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 .
Status of Claims
Claims 1, 7-9, 11, 13-17, 26, 28, 55, 60-63, 67 and 69-72 are currently pending. Claims 1, 7, 63, 67 and 69-72 have been amended by Applicants’ amendment filed 10-07-2025. Claims 57, 59, 64-66 and 68 have been canceled by Applicants’ amendment filed 10-07-2025. No claims have been added by Applicants’ amendment filed 10-07-2025.
Applicant's election with traverse of Group I, claims 1 and 7-13 (claims 10 and 12, now canceled), directed to a method, and the election of Species as follows:
Species (A): wherein attaching comprises ligating the first oligonucleotide of the plurality of oligonucleotides to the first biological molecule (claim 7);
Species (B): wherein the plurality of oligonucleotides further comprises one or more adaptor sequences (claim 11);
Species (C): wherein the tissue section is a biopsy sample (claim 17); and
Species (D): wherein the first signal sequence is a tag oligonucleotide (claim 28), in the reply filed on September 23, 2019 was previously acknowledged.
Claims 14-18, 26, 28-32, 53 and 54 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on September 23, 2019.
Claims 8, 9 and 12 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
The restriction requirement was deemed proper and was made FINAL.
The restriction requirement was deemed proper and was made FINAL.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1, 7, 11, 13, 55, 60-63, 67 and 69-72 are under consideration to which the following grounds of rejection are applicable.
Interview Summary
Applicant’s representative Ashley Sperbeck contacted the Examiner to set up an interview, where such interview was held on August 11, 2025. The novelty of the invention, organosilane initiator species, and Applicant’s proposed amendments to the claims were discussed including whether the proposed amendments may be taught in the prior art references. The Examiner indicated that providing additional limitations to claim 1 may assist in moving prosecution forward.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on October 7, 2025 has been considered. An initialed copy of the IDS accompanies this Office Action.
Priority
The present application, filed September 29, 2017, is a 35 U.S.C. 371 national stage filing of
International Application No. PCT/US16/28118, filed on April 18, 2016, which claims the benefit of claims
the benefit of US Provisional Patent Application 62/149,385, filed April 17, 2015; US Provisional Patent Application 62/148,747, filed April 17, 2015 (now abandoned); and US Provisional Patent Application 62/148,758, filed April 15, 2015.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed October 7, 2025 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Claim Rejections - 35 USC § 112(a) – New Matter
The rejection of claims 1, 7, 11, 13, 55, 57 and 59-72 is withdrawn under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention due to Applicant’s amendments to the claims, in the reply filed October 7, 2025.
Maintained Objections/Rejections
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 7, 11, 13, 55, 60-63, 67 and 69-72 is maintained under 35 U.S.C 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claims 1 and 63 are indefinite for the recitation of the term “a surface of the substrate comprises an initiator species” such as recited in claim 1, line 6 because the purpose of the initiator species in the method of claims 1 and 63 is completely unclear. Instant claims 1 and 63 recite a surface of a substrate comprising an initiator species; however, this species is not recited to have any function or to serve any purpose in the method of claims 1 and 63 and, thus, the metes and bounds of the claim cannot be determined.
Claims 1 and 63 are indefinite for the recitation of the terms “wherein each surface bonding group of the at least two surface bonding groups differs” such as recited in claim 1, lines 9-10 because the surface bonding groups of one organosilane, such as MeO3Si, (MeO)3Si, (EtO)3Si, (AcO)3Si, (MeN)3Si, and (OH)3Si) are all the same (e.g., they do not differ as required). For example, the surface bonding groups of (MeO)3Si are the three (3) OMe groups as evidenced by Acres (Abstract), wherein mono-pedal, bi-pedal and tri-pedal structures are illustrated below:
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and, thus, the metes and bounds of the claim cannot be determined.
Claims 1 and 63 are indefinite for the recitation of the term “each surface bonding group of the at least two surface bonding groups is selected from the group consisting of MeO3Si” such as recited in claim 1, lines 11-12 because MeO3Si because MeO3Si is an improper structure that does not have at least two surface bonding groups (e.g., as compared to (MeO)3Si). Moreover, it is unclear whether the surface bonding groups are bound to anything including the surface of the substrate, where such binding would require pre-hydrolysis of one or more of the bonding groups of the initiator species and, thus, the metes and bounds of the claim cannot be determined.
