PATENT COOPERATION TREATY
`
`PCT
`
`INTERNATIONAL SEARCH REPORT
`
`(PCT Article 18 and Rules 43 and 44)
`
`Applicant's or agent's file reference
`47697—709601
`
`FOR FURTHER
`ACTION
`
`see Form PCT/lSA/220
`as well as, where applicable, item 5 below.
`
`(Earliest) Priority Date (day/month/year)
`International filing date (day/month/year)
`1nternational application NO'
`PCT/US2018/027393
`12 April 2018
`12 April 2017
`
`Applicant
`
`KARIUS, INC.
`
`This international 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 7 sheets.
`D 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:
`
`The international application in the language in which it was filed.
`
`A translation of the international application into , which is the language ofa translation furnished for the purposes of
`international search (Rules 12.3(a) and 23.1(b)).
`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 43.6bis(a)).
`
`With regard to any nucleotide and/0r amino acid sequence disclosed in the international application, see Box No. 1.
`
`|:| as sclcctcd by this Authority, because this figurc bcttcr charactcrizcs thc invcntion.
`
`Certain claims were found unsearchable (See Box No. 11).
`
`Unity of invention is lacking (See Box No. 111).
`
`With regard to the title,
`
`the text is approved as submitted by the applicant.
`
`the text has been established by this Authority to read as follows:
`
`With regard to the abstract,
`
`D 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 N 0. 1V. The applicant may, Within one
`month from the date of mailing ofthis 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. 1
`
`as suggested by the applicant.
`
`|:| as selected by this Authority, because the applicant failed to suggest a figure.
`
`b. D none of the figures is to be published with the abstract.
`
`Form PCT/ISA/Zl 0 (first sheet) (January 2015)
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/U820 18/027393
`
`Box No. II Observations where certain claims were found unsearchable (Continuation of item 2 of first sheet)
`
`This international search report has not been established in respect of certain claims under Article l7(2)(a) for the following
`reasons:
`
`1. El Claims Nos.:
`because they relate to subject matter not required to be searched by this Authority, namely:
`
`the subject matter listed in Rule 39 on which, under Article l7(2)(a)(i), an international search is not required to be
`carried out, including
`
`|:| 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:
`
`|:| Claims Nos:
`because they are dependent claims and are not drafted in accordance with the second and third sentences of Rule 6.4(a)
`
`Box No. III Observations where unity of invention is lacking (Continuation of item 3 of first sheet)
`
`This International Searching Authority found multiple inventions in this international application, as follows:
`
`See Supplemental Box for Details
`
`D As all required additional search fees were timely paid by the applicant, this international search report covers all
`searchable claims.
`
`D As all searchable claims could be searched without effort justifying additional fees, this Authority did not invite
`payment of additional fees.
`
`D As only some of the 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.:
`
`
`
`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.:
`1-18, 75-77, 92-101, 108-114
`
`Remark on Protest
`
`|:| The additional search fees were accompanied by the applicant's protest and, where applicable,
`the payment of 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.
`
`|:| No protest accompanied the payment of additional search fees.
`
`Form PCT/lSA/Z] 0 (third sheet) (January 2015)
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/USZO 18/027393
`
`Box No. IV Text of the Abstract (Continuation of item 5 of the first sheet)
`
`The disclosure provides methods, compositions, systems, and kits for the concurrent detection and analysis of different structural
`and chemical forms of nucleic acids in a sample. Different nucleic acid forms are tagged using DNA-dependent polymerase and
`reverse transcriptase enzymes with non—templated activity or with ligase enzymes that display a preference for the different nucleic
`acid forms.
`
`
`
`Form PCT/ISA/Zl 0 (4th sheet) (January 2015)
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application No.
`PCT/USZOIS/027393
`
`A. CLASSIFICATION OF SUBJECT MATTER
`
`c12a 1/68 (2018.01)
`
`c120 1/70 (2006.01)
`
`Accordin; to International Patent Classification IPC or to both national classification and IPC
`
`B. FIELDS SEARCHED
`
`Minimum documentation scarchcd (classification systcm followed by classification symbols)
`
`Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched
`
`
`
`Electronic data base consulted during the international search (name of data base and, where practicable, search terms used)
`
`Databases: EPOQUE; PATENW. STN; CAPLUS, MEDLINE, EMBASE, BIOSIS, CABA. Google, Google Scholar,
`PubMed, Espacenet, Auspat.
