DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Applicant’s amendment to the claims submitted on 1/9/2026 is acknowledged.
Claims 77-105 are currently pending and being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (for example see pg 16, ln 12-14 and pg 61, Bibliography). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Response to Remarks
No IDS was filed with the response to amendment submitted on 1/9/2026, therefore the references in the specification remain unconsidered unless otherwise cited by the examiner on form PTO-892.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825. This application contains a “Sequence Listing” as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3)). A copy of the "Sequence Listing" in computer readable form (CRF) has been submitted; however, the content of the CRF does not comply with one or more of the requirements of 37 CFR 1.822 through 1.824, as indicated in the "Error Report" that indicates the "Sequence Listing" could not be accepted. Refer to attachment or document "Computer Readable Form (CRF) for Sequence Listing – Defective" dated 1/12/2026.
Required response – Applicant must provide:
A replacement "Sequence Listing" part of the disclosure, as described above in item 1); together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the replacement "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter and
An amendment to the specification to remove the “Sequence Listing previously submitted as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3))
If the replacement "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, Applicant must also provide:
A CRF in accordance with 1.821(e)(1) or 1.821(e)(2) as required by 37 CFR 1.825(b)(6)(ii); and
Statement according to item 2) a) or b) above.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d) (see Figure 2). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Response to Remarks
Applicant’s inclusion of a sequence listing XML file on 1/9/2026 is acknowledged. However, the sequence listing was submitted in the incorrect format. Sequence listings submitted in either PCT applications or U.S. national phase applications submitted under 35 U.S.C. 371(c) that have an international filing date BEFORE July 1, 2022 must be in ASCII test format and comply with WIPO Standard ST.25 and/or 37 CFR 1.821 through 1.825. The sequence listing submitted on 1/9/2026 was filed as ST.26, when the international filing date is 6/11/2021 (BEFORE 7/1/2022). Correction is required.
Applicant has correctly pointed out that the sequences in Figure 2 are referenced in the specification. However, the manner in which the SEQ ID NOs are referenced does not clearly indicate which sequence corresponds to which SEQ ID NO. “respectively, in order of appearance” does not adequately convey the sequence identity of the sequences in the figure, given that the “order of appearance” could be interpreted in numerous ways given the layout of the figure. Correction is required.
Specification
Applicant’s amendment to the specification (submitted 1/9/2026) to properly denote trade names and marks used in commerce is acknowledged. Given that this was not a formal objection to the specification, there is no objection to be withdrawn.
Claim Objections
Withdrawn:
The objection to claim 84 is withdrawn in light of Applicant’s amendment to the claim.
The objection of claims 89-91 as being in improper form because a multiple dependent claim cannot depend from any other multiple dependent claim is withdrawn due to applicant’s amendment to claim 89 to depend directly from claim 77.
Maintained:
Claims 92-99 are objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim cannot depend from any other multiple dependent claim. See MPEP § 608.01(n). Accordingly, the claims have not been further treated on the merits.
Response to Remarks
Applicant’s amendments to make claim 89 depend directly from claim 77 and remove the multiple dependencies rectifies the objection made to claims 89-91. However, claims 92-99 remain in improper form, given that claim 92 depends from “any of claims 77-82, 84-88, or 90-91”. Claim 84 depends from claim 83, which is a multiple dependent claim and therefore places claim 92 (and its dependent claims), in improper form for depending from another multiple dependent claim.
Claim Rejections - 35 USC § 112b - Indefiniteness
The rejection of claims 77-88 and 104-105 under 35 U.S.C. 112(b) are withdrawn in light of Applicant’s amendments to the claims.
Claim Rejections - 35 USC § 112d
The rejection of claim 79 under 35 U.S.C. 112(d) is withdrawn in light of Applicant’s amendments to the claims.
Claim Rejections - 35 USC § 103
Withdrawn:
The rejections of claims under 35 U.S.C. 103 as presented in the Office Action of 7/11/2025 are withdrawn in light of Applicant’s amendments to the claims. New rejections to address said amendments are presented below.
New (Necessitated by Amendments):
Claims 77-82, 85, and 87-89 are rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025) and Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1).
Adey 2012 teaches a method for whole-genome bisulfite sequencing using tagmentation via transposases with adapter pairs (Abstract and Figure 1B).