Claims 1 and 63 are indefinite for the recitation of the term “each feature of the plurality of features comprises an oligonucleotide attached to an area on a surface of the substrate” such as recited in claim 1, lines 14-15 because the structure of the substrate surface is completely unclear with regard to how the initiator species (e.g., organosilanes) is related to the features and/or to the oligonucleotides attached to the surface of the substrate including whether the substrate surface comprises: (i) organosilanes bound to (or not bound to) a feature; (ii) organosilanes and oligonucleotides bound to separate features on the surface of the substrate; (iii) whether each oligonucleotide is bound to an initiator species located in a feature of the substrate surface; or (iv) whether the substrate surface comprises some other structure and, thus, the metes and bounds of the claim cannot be determined.
Claims 1 and 63 are indefinite for the recitation of the term “identifying, using the spatial barcode array, a position of one or more mutations or epigenetic modifications to within 0.5 mm” such as recited in claim 1, lines 37-38 because it is unclear what the one or more mutations or epigenetic modifications is identified within (e.g., one the spatial barcode array, in the biological sample, etc.); and it is unclear what the 0.5 mm is relative to (e.g., to within 0.5 mm of the next modification, of the next feature, to the nearest oligonucleotide, etc.) and, thus, the metes and bounds of the claim cannot be determined.
Claim 7 is indefinite for the recitation of the term “prior to ligating” such as recited in claim 7, line 2 because claim 7 depends from claim 1, wherein claim 1 does not recite a step of ‘ligating’ and, thus, the metes and bounds of the claim cannot be determined.
Claim 70 is indefinite for the recitation of the term “a surface of the substrate comprises a coating of a polymer” such as recited in claim 70, lines 1-2 because claim 70 depends from claim 1, wherein claim 1 does not recite that the substrate comprises a polymer coating. Moreover, claim 1 recites that the substrate surface comprises an initiator species, such that claim 70 cannot recite that the substrate surface comprises something different from what is indicated in the independent claim and, thus, the metes and bounds of the claim cannot be determined. The Examiner suggests that Applicant amend the claim to recite, for example, “a surface of the substrate further comprising…”.
Claim 70 is indefinite for the recitation of the term “the coating of the polymer is below 200 (sub-200) nanometer (nm) coating” in lines 2-3 because it is unclear whether the term refers to a plurality of coating layers (e.g., a coating below a 200 nm coating); whether the term refers to a structural dimension of the polymer coating such as length, width, thickness, etc.; or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 70 is indefinite for the recitation of the term “(sub-200)” such as recited in claim 70, line 3 due to the use of use parentheses to comment on or qualify part of the sentence. It is unclear whether the limitation in parentheses is meant to be a limitation in the claims or whether it is only a suggestion, an example of a preferred embodiment, or a synonym. Accordingly, the metes and bounds of the claim are not clear.
Claims 11, 13, 55, 60-62 and 71 are indefinite insofar as they ultimately depend from claim 1. Claims 67, 69 and 72 are indefinite insofar as they ultimately depend from claim 63.
Claim Rejections - 35 USC § 112(d)
The rejection of claim 70 is maintained, and claim 7 is newly rejected, under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it
depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 7 recites (in part) “phosphorylating or adenylating a 5’ end of the first oligonucleotide prior to ligating” in lines 1-2. Claim 7 depends from instant claim 1, wherein claim 1 does not recite a step of ligating. Thus, claim 7 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 70 recites (in part) “wherein a surface of the substrate comprises a coating of a polymer, and wherein the coating of the polymer is below 200 (sub-200) nanometer (nm) coating” in lines 1-3 because claim 70 depends from instant claim 1, wherein claim 1 already recites that the substrate surface comprises an initiator species. Thus, claim 70 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 7, 11, 13, 55, 60-63, 67 and 69-72 is maintained under 35 U.S.C. 103 as being unpatentable over Eltoukhy et. al. (hereinafter “Eltoukhy”) (US Patent Application Publication No. 20160046986, filed on September 22, 2015, published February 18, 2016; International Application PCT/US2014/072383, filed December 24, 2014; of record) in view of Rajasekaran et. al. (hereinafter “Rajasekaran”) (US Patent Application No. 20140349888, published November 27, 2014; PCT/US2013/025190, fled February 7, 2013; of record) as evidenced by Holt et al. (hereinafter “Holt”) (Genome Research, 2008, 18, 839-846; of record); and Gunderson et al. (hereinafter “Gunderson”) (US Patent No. 10619204, issued April 14, 2020; PCT/EP2015/076353, filed November 11, 2015; of record); and Illumina (Illumina, 2009, 1-4); and Beckman Coulter (Beckman Coulter, 2000, 1-4).
