaches a method for sequencing genomic DNA(para [0117], methods of sequencing a nucleic acid molecule,
`methods of sequencing a nucleic acid tibrary.), comprising:
`
`
`(a) contacting a composition comprising a first polynucleotide library comprising at least 30,000 polynucleotides, (para [0187], "A set of
`capture probes(also referred to as a capture probelibrary) can be used to enrich a plurality of nucleic acid molecules (for example, in a
`sequencinglibrary which may or may not be amplified, for example using PCR). The capture probes comprise a nucleic acid sequence
`
`
`complementary to various portions within the region ofinterest. In some embodiments, a set of