Regarding claims 77 and 85: Adey 2012 teaches fragmenting a plurality of genomic DNA samples comprising one or more loci of interest with a transposase loaded with a pair of adapters resistant to conversion of cytosines (Figure 1B, “adaptors to be incorporated were methylated at all cytosine residues to maintain cytosine identity” Introduction paragraph 5). The plurality of samples were differentially barcoded lymphoblastoid cell lines to construct multiple libraries of genomic DNA (Results – Ultra-low-input transposase-based WGBS library performance). Adey 2012 teaches converting unmethylated cytosine to uracil in the fragmented genomic DNA from the plurality of samples (“The fragmented, adapted, double-stranded genomic DNA is then subjected to standard bisulfite treatment for the conversion of unmethylated cytosine to uracil”, Introduction paragraph 5). Adey 2012 teaches then amplifying the converted…fragmented genomic DNA and sequencing to determine methylation status (Introduction paragraph 5 and Methods-Tn5mC-seq library construction and sequencing).
Adey 2012 does not teach that the adapters attached to the transposase contain a barcode sequence (claim 77a) or enrichment of one or more loci of interest from the fragmented genomic DNA (claim 77c and claim 85). However, inclusion of a barcode sequence in adapters used in tagmentation and in-solution target enrichment of specific genomic loci of interest was known in the art, as taught by Adey 2010.
Adey 2010 teach a method in which “transposase-catalyzed adaptor insertion” can be used to barcode a plurality of individual samples prior to pooling (96-plex sample indexing). Adey 2010 teach that the adapters themselves could contain the barcode sequence (96-plex sample indexing and Table S4). In this method, 96 individual libraries were fragmented in individual reaction volumes in which each volume was assigned a unique barcode placed on one of the adapters. After barcode incorporation samples were then pooled (96-plex sample indexing). Adey 2010 also teach that specific genomic loci can be enriched by targeted sequence capture prior to fragmenting by the transposome (Low input targeted sequence capture of the human exome). Adey 2010 specifically employs an in-solution enrichment method from Nimblegen comprised of biotinylated DNA probes (relevant to claim 85; “Nimblegen SeqCap EZ Exome probes v1.0”). Adey 2010 teaches amplifying and then sequencing the enriched, fragmented, genomic DNA (Materials and methods - Targeted sequence capture of the human exome).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 with the method of Adey 2010 to include barcodes in the adapter sequences and enrich for target sequences. One would be motivated to include barcodes on the adapters given that inclusion of barcode sequences allows for multiplexing of samples and increases the throughput of the sequencing assay, as taught by Adey 2010 (96-plex sample indexing). One would have a reasonable expectation of success given that Adey 2010 successfully generated 96 different barcoded adapters that were then used to multiplex 96 different libraries. One would be motivated to enrich for target sequences given the assertion by Adey 2010 that enrichment of specific genomic loci allows for “significantly lower input requirement for genomic DNA” (Low input targeted sequence capture of the human exome). One would have a reasonable expectation of success given that Adey 2010 successfully enrich for the human exome using a commercially available kit for Nimblegen SeqCap that they specifically adapt for their adaptor sequences (Low input targeted sequence capture of the human exome).
Adey 2012 in view of Adey 2010 teaches tagmentation of genomic DNA with adapters that include barcodes. Adey 2012 teaches that the adapters used in tagmentation are resistant to conversion of cytosines by the inclusion of fully methylated cytosines, specifically so that “cytosine identity” was maintained during bisulfite treatment. Adey 2010 does not teach that the barcodes used in their methodology are resistant to bisulfite conversion, given that bisulfite conversion was not used in their method and therefore Adey 2012 in view of Adey 2010 does not explicitly teach the use of barcodes that are resistant to bisulfite conversion. However, use of barcodes that are resistant to bisulfite conversion is known in the art, as taught by Adey 2018.