`
`Classification symbols: C12Ql/68, C12Q1/70
`
`Searched for keywords: DNA, RNA, Single—stranded, nucleic acid form, simultaneous, parallel, concun'ent, adapter, ligation, non-
`template or like terms and applicant/inventor search.
`
`
`
`C. DOCUMENTS CONSIDERED TO BE RELEVANT
`
`Citation of document, with indication, where appropriate, of the relevant passages
`
`Relevant to
`claim No.
`
`Documents are listed in the continuation of Box C
`
`Further documents are listed in the continuation of Box C
`
`See patent family annex
`
`Special categories of cited documents:
`document defining the general state of the an which is not
`considered to be of particular relevance
`
`earlier application or patent but published on or after the
`international filing date
`
`"0"
`
`
`
`document which may throw doubts on priority claim(s) or
`which is cited to establish the publication date of another
`citation or other special reason (as specified)
`document referring to an oral disclosure, use, exhibition
`or other means
`document published prior to the international filing date
`"P"
`
`but later than the priority date claimed
`Date of the actual completion of the international search
`
`later document published after the international filing date or priority date and not in
`conflict with the application but cited to understand the principle or theory
`underlying the invention
`document ofparticular relevance; the claimed invention cannot be considered novel
`or cannot be considered to involve an inventive step when the document is taken
`alone
`document of particular relevance; the claimed invention cannot be considered to
`involve an inventive step when the document is combined with one or more other
`such documents, such combination being obvious to a person skilled in the art
`
`document member of the same patent family
`
`Date of mailing of the international search report
`
`16 July 2018
`Name and mailing address of the ISA/AU
`
`AUSTRALIAN PATENT OFFICE
`
`PO BOX 200, WODEN ACT 2606, AUSTRALIA
`Email address: pct@ipaustralia.gov.au
`
`Form PCT/ISA/Zl 0 (fifth sheet) (January 2015)
`
`l6July2018
`Authorised officer
`
`Jason McArthur
`
`AUSTRALIAN PATENT OFFICE
`(ISO 9001 Quality Certified Service)
`Telephone No. +6126283 2594
`
`

`

`C (Continuation).
`
`DOCUMENTS CONSIDERED TO BE RELEVANT
`
`PCT/US2018/027393
`
`INTERNATIONAL SEARCH REPORT
`
`International application NO.
`
`Category*
`
`Citation of document, with indication, where appropriate, of‘ the relevant passages
`
`Relevant to claim No.
`
`WO 2013/138536 A1 (SWIFT BIOSCIENCES, INC.) 19 September 2013
`[0113], [0196], Figures 10 and 11
`
`[0113], Figures 10 and ll
`
`1-8, 92-101
`
`9-18, 75-77, 108-114
`
`WC 2015/ 173402 A1 (RUPRECHT—KARLS-UNIVERSITAT HEIDELBERG et a1.) 19
`November 2015
`
`p5, lines 4-16; p16, lines 23-27; p17 lines 17-18; p21, lines 11-13; p26, lines 31-33;
`p30, lines 24-30; Figure 1
`p16, lines 23-27; p17 lines 17-18; p21, lines 11-13; p26, lines 31—33; p30, lines 24-30;
`Figure 1
`
`1-8, 92-101
`
`9-187 75-777 108-114
`
`Dcy S. et 211., “Integrated genome and transeriptomc sequencing from the same cell” Nat
`Biotechnol. 2015, 33(3), p2857289.
`On1ine Methods and Figure 1
`
`WO 2018/057820 A1 (PREDICINE, INC.) 29 March 2018
`
`paragraph [005], Figure 7
`
`WO 2018/119452 A1 (GUARDANT HEALTH, INC.) 28 June 2018
`Abstract
`
`
`
`Form PCT/ISA/210 (fifth sheet) (January 2015)
`
`

`

`INTERNATIONAL SEARCH REPORT
`
`International application NO.
`PCT/U82018/027393
`
`Supplemental Box
`
`Continuation of: Box III
`
`This International Application does not comply with the requirements of unity of invention because it does not relate to one
`invention or to a group of inventions so linked as to form a single general inventive concept. Please note, there are extensive clarity
`issues resulting from numerous claims being appended to “any preceding claim”. For the purpose of this Lack of Unity assessment,
`claims appended to “any preceding claim” were construed to be appended to any claim up to and including the immediately
`preceding independent claim only.