Regarding claims 1 (in part), 11, 13 and 63 (in part), Eltoukhy teaches methods to reduce or combat the errors introduced by the sample preparation and sequencing processes for all molecules that are converted and sequenced (paragraph [0005]). Eltoukhy teaches providing cell free polynucleotides from bodily fluid of (a) a test sample and (b) a control sample; then tagging polynucleotides, wherein the tag includes a source identifier (test or control) and, optionally a further identifier (optionally with duplex tags), such that polynucleotides can be uniquely or non-uniquely tagged (interpreted as contacting a biological sample with spatial barcode array; tagged the same and/or differently; the oligonucleotide has a 5’ end and the biological molecule has a 3’ end; and at least two distinct barcodes, claims 1a, 1d, 63a and 63d) (Figure 8). Eltoukhy teaches a method for detecting and/or quantifying rare deoxyribonucleic acid (DNA) in a heterogeneous population of original DNA fragments, comprising tagging the original DNA fragments in a single reaction including within a single reaction vessel using a library of a plurality of different tags such that >30% or >50% of the fragments are tagged at both ends, wherein the plurality of different tags can be no more than any of 100, 500, 1000, 10,000 or 100,000 different tags (interpreted as at least two distinct tags, claims 1 and 63) (paragraph [0007]). Eltoukhy teaches that a barcode can comprise contiguous or non-contiguous sequences; and at least 1, 2, 3, 4, 5 or more nucleotides (interpreted as barcodes is at most 35 bases, claims 1a and 63a) (paragraph [0121]). Eltoukhy teaches that the invention provides a set of library adaptors that can be used to tag the molecules of interest (e.g., by ligation, hybridization, etc.), wherein the set of library adaptors can comprise plurality of polynucleotide molecules with molecular barcodes including polynucleotide molecules are less than or equal to 80 nucleotide bases in length, wherein the molecular barcodes are at least 4 nucleotide bases in length, and wherein the molecular barcodes are: (a) different from one another and have an edit distance of at least 1 between one another; (b) located at least one nucleotide base away from a terminal end of their respective polynucleotide molecules; (c) optionally, at least one terminal base is identical in all of the polynucleotide molecules; and (d) none of the polynucleotide molecules contains a complete sequencer motif (interpreting the polynucleotide molecules as tagged biological molecules; an edit distance of at least one; ligating; and oligonucleotides comprises adapters, claims 1b, 11 and 63b) (paragraph [0008]). Eltoukhy teaches that a library of polynucleotides comprising a plurality of polynucleotide molecules can also have distinct (with respect to each other) molecular barcode sequences with respect to at least 4, 10, 20, 30, 40, 50 or more nucleic acid bases, wherein the molecular barcode (also "barcode" or "identifier" herein) sequence is a nucleotide sequence that distinguishes one polynucleotide from another (interpreted as distinct barcode sequences including at least four distinct barcode sequences; identifies the oligonucleotide location to within 0.5 microns; and encompassing identifying x and y coordinates on an array, claims 1a, 13, 63a, 70 and 71) (paragraph [0126]). Eltoukhy teaches that a sequencing adaptor can comprise one or more barcodes including a sample barcode, which can comprise a predetermined sequence that can be used to identify the source of the polynucleotides (interpreted as tagged biological molecules, claim 1b and 63b) (paragraph [0137], last ten lines). Eltoukhy teaches analyzing a sample comprising nucleic acids from a subject, wherein the system includes a sequencer, bioinformatic software and internet connection for report analysis by, for example, a hand-held device or desktop computer (interpreted as analyzing sequencing information; generating a gene expression profile; and detecting a target sequence, claims 1c, 1d, 1f, 63c, 63d and 63f) (paragraph [0276]). Eltoukhy teaches a method for detecting copy number variation in a DNA molecule in a biological sample of a subject, comprising: (a) attaching adapters to ends of fragments generated from said DNA molecules