Adey 2018 teaches a method of preparing a sequencing library for determination of methylation status of nucleic acids (Abstract). Adey 2018 teaches indexing nucleic acids with at least one index sequence (tag or barcode) using the transferred strand from the tagmentation process (paragraph [0060]). Adey 2018 teaches that these index sequences are fully methylated or do not contain cytosine (paragraph [0063]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010 with the method of Adey 2018 to ensure that the barcode within the resistant adapter was also resistant to bisulfite conversion. One would be motivated to do so given the teaching by Adey 2012 that fully methylated cytosines are resistant to bisulfite conversion and enable the maintenance of cytosine identity, and thus sequence identity, of the adapter. One would have a reasonable expectation of success given that Adey 2018 teaches that these adapters with barcode sequences that are fully methylated or cytosine-depleted can be successfully used to tagment nucleic acids and “do not have a significant impact on transposase efficiency” (paragraph [0063]).
Regarding claim 78: Adey 2012 teaches fragmentation of genomic DNA samples from humans (“lymphoblastoid cell line (GM20847)”; Ultra-low-input transposase-based WGBS library performance).
Regarding claim 79: Adey 2018 teaches that the barcode does not contain cytosine nucleotides (paragraph [0063]).
Regarding claim 80: Adey 2012 teaches that the pair of adapters comprises fully methylated cytosines (“the adaptors to be incorporated were methylated at all cytosine residues to maintain cytosine identity during bisulfite treatment”; Introduction paragraph 5).
Regarding claim 81 and 82: Adey 2012 teaches that the transposase used is a hyperactive transposase Tn5 (“a hyperactive derivative of the Tn5 transposase”, Introduction paragraph 4; “Ez-Tn5 transposase”, Methods-Tn5mC-seq library construction and sequencing).
Regarding claim 87: Adey 2012 teaches that the that the unmethylated cytosine is converted into uracil via bisulfite treatment (“The fragmented, adapted, double-stranded genomic DNA is then subjected to standard bisulfite treatment for the conversion of unmethylated cytosine to uracil”, Introduction paragraph 5).
Regarding claim 88: Adey 2012 teaches that PCR amplification is performed using primers specific to the pair of adapters (Figure 1b).
Regarding claim 89: Adey 2012 teaches sequencing the sequencing library (Methods - Tn5mC-seq library construction and sequencing).
Claim 86 is rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025) and Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1) as applied to claims 77-82, 85, and 87-89 above, and further in view of Gnirke et al. (WO 2009/099602 A1; cited on PTO-892 of 7/11/2025).
The teachings of Adey 2012 in view of Adey 2010 and Adey 2018 are detailed above. Relevant to the instantly rejected claims, Adey 2012 in view of Adey 2010 and Adey 2018 teach enriching for specific loci of interest in-solution, namely the human exome (Claim 77c and Claim 85).
Adey 2012 in view of Adey 2010 and Adey 2018 does not teach enriching for target sequences using biotinylated RNA baits that are specific to the target loci of interest. However, enriching for genomic loci of interest using biotinylated RNA bait was known in the art, as taught by Gnirke et al.
Gnirke et al. teaches generation of biotinylated RNA bait sequences that can be used for capture enrichment of target DNA sequences (pg 5, ln 9-18; pg 7, ln 6-7; Fig 3).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010 and Adey 2018 with the method of Gnirke et al. One would be motivated to use biotinylated RNA baits given the assertion by Gnirke et al. that "RNA-DNA duplex is more stable than a DNA-DNA duplex, and therefore provides for potentially better capture of nucleic acids" (pg 37, ln 3-5). One would have a reasonable expectation of success given that Gnirke et al. demonstrate the successful generation of biotinylated RNA baits that are then used to enrich genomic DNA samples for target sequences in their working examples 1 and 2 (pg 42-72).
Claims 83-84 are rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025), Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1) and Gnirke et al. (WO 2009/099602 A1; cited on PTO-892 of 7/11/2025) as applied to claims 77-82 and 85-89 above, and further in view of Spektor et al. (Genome Research, 2019; cited on PTO-892 of 7/11/2025) and Weichenhan et al. (Lymphoma, 2019; cited on PTO-892 of 7/11/2025).
The teachings of Adey 2012 in view of Adey 2010, Adey 2018, and Gnirke et al. are detailed above. Relevant to the instantly rejected claims they teach the construction of a transposome consisting of a transposase with a pair of barcoded adapters which is used to fragment genomic DNA and append the pair of adapters to either end of the DNA fragments. Adey 2012 teaches end repair and gap filling of the genomic DNA fragment-adapter complexes by hybridizing a fully methylated oligonucleotide to each adapter, and then performing gap repair with a T4 DNA polymerase (Figure 1B and Methods-Tn5mC-seq library construction and sequencing).