`
`This Authority has found that there are different inventions based on the following features that separate the claims into 3 distinct
`groups:
`
`Group 1: Claims 1—18, 75-77, 92-101, 108-1 14 directed to methods. kits and reaction mixtures for characterising multiple forms of
`DNA and RNA separately in a sample comprising tagging DNA/RNA strands via primer extension with non—templated polymerase
`or non-templated reverse transcriptase enzymes.
`
`Group 2: Claims 19-49 directed to a method of sequencing nucleic acids present in a sample containing a mixture of single stranded
`and double stranded nucleic acids.
`
`
`
`Group 3: Claims 50-74, 78—91, 102-107 directed to methods, kits and reaction mixtures for characterising multiple forms of DNA
`and RNA separately in a sample comprising tagging DNA/RNA strands with adapters using ligases that have a preference for the
`different nucleic acid forms present in the sample.
`
`PCT Rule 13.2, first sentence, states that unity of invention is only fulfilled when there is a technical relationship among the
`claimed inventions involving one or more of the same or corresponding special technical features. PCT Rule 13.2, second sentence,
`defines a special technical feature as a feature which makes a contribution over the prior art. When there is no special technical
`feature common to all the claimed inventions there is no unity of invention.
`
`The above groups of claims do not share any common feature capable of providing a contribution over the prior art. The only
`feature common to all of the claimed inventions and which provides a technical relationship among them is the concurrent
`processing of multiple types of nucleic acids in the same sample without physical separation. However this feature does not make a
`contribution over the prior art because it is disclosed in:
`
`Dey S. et al., “Integrated genome and transcriptome sequencing from the same cell” Nat Biotechnol. 2015, 33(3), p2857289 (see
`Figure 1)
`
`In the light of this document this common feature cannot be a special technical feature. Therefore there is no special technical
`feature common to all the claimed inventions and the requirements for unity of invention are consequently not satisfied a posteriori.
`
`For the fee already paid, the ISA has searched and examined the first invention claimed (i.e. Group 1).
`
`Form PCT/ISA/Zl 0 (Supplemental Box) (January 20] 5)
`
`

`

`19 Sep 2013
`
`18 Sep 2014
`
`19 Sep 2013
`04 Mar 2015
`
`30 Jan 2018
`
`21 Jan 2015
`
`08 Jan 2016
`
`13 Apr 2015
`30 Oct 2014
`
`26 Mar 2015
`
`20 Feb 2018
`
`19N0V 2015
`
`05 Jan 2017
`
`19 Nov 2015
`
`22 Feb 2017
`
`31 May 2017
`22 Mar 2017
`
`WO 2015/173402 Al
`
`19 November 2015
`
`WO 2015173402 A]
`
`AU 2015261440 Al
`
`CA 2948951 Al
`
`CN 106460052 A
`
`EA 201692157 A1
`
`EP 3143139 A1
`
`WO 2018/057820 A1
`
`29 March 2018
`
`WO 2018057820 A]
`
`WO 2018/119452 A1
`
`28 June 2018
`
`None
`
`End of Annex
`
`INTERNATIONAL SEARCH REPORT
`
`Information on patent family members
`
`International application NO.
`
`PCT/[1820181027393
`
`This Annex lists known patent family members relating to the patent documents cited in the above—mentioned international search
`report. The Australian Patent Office is in no way liable for these particulars which are merely given for the purpose of information.
`
`Patent Document/s Cited in Search Report
`
`Patent Family Member/s
`
`Publication Number
`
`Publication Date
`
`Publication Number
`
`Publication Date
`
`WO 2013/138536 A1
`
`19 September 2013
`
`WO 2013138536 A]
`
`AU 2013232131 A1
`
`CA 2866625 A1
`
`CN 104395480 A
`
`CN 104395480 B
`
`EP 2825672 A1
`
`HK 1206395 Al
`
`JP 2015510766 A
`
`SG 11201405669X A
`
`US 2015087027 A1
`
`US 9896709 B2
`
`29 Mar 2018
`
`listin_ ma not include 10 di_it Australian a ulications filed since Ma 2001.