in said biological sample of said subject, wherein said adapters tag a 5' end of a strand of an individual fragment among said fragments with a first tag and a 3' end of a complementary strand of said individual fragment with a second tag, thereby providing tagged fragment molecules (interpreted as attaching an oligonucleotide having a 5’ end and a biological molecule has a 3’end, claim 1d and 63d) (pg. 32, col 2, claim 19). Eltoukhy teaches in Figure 9B that the library of adaptors are ligated at both ends of the target polynucleotide molecules to provide a tagged target polynucleotide molecule, wherein the library adaptor is less than or equal to 80 nucleotide bases in length (interpreted as attaching an oligonucleotide having a 5’ end and a biological molecule has a 3’end, claim 1d and 63d) (paragraph [0152], lines 7-11; and Figure 9B). Eltoukhy teaches analyzing the nucleotide sequences with a programmed computer processor to identify one or more genetic variants in the nucleotide sample of the subject including one or more genetic variants are selected from the group consisting of base change(s), insertion(s), repeat(s), deletion(s), copy number variation(s) and transversion(s), wherein the one or more genetic variants include one or more tumor associated genetic alterations (interpreted as generating a gene expression profile; deletions, insertions, or substitutions; using barcodes to target nucleic acid positioning comprising one or more mutations or epigenetic modifications, claims 1e, 1f, 63e and 63f) (paragraph [0027]). Eltoukhy teaches that the substrate can be a bead or planar surface including a surface of a bead for an Illumina flow cell; and that the sample is subjected to proteinase K digestions, DNA is precipitated, and captured on a DNA purification column, where DNAs below 500 bp are selected with Ampure SPRI magnetic bead capture (interpreted as each feature having a size less than 0.5 mm, claims 1 and 63) (paragraphs [0131]; and [0287]), where it is known that SPRI beads are coated with carboxy groups, and have a size of 1 mm as evidenced by Beckman Coulter (pg. 3, first full paragraph). Eltoukhy teaches that the polynucleotides can be amplified including by PCR, and sequenced by massively parallel sequencing to simultaneously sequence any of at least 100, 1000, 10,000, 100,000, 1 million, 100 million, or 1 billion polynucleotide molecules, wherein sequencing methods include high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next Generation Sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLiD, Ion Torrent, or Nanopore platforms (interpreted as encompassing oligonucleotides on an array located in a feature size within 0.5 microns; and amplification and sequencing, claims 1 and 63) (paragraphs [0156]; and [0159]); wherein it is known that the 454 flow cell comprises a fiber optic slide with ~1.6 million 75-piocliter wells; and that in the Illumina system, templates are applied at high density to the flow cells, while Helicos applies templates at very high density as evidenced by Holt (pg. 840, col 1, first full paragraph; and col 2, first full paragraph; and pg 842, col 2, first full paragraph); and it is known that the number of features within a microarray includes about 5,000,000 templates/cm2 or higher as evidenced by Gunderson (col 70, lines 19-20). Eltoukhy teaches that the a sequencing adaptor is adapted to permit a sequencing instrument to sequence a target polynucleotide, wherein the sequencing adaptor comprises a nucleotide sequence that hybridizes or binds to a capture polynucleotide attached to a solid support of a sequencing system such as a flow cell (interpreting sequencing adaptors as tagged oligonucleotides; and interpreting attachment to a flow cell as contacting a biological sample with a spatial barcode array comprising a substrate comprising a plurality of features, claims 1a and 63a) (paragraph [0087]). Eltoukhy teaches that tagged cell-free DNA fragments are amplified by PCR, the amplified fragments are enriched using beads comprising oligonucleotide probes that specifically bind to a group of cancer-associated genes (interpreted as amplification and sequencing; oligonucleotides; a solid support; tagged fragments; generating a gene expression profile; and a target sequence, claims 1c, 