Adey 2012 in view of Adey 2010, Adey 2018, and Gnirke et al. does not explicitly teach methylated end repair using individual nucleotides that comprise methylated cytosine. However, end repair in the process of tagmentation with methylated cytosines was known in the art, as taught by Spektor et al.
Spektor et al teach using a transposome with adapters to fragment and append adapters to genomic DNA. They then teach applying a mixture of dNTPs, which comprise 5-mdCTP, to end repair the fragment-adapters which are incorporated using a Klenow (Methods - methyl-ATAC-seq).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010, Adey 2018 and Gnirke et al. with the method of Spektor et al. One would be motivated to employ methylated end repair given the teaching by Weichenhan et al. (who first employ this method) that end repair through incorporation of dNTPs is more efficient than the methylated oligonucleotide incorporation step taught by Adey 2010 and Adey 2012 (Abstract). Weichenhan et al. first employ the method using a BstI DNA polymerase (large fragment) on phage DNA to demonstrate the technique (2.4 Gap Repair and Strand Displacement). Spektor et al. use a Klenow fragment polymerase which successfully performs the same function of methylated gap end repair on human DNA, demonstrating that this type of polymerase can be used for experiments involving human genomic DNA.
Claims 90-91 are rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025) and Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1) as applied to claims 77-82, 85, and 87-89 above, and further in view of Liu et al. (US 2019/0177792 A1).
The teachings of Adey 2012 in view of Adey 2010 and Adey 2018 are outlined in the rejections above. Relevant to the instantly rejected claims, Adey 2012 in view of Adey 2010 and Adey 2018 teaches a method of constructing a sequencing library through tagmentation with barcoded adapters, pooling, enriching, converting, and ultimately sequencing said sequencing library.
Adey 2012 in view of Adey 2010 and Adey 2018 do not teach using shallow sequencing, with a coverage of about 1 to about 2 reads per CpG. However, use of shallow sequencing for methylation sequencing is known in the art, as taught by Liu et al.
Liu et al. teach a method of methylation sequencing analysis of gDNA (paragraph [0007 and 0095]). Specifically, Liu et al. teach performing ultra-low pass whole genome bisulfite sequencing (ULP-WGBS; paragraph [0089]). Liu et al. teaches that ultra-low pass sequencing is 0.01-3X coverage, and teaches that sequencing coverage using ULP-WGBS is 1X or 2X (reads on about 1 to about 2 reads per CpG; paragraph [0015 and 0089]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010 and Adey 2018 to employ shallow sequencing as taught by Liu et al. One would be motivated to do so given the assertion by Liu et al. that shallow sequencing “provides for the accurate characterization of genomic DNA at a significant savings of cost and time” (paragraph 0098]). One would have a reasonable expectation of success given that Liu et al. successfully performs low coverage/shallow sequencing using a whole genome bisulfite sequencing approach to determine methylation levels (paragraph [0110]).
Claims 100-103 are rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025), Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1) and Ahern (1995; cited on PTO-892 of 7/11/2025).
The teachings of Adey 2012 in view of Adey 2010 and Adey 2018 are outlined in the rejections above. Relevant to the instantly rejected claims, Adey 2012 in view of Adey 2010 and Adey 2018 teaches a method of constructing a sequencing library for determining the methylations status of one or more loci of interest for a plurality of samples comprising a pair of transposon adapters resistant to conversion of cytosines and comprising a barcode sequence, wherein the barcode sequence is resistant to conversion of cytosines during bisulfite treatment, wherein the barcode sequence is a sequence on one of the adapters (claim 100). They also teach that the transposase is a hyperactive transposon 5 (Tn5) (claims 101-103).
Adey 2012 in view of Adey 2010 and Adey 2018 does not teach incorporating all of these materials into a kit. However, inclusion of necessary reagents for performing a reaction in a kit was known in the art, as taught by Ahern.