`Due to data inte ration issues this famil
`Form PCT/ISA/Z 10 (Family Annex)(January 2015)
`
`

`

`PATENT COOPERATION TREATY
`
`From the:
`INTERNATIONAL SEARCHING AUTHORITY
`
`PCT
`
`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`(PCT Rule 43bis.1)
`
`Date of mailing (day/month/year)
`16 July 2018
`
`
`
`KUMAR, Rachana A.
`
`Wilson Sonsini Goodrich & Rosati, PC.
`650 Page Mill Road
`
`Palo Alto, CA 94304-1050
`United States of America
`
`
`
`
`
`Applicant's 0r agent‘s file reference
`
`FOR FURTHER ACTION
`
`International application No.
`
`International filing date (day/month/year)
`
`Priority date (day/month/year)
`
`International Patent Classification (IPC) or both national classification and IPC
`
`C120 1/68 (2018.01) C120 1/70 (2006.01)
`
`
`
`
`
`Applicant
`KARIUS, INC.
`
`This opinion contains indications relating to the Following items:
`
`Box \lo, I
`
`Basis of the opinion
`
`Box V0. 11
`
`Box \lo.
`
`. IV
`
`. V
`
`. VI
`
`. VII
`
`. VIII
`
`Priority
`
`Non—establishment of opinion with regard to novelty, inventive step and industrial applicability
`
`Lack of unity of invention
`
`Reasoned statement under Rule 43h1‘s.1(a)(i) with regard to novelty, inventive step and industrial applicability;
`citations and explanations supporting such statement
`Certain documents cited
`
`Certain defects in the international application
`
`Certain observations on the international application
`
`Date of completion of this opinion Authorised Officer
`
`ESEHEDEE
`
`
`
`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") 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 International Bureau under Rule 66.1bis(b) that written opinions of this International
`Searching Authority will not be so considered.
`If this opinion is, as provided above, considered to be a written opinion of the IPEA, the applicant is invited to submit to the IPEA a
`written reply together, where appropriate, with amendments, before the expiration of 3 months from the date of mailing of Form
`PCT/ISA/ZZO or before the expiration of 22 months from the priority date, whichever expires later.
`For further options, see Form PCT/ISA/220.
`Name and mailing address of the ISA
`
`AUSTRALIAN PATENT OFFICE
`PO BOX 200, WODEN ACT 2606,
`AUSTRALIA
`Email address: pct@ipaustralia.gov.au
`
`16 July 2018
`
`Jason McArthur
`AUSTRALIAN PATENT OTFICE
`(ISO 9001 Quality Certified Service)
`Telephone No. +61262832594
`
`Form PCT/ISA/237 (Cover sheet) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`
`
`Box No. I
`
`Basis of this opinion
`
`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
`
`
`International application No.
`
`PCT/U82018/027393
`
`
`
`D A translation of the international application into, , Which is the language of a translation filrnished for the purposes of
`international search (under Rules 12.3(a) and 23.1(b)).
`
`This opinion has been established taking into account the rectification of an obvious mistake authorized by or notified
`to this Authority under Rule 91 (Rule 43bis.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 sequence listing:
`
`a. El forming part of the international application as filed:
`
`CI in the form of an Annex C/ST.25 text file.
`
`D on paper or in the fonn of an image file.
`
`b.
`
`|:|
`
`furnished together with the international application under PCT Rule 13ter.l(a) for the purposes of
`international search only in the form of an Annex C/ST.25 text file.
`
`0. El furnished subsequent to the international filing date for the purposes of international search only:
`
`D in the form of an Annex C/ST.25 text file (Rule l3ter. 1(a)).
`
`D on paper or in the form of an image file (Rule 13ter.l(b) and Administrative Instructions, Section 713).
`
`. D In addition, in the case that more than one version or copy of a sequence listing 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.
`
`Additional comments:
`
`Form PCT/ISA/237(Box1) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International application No.
`
`PCT/U82018/027393
`
`
`
`Box No. II Priority
`
`1. CI The validity of the priority claim has not been considered because the International Searching Authority does not have in
`its posscssion a copy of the earlier application Whosc priority has bccn claimcd or, where required, a translation of that
`earlier application. This opinion has nevertheless been established on the assumption that the relevant date (Rules
`43bis.l and 64.1) is the claimed priority date.
`
`2. D This opinion has been established as if no priority had been claimed due to the fact that the priority claim has been found
`invalid (Rules 43])i.\'.l and 64.1). Thus for the purposes of this opinion, the international filing date indicated above is
`considered to be the relevant date.