1d, 1f, 63c, 63d and 63f) (paragraph [0336]). Eltoukhy teaches that the method comprises quantifying polynucleotides in the sample bearing a nucleotide sequence variant at each of a plurality of genetic loci; determining copy number variation (CNV) at each of the plurality of genetic loci, wherein the CNV indicates a genetic dose of a locus in the disease cell polynucleotides; determining with a programmed computer processor a relative measure of quantity of polynucleotides bearing a sequence variant at a locus per the genetic dose at the locus for each of a plurality of the loci; and comparing the relative measures at each of the plurality of loci, wherein different relative measures is indicative of tumor heterogeneity (interpreted as generating a quantitative gene expression profile; spatial information including obtaining information on the location of biological molecules with in the sample, claims 1g and 63g) (paragraph [0066]). Eltoukhy teaches that sequence reads or consensus sequences can be mapped to one or more selected genetic loci (e.g., as shown step (110), Figure 1), wherein a genetic locus can be, for example, a specific nucleotide position in the genome, a sequence of nucleotides (for example, an open reading frame), a fragment of a chromosome, a whole chromosome, or an entire genome (interpreted as spatial information including obtaining information on the location of biological molecules with in the sample, claims 1g and 63g) (paragraph [0176]). Eltoukhy teaches that a consensus sequence can be generated using any collapsing method disclosed herein, and then the consensus sequence can be mapped to locations in the genome, and reads mapped to a locus can be quantified (e.g., counted) (interpreted as generating a quantitative gene expression profile; spatial information including obtaining information on the location of biological molecules with in the sample, claims 1g and 63g) (paragraph [0178]). Eltoukhy teaches that each of the library adaptors comprises a molecular barcode that is at least 5, 6, 7, 8, 9 and 10 nucleotide bases in length and/or the library adaptors is from 10 nucleotide bases to 80 in length, and that in some cases, at least 1, 2, 3, or 4 terminal bases are identical in all library adaptors (interpreted as encompassing wherein the barcode sequence of 5-35 bases; and comprising an adaptor, claims 1, 11 and 63) (paragraph [0012]). Eltoukhy teaches that the present disclosure can be used to detect genetic variation in non-uniquely tagged initial starting genetic material (e.g., rare DNA) at a concentration that is less than 5% (interpreted as an initiator species) (paragraph [0251], lines 1-4). Eltoukhy teaches that a library of polynucleotides comprising a plurality of polynucleotide molecules can also have distinct (with respect to each other) molecular barcode sequences with respect to at least 4, 10, 20, 30, 40, 50 or more nucleic acid bases, wherein the molecular barcode (also "barcode" or "identifier" herein) sequence is a nucleotide sequence that distinguishes one polynucleotide from another (interpreted as distinct barcode sequences encompassing 5-35 bases, claims 1a and 63a) (paragraph [0126]).
Regarding claim 7, Eltoukhy teaches high-efficiency DNA tagging (>80%) is performed by blunt-end repair and ligation with 8 different octamers with overloaded hairpin adaptors (interpreting blunt-end repair and ligation as including phosphorylation of the oligonucleotide, claim 7) (paragraph [0289]). Eltoukhy teaches that a polynucleotide can include one or more subunits selected from a group including adenosine (interpreted as encompassing adenylation, claim 7) (paragraph [0082], lines 1-4). Eltoukhy teaches that a sequence adaptor can be a polynucleotide that comprises a sequence that hybridizes to one or more sequencing adaptors or primers, wherein the sequencing adaptor can comprise a sequence that hybridizes to a solid support, such as a flow cell sequence; and that the term "flow cell sequence" refers to a sequence that permits hybridization to a substrate, for example, by way of a primer attached to the substrate, wherein the substrate can be bead or a planar surface (interpreting beads etc. as a solid support; and interpreting the planar surface as a flat surface, claim 63a) (paragraph [0131]).