Ahern teaches aspects of kits of reagents. Ahern teaches that a kit supplies all of the necessary reagents for a particular application and provides detailed instructions to follow (p.20 - The kit concept, Saving time and money).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010 and Adey 2018 to include the reagents necessary for sequencing library construction in a kit, as taught by Ahern. One would be motivated to include these reagents in a kit given the assertion by Ahern that inclusion of reagents in a kit saves time and money and is highly convenient (p 20. The kit concept, Saving time and money).
Claim 104 is rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025), Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1) and Ahern (1995; cited on PTO-892 of 7/11/2025) as applied to claims 100-103 above, and further in view of Gnirke et al. (WO 2009/099602 A1; cited on PTO-892 of 7/11/2025).
The teachings of Adey 2012 in view of Adey 2010, Adey 2018, and Ahern are detailed above. Relevant to the instantly rejected claim, they teach inclusion of reagents in a kit for performing a method of constructing a sequencing library for methylation sequencing.
Adey 2012 in view of Adey 2010, Adey 2018, and Ahern do not teach including biotinylated RNA bait specific to loci of interest in their kit.
However, usage of biotinylated RNA baits for targeted enrichment of loci of interest was known in the art, as taught by Gnirke et al. (pg 5, ln 9-18; pg 7, ln 6-7; Fig 3).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010, Adey 2018, and Ahern to include the reagents necessary for target enrichment of loci of interest, as taught by Gnirke et al. One would be motivated to include this reagent in the kit given the teachings of Gnirke et al. and Adey 2010 that targeted enrichment of loci of interest decreases the amount of input DNA required for the assay.
Claim 105 is rejected under 35 U.S.C. 103 as being unpatentable over Adey et al. 2012 (hereinafter “Adey 2012”; Genome Research, 2012; cited on PTO-892 of 7/11/2025) in view of Adey et al. 2010 (hereinafter “Adey 2010”; Genome Biology, 2010; cited on PTO-892 of 7/11/2025), Adey et al. 2018 (hereinafter “Adey 2018”; US 2018/0355348 A1), Ahern (1995; cited on PTO-892 of 7/11/2025), and Gnirke et al. (WO 2009/099602 A1; cited on PTO-892 of 7/11/2025) as applied to claims 100-104 above, and further in view of Horvath (WO 2015/048665 A2; cited on PTO-892 of 7/11/2025).
The teachings of Adey 2012 in view of Adey 2010, Adey 2018, Ahern, and Gnirke et al. are detailed above. Relevant to the instantly rejected claims, they teach a kit in which reagents are included for tagmentation using transposase with barcoded adapters and biotinylated RNA bait specific for loci of interest.
Adey 2012 in view of Adey 2010, Adey 2018, Ahern, and Gnirke et al. do not teach that the loci of interest are associated with an epigenetic clock. However, enrichment of target loci that are associated with epigenetic clocks was known in the art, as taught by Horvath.
Horvath teaches a method in which analyzing methylation status at a subset of CpG sites in the genome can be used to determine chronological/biological age of a sample (pg 3, ln 8-22). Horvath teaches that a kit can be supplied in which probes specific “for at least one genomic DNA sequence in a biological sample, wherein the genomic DNA sequences comprises a CG loci” (pg 26, ln 21-23).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Adey 2012 in view of Adey 2010, Adey 2018, Ahern, and Gnirke et al. to include the reagents necessary for target enrichment of loci that are associated with an epigenetic clock, as taught by Horvath. One would be motivated to examine these CpG sites given the assertion by Horvath that determination of chronological age can be used to “study the effects of medication, food compounds and/or special diets on the biological age of humans” (pg 5, ln 7-8). One would have a reasonable expectation of success given that Horvath has taught the sequences of sets of specific loci associated with epigenetic clocks (Tables 1-5).
Response to Remarks
Applicant's arguments filed 1/9/2026 have been fully considered but they are not persuasive. Applicant’s traversal of the 103 rejections of the claims over Adey 2012 in view of Adey 2010 (pg 12-14 of Remarks), Gnirke, Spektor, and Weichenhan (pg 15 of Remarks), and Horvath (pg 15-16 of Remarks) were solely in reference to an amended limitation added to the claims in the response submitted on 1/9/2026. The previous rejections have been withdrawn, rendering Applicant’s arguments against said rejections moot. This additional limitation (“wherein the barcode sequence is resistant to conversion of cytosines during bisulfite treatment”) has been addressed in the new rejections presented above.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683