`
`3. Additional observations, if necessary:
`
`The claimed priority date is found to be valid.
`
`Form PCT/ISA/237 (Box 11) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`
`International application No.
`
`
`PCT/U82018/027393
`
`Box No. IV
`
`Lack of unity of invention
`
`In response to the invitation (Form PCT/lSA/206) to pay additional fees the applicant has, within the applicable time
`
`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 additional fees
`
`D This Authority found that the requirement of unity of invention is not complied with and chose not to invite the
`applicant to pay additional fees.
`
`This Authority considers that the requirement of unity of invention in accordance with Rule 13.1, 13.2 and 13.3 is
`
`El complied with
`
`not complied with for the following reasons:
`
`limit: paid additional fees
`
`See Supplemental Box for Details
`
`4. Consequently, this opinion has been established in respect of the following parts of the international application:
`
`El all parts
`
`the parts relating to claims Nos. 1—18,75—77,92—101,108—114
`
`Form PCT/lSA/237 (Box IV) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International Application No.
`
`PCT/U52018/027393
`
`Box No. V
`
`Reasoned statement under Rule 43bis.1(a)(i) with regard to novelty, inventive step or industrial applicability;
`citations and explanations supporting such statement
`
`1.
`
`Statement
`
`Novelty (N)
`
`Claims 9-18, 75-77, 92-101, 108-114
`Claims 1—8
`
`Inventive step (IS)
`
`Claims NONE
`
`Industrial applicability (IA)
`
`Claims 1-18, 75-77, 92-101, 108-114
`
`Claims 1—18, 75—77, 92—101, 108—114
`Claims NONE
`
`
`
`2. CITATIONS AND EXPLANATIONS:
`
`CITATIONS
`
`Dl: WO 2013/138536 A1 (SWIFT BIOSCIENCES, INC.) 19 September 2013
`D2: WO 2015/173402 A1 (RUPRECHT-KARLS-UNIVERSITAT HEIDELBERG et a1.) 19 November 2015
`
`D3: Dey S. et 31., “Integrated genome and transcriptonie sequencing from the same cell” Nat Bioteclmol. 2015, 33(3), p285—289.
`
`NOVELTY 1N!
`
`Dl discloses compositions and methods for the processing of nucleic acid populations containing different forms. The method
`comprises attaching a first adapter to DNA (including ssDNA) and attaching a second adapter to RNA (including ssRNA). The
`adapter comprises an oligonucleotide of known sequence that is ligated to the 3' —hydr0xy end of single stranded nucleic acids (see
`Figure 10), The adapters may be incorporated using template independent DNA/RNA polymerases such as terminal transferases and
`poly (A, U or C)-polymerases (see [0113]). A priming oligonucleotide is then annealed to the previously added nucleotide sequence
`and is extended to form a double-stranded DNA or a double-stranded DNA-RNA hybrid (see Figure 10). Annealed primers may be
`extended by DNA polymerases (e.g. Taq, Klenow (exo-)) or by a reverse transcriptase that have terminal transferase activity which
`allows nucleotides to be added in a template independent manor to produce an overhang at the 3' -prime end of the newly
`synthesized strand (see Figure 11). Additional adapters may be hybridised t0 the overhangs produced (see Figure l 1). D1 also
`discloses a kit comprising a template independent DNA/RNA polymerase, a ligase and a reverse transeriptase (see [0196]).
`Therefore claims 1-8 are not novel in light of D1.
`
`D2 discloses a method for the synthesis of double-stranded nucleic acids from multiple types of nucleic acids present in a sample
`(see p21, lines 1 1-13). The method comprises attaching a first adapter to single-stranded DNA (SSDNA) and attaching a second
`adapter to single-stranded RNA (ssRNA). The adapter comprises an oligonucleotide of known sequence that is ligated to the 3’ -
`hydroxy end of single stranded nucleic acids (see p17 lines 17—18). The adapters may be incorporated using template independent
`DNA/RNA polymerases such as DNA/RNA ligases, terminal transferases and poly (A, U or C)—polymerases (see p16, lines 23-27).