Regarding claims 55, 60 and 61, Eltoukhy teaches that the polynucleotides can be amplified including by PCR, and sequenced by massively parallel sequencing to simultaneously sequence any of at least 100, 1000, 10,000, 100,000, 1 million, 100 million, or 1 billion polynucleotide molecules, wherein sequencing methods include high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next Generation Sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLiD, Ion Torrent, or Nanopore platforms (interpreted as encompassing oligonucleotides on an array located in a feature size within 0.5 microns, 0.4 microns, 0.2 microns, and 0.1 microns; and amplification and sequencing, claims 1, 55, 60, 61 and 63) (paragraphs [0156]; and [0159]); wherein the feature size for Solexa sequencing is 1.0 microns to submicron levels as evidenced by Illumina (pg. 3, col 2, Data Density); and wherein it is known that the 454 flow cell comprises a fiber optic slide with ~1.6 million 75-piocliter wells; and that in the Illumina system, templates are applied at high density to the flow cells, while Helicos applies templates at very high density as evidenced by Holt (pg. 840, col 1, first full paragraph; and col 2, first full paragraph; and pg 842, col 2, first full paragraph); and it is known that the number of features within a microarray includes about 5,000,000 templates/cm2 or higher as evidenced by Gunderson (col 70, lines 19-20). Eltoukhy teaches that a library of polynucleotides comprising a plurality of polynucleotide molecules can have an edit distance of at least one, wherein in some cases the plurality of polynucleotide molecules can have an edit distance of at least 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more; and the edit distance can be a Hamming distance (interpreted as including an edit distance of 4, claims 1a, and 63a) (paragraph [0130]). Eltoukhy teaches that DNA fragments, comprising tagging the original DNA fragments in a single reaction including within a single reaction vessel using a library of a plurality of different tags such that >30%or >50% of the fragments are tagged at both ends, wherein the plurality of different tags (interpreted as barcode sequences for each oligonucleotide are different, claims 1 and 63) (paragraph [0008]).
Regarding claims 62, Eltoukhy teaches that sequencing adaptor can further comprise a sequence hybridizing to a solid support including a planar surface, such as a flow cell sequence (interpreted as a solid support; and a flat surface, claims 62 and 67, in part) (paragraphs [0131]; and [0137], lines 4-6). Eltoukhy teaches that selective enrichment can be performed using a solid support (e.g., beads), wherein the beads can comprise probes (e.g., oligonucleotides) specifically hybridizing to certain sequences (interpreted as a solid support, claim 62) (paragraph [0213], lines 4-6).
Regarding claims 71 and 72, Eltoukhy teaches that the molecular barcodes are located at least 10 nucleotide base away from a terminal end of an adapter, wherein the plurality of library adapters includes at least 2, 4, 6, 8, 10, 20, 30, 40 or 50 different molecular barcodes, or from 2-100, 4-80, 6-60 or 8-40 different molecular barcodes (interpreted as each oligonucleotide comprising an adaptor, and at least three distinct barcode sequences, claims 1, 63, 71 and 72) (paragraph [0013]). Eltoukhy teaches that a library of polynucleotides comprising a plurality of polynucleotide molecules can also have distinct (with respect to each other) molecular barcode sequences (interpreted as distinct barcode sequences, claims 71 and 72) (paragraph [0126]).
Eltoukhy does not specifically exemplify the initiator species as recited in claims 1 and 63 (claims 1 and 63, in part); a polymer gel coats the initiator species (claim 67); a polyacrylamide gel and/or a PDMS gel (claim 69); and a polymer coating below 200 nm (claim 70).
Regarding claims 1 (in part) and 63 (in part), Rajasekaran teaches formulations, substrates and arrays, and methods for identifying peptide sequences useful for diagnosis and treatment of disorders, wherein substrates and arrays comprise a porous layer for synthesis and attachment of polymers or biomolecules (interpreted as substrates and arrays, claims 1 and 63) (Abstract). Rajasekaran teaches that the uses of such an array include, but are not limited to, diagnostic microbiology, including the detection and identification of pathogens, investigation of anti-microbial resistance, epidemiological strain typing, investigation of oncogenes, analysis of microbial infections using host genomic expression, and polymorphism profiles; as well as, determining binding specificity of a plurality of antibodies to one or more features of the array; and imaging an intensity profile (interpreted as generated a gene expression profile, claim 1) (paragraphs [0003]; [0050]; and [0348]). Rajasekaran teaches peptide arrays with distinct analyte-detecting regions or probes can be assembled on a single substrate (paragraph [0005]). Rajasekaran teaches an array of features attached to a surface at positionally-defined locations (interpreted as an array of features on a solid support having an x and y location, claims 1 and 63) (paragraph [0014]). Rajasekaran teaches that the method includes producing an array of features, comprising: obtaining a surface; attaching the features to the surface, the features each comprising a collection of peptide chains of determinable sequence and intended length, wherein