`A priming oligonucleotide is then annealed to the previously added nucleotide sequence and is extended to form a double—stranded
`DNA or a double—stranded DNA-RNA hybrid (see Figure l and p26, lines 31—33). Annealed primers are extended by DNA/RNA
`polymerases that have terminal transferase activity which allows nucleotides to be added in a template independent manner to
`produce an overhang at the 3' -prime end of the newly synthesized strand (see p30, lines 24-30). Additional adapters may be
`hybridised t0 the overhangs produced (see Figure 1). D2 also discloses a kit comprising a template independent DNA/RNA
`polymerase and a reverse transcriptase (see p5, lines 4—16). Therefore claims 1-8 are not novel in light of D2.
`
`In summary, the subject matter of claims 1—8 is not new and does not meet the requirements of Article 33(2) of the PCT with regard
`to novelty.
`
`Claims 9-12, 13-18, 75-77, 92-101 and 108-114 meet the criteria set forth in PCT Article 33(2) for novelty. The prior art published
`before the priority date does not disclose a method for processing different nucleic acid forms that uses a polymerase that is
`selective for DNA templates or uses two polymerases with non-template activity that add different non-templated nucleotides.
`Therefore the subject matter of these claims is new and meets the requirements of Article 33(2) of the PCT with regard to novelty.
`
`Form PCT/ISA/237 (Box V) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International Application No.
`
`PCT/U52018/027393
`
`INVENTIVE STEP 11S!
`Claims 1—8 are not novel and therefore are also considered to be obvious and do not meet the requirements of Article 33(3) of the
`PCT with regard to inventive step.
`
`Claims 9-12, 13-18, 75-77 and 108-114 are not inventive when the disclosure ofDl is combined with D2.
`
`The problem addressed by the current application is the provision ofan improved method ofprocessing multiple nucleic acid forms
`present in a sample.
`
`The disclosures ofDl and D2 are discussed above in Novelty.
`
`Claims 9—12, 75—77 and 108—1 14 differ from the disclosure of D1 by the inclusion of a second polymerase with non—templated
`activity that adds distinct non-templated nucleotides when compared to the first polymerase used.
`
`When faced with the problem of providing an improved method of processing multiple nucleic acid forms present in a sample, it is
`considered that a person skilled in the an would understand from the teachings of D1 that DNA and RNA can be processed
`simultaneously using both DNA polymerase and reverse transcriptase enzymes with non—templated activity to generate nucleotide
`overhangs at the 3' —prime end of the newly synthesized strand which can be used for further adapter incorporation. Furthermore,
`the PSA would be motivated to use additional reverse transcriptase enzymes with non—templated activity as disclosed in D2 to add
`distinct nucleotide overhangs at the 3' -prime end of the newly synthesized DNA strand in an improved method of processing
`multiple nucleic acid forms present in a sample. Additionally, it is considered that the person skilled in the art would have a
`reasonable expectation of success and would encounter no technical difficulties when doing so. Claims 9-12, 75-77 and 108-1 14 are
`therefore considered not to involve an inventive step in View of D1 in combination with D2.
`
`Claims 13—18 further differ from the disclosure ofDl combined with D2, and from the disclosure of D3 when considered
`separately, in the use of a sample comprising a mixture of a first DNA and a first RNA, wherein said first DNA does not comprise a
`sequence complementary to said first RNA. However, no surprising unexpected effect appears to have been identified in using a
`sample comprising a first DNA and first RNA, wherein the first DNA does not contain a sequence complimentary to the first RNA.
`Furthermore, it is considered that supplying such a sample is something the person skilled in the art would do routinely when
`performing the claimed invention, without requiring the use of any inventive ingenuity, when presented with such a sample. Claims
`13 to 18 are therefore also considered not to involve an inventive step.
`
`Claims 92—101 lack an inventive step in light of each of D1 and D2. These claims are directed towards a kit of known polymerase
`enzymes. As such, this merely represents a juxtaposition of known features and does not confer an inventive step on these claims
`(see PCT International Search and Preliminary Examination Guidelines, Part 11, Chapter 13, page 112, paragraph 13.05 and page
`115, paragraph 13.140 and 13.14d).
`
`Therefore the subject matter of claims 1-18, 75-77, 92-101 and 108-1 14 is obvious and does not meet the requirements of Article
`33(3) of the PCT with regard to inventive step.
`
`
`
`INDUSTRIAL APPLICABILITY 11A!
`
`The invention defined in the claims is considered to meet the requirements of Industrial Applicability under Article 33(4) of
`the PCT because it can be made by, or used in, industry.
`
`P Category Document/s listed in Box VI:
`There is a document(s) listed as a P category document in Box VI because it:
`o
`discloses subject matter that is of particular relevance to this application and
`0
`is published before the international filing date but after the priority date of this application.
`
`Under the PCT, only documents published before the priority date of the instant application can deprive the claims of that
`application of novelty or inventive step.
`
`However, the relevance of a document published after the priority date of the application under consideration is dependent on
`national law in individual countries.
`
`Form PCT/ISA/237 (Box V) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`
`INTERNATIONAL SEARCHING AUTHORITY
`
`International Application N 0.
`
`PCT/U52018/027393
`
`P category document/s may become significant in the National Phase.
`
`E Category Document/s listed in Box VI:
`There is a document(s) listed as an E catego1y document in BOX VI because it:
`o
`discloses subject matter that is of particular relevance to this application and
`is an earlier application or patent but published on or after the international filing date of this application
`
`E category document/s may become significant in the National Phase.
`
`Under the PCT, only documents published before the priority date of the instant application can deprive the claims of that
`application of novelty.
`
`However, the relevance of a document published after the priority date of the application under consideration is dependent on
`national law in individual countries.
`
`Form PCT/ISA/237 (Box V) (July 2011)
`
`

`

`WRITTEN OPINION OF THE
`
`INTERNATIONAL SEARCHING AUTHORITY
`
`International Application N o.
`
`Box No. VI PCT/USZOlS/027393 Certain documents cited
`
`
`
`
`1. Certain published documents (Rules 43bis.l and 70.10)
`
`Application No.
`Patent NO.
`
`P,X : WO 2018/057820 A1
`E1WO 2018/119452 Al
`
`Publication date
`(dd y/morzth/zear)
`
`29 March 2018
`28 June 2018
`
`Filing date
`(da z/mortth/year)
`
`Priority date (valid claim)
`(day/mortth/zear)
`
`21 September 2017
`22 December 20l7
`
`21 September 2016
`22 December 2016
`
`See Supplemental Box for Details
`
`2. Non-written disclosures (Rules 43bis.l and 70.9)
`
`Kind of non-written disclosure
`
`Date of non-written disclosure
`(day/mont/z/year)
`
`Date of written disclosure
`
`referring to non-written disclosure
`(day/month/Vear)
`
`
`
`Form PCT/ISA/237 Box VI
`
`

`

`WRITTEN OPINION OF THE
`INTERNATIONAL SEARCHING AUTHORITY
`
`International Application No.
`
`Box No. VIII Certain observations on the international application
`
`PCT/U82018/027393
`
`The following observations on the clarity of the claims, description, and drawings or on the question whether the claims are fully
`supported by the description, are made:
`
`Claim 13 (and appended claims thereto) is not clear. The claim defines at part a) “a sample comprising a mixture of a first DNA and
`a first RNA. whcrcin said first DNA docs not comprise a scqucncc complimcntary to said first RNA”. As thc dcgrcc of
`complementarity between the first DNA and the first RNA is not defined, the length of complementary nucleotides required to
`identify a first DNA as not comprising a sequence complementary to a first RNA cannot be ascertained. Therefore, the scope of
`claim 13 cannot be determined.
`
`Please note, claim 15 is appended to claim 23. For the purpose ofthis report, I have construed the claim to be appended to claim 13
`as this claim recites tagging DNA and RNA with a first and second tag.
`
`Please note. the use of the phrase “any one of the preceding claims” to append many of the claims produces numerous inherent
`inconsistencies that results in a number of clarity issues. For the purpose of this report, my construction of claims presenting this
`problem is given below;
`
`Claim 10 has been construed as being appended to claim 9 which recites a second overhang.
`
`Claim 1 1 has been construed as being appended to claim 10 which recites a third and fourth adapter.
`
`Claim 12 has been construed as being appended to claim 1 l which recites sequencing said third and fourth adapters.
`
`Claim 17 has been construed as being appended to any one of claims 13—16 which recite a first RNA and a first DNA.
`
`Claim 18 has been construed as being appended to any one of claims 13—17 which recite a first RNA and a first DNA.
`
`Claim 76 has been construed as being appended to claim 75 which recites a reaction mixture.
`
`Claim 77 has been construed as being appended to any one of claims 75-76 which recites a reaction mixture.
`
`Claim 94 has been construed as being appended to any one of claims 92-93 which recites a kit.
`
`Claim 95 has been construed as being appende