within an individual feature, the fraction of peptide chains within the collection having the intended length is characterized by an average coupling efficiency for each coupling step of at least 98% (interpreted as features on a surface or solid support, claims 1 and 63) (paragraph [0021]). Rajasekaran teaches that substrates can be surfaced derivatized in a semiconductor module as explained in US Patent Application 2010/0240555, herein incorporated by reference in its entirety, for all purposed, wherein surface derivatization is a method wherein an amino silane group is added to the substrate so that free amino groups are available for coupling a biomolecule (interpreted as encompassing organosilanes for coupling biomolecules; and binding biomolecules, claims 1 and 63) (paragraph [0228]). Rajasekaran teaches that the wafer surface is derivatized using aminopropyl triethoxysilane (APTES) (interpreted as comprising at least two surface bonding groups; and (EtO)3Si, claims 1 and 63) (paragraph [0283]). Rajasekaran teaches wafer fabrication, silane deposition is generally needed to promote the chemical adhesion of an organic compound (photoresist) to a non-organic substrate (wafer), wherein the silane acts as a sort of "bridge," with properties that will bond to both the photoresist and wafer surface including hexamethyldisilizane (HMDS) (interpreted as an organosilane initiator species, claim 66) (paragraph [0217], lines 8-14). Rajasekaran teaches that the plurality of pillars are present at a density of greater than 10,000/cm2; that the surface area of each pillar is 1 mm2; distance between the surface of each pillar and the lower surface of the layer is 2,000-7,000 angstroms; and the center of each pillar is at least 2,000 angstroms from the center of any other pillar (interpreted as encompassing less than 0.5 microns to 0.1 microns, claims 55, 60 and 61) (paragraphs [0023]; and [0034]).
Regarding claims 67, 69 and 70, Rajasekaran teaches that porous layers are permeable, polymeric materials of porous structure which have a functional group native to the constituent polymer or which is introduced to the porous layer for attachment of the first peptide building block, wherein the polymeric material includes polyacrylamides, wherein the porous layer can range from 0.01 microns to about 1,000 microns (interpreted as polyacrylamide polymer, claims 67 and 70) (paragraph [0199]). Rajasekaran teaches that Figures 2A and 2B illustrate a derivatized surface (e.g., a surface derivatized wafer) with a linker molecule attached is spun coat with a photoactive formulation (photoresist) as described herein, wherein the resist thickness can be 100 nm to 200 nm to enable better photoacid diffusion; and the spin speed can be modified to achieve the desired thickness of the resist (interpreted as a coating including a sub-200 nm coating of a polymer including polyacrylamide, claims 67 and 70) (paragraph [0238]; and Figure 2). Rajasekaran teaches in Figure 2F, a cap film solution coat is applied on the wafer to prevent the unreacted amino groups on the substrate from reacting with the next coupling molecule (interpreted as coating with polymer, claims 67, 69 and 70) (paragraph [0247], lines 1-3; and Figure 2F). Rajasekaran teaches that a substrate can include a gelatinous form of a water soluble polymer in contact with the surface or at least one of said pillars; and that surface materials include, for example, silicon, bio-compatible polymers such as poly(methyl methacrylate) (PMMA) and polydimethylsiloxane (PDMS), glass, and silicon dioxide (interpreted as a polymer gel including PDMS or polyacrylamide gel coating the initiator species, claims 67, 69 and 70) (paragraphs [0194]; and [0204]).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of preparing a substrate for use as a high density arrays as exemplified by Rajasekaran, it would have been prima facie obvious before the effective filing date of the claimed invention to modify the method of efficiently and differentially tagging DNA fragments, and reducing errors introduced by sample preparation and sequencing processes as disclosed by Eltoukhy to include the methods of producing high density peptide and polypeptide arrays including through the use of photoactive formulations as taught by Rajasekaran with a reasonable expectation of success in producing a substrate binding assay having significantly improved tagging, coupling efficiency, performance, and/or processability; and/or in using the improved array substrates and efficient tagging methods for the accurate detection and quantification of polynucleotides including for the early detection, monitoring, and treatment of diseases such as cancer; as well as, in reducing sequencing noise, amplification bias and/or in reducing redundancy in sequencing reads to provide for the efficient and accurate detection of rare sequence variants.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103(a) as obvious over the art.
Response to Arguments
Applicant’s remarks filed October 7, 2025 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Eltoukhy is silent regarding the limitations: (i) a surface comprising an initiator species; (ii) wherein the initiator species comprises an organosilane with at least two surface bonding groups; (iii) wherein each surface bonding group of the at least two surface bonding groups differs; (iv) wherein a size of each feature of the plurality of features is smaller than 0.5 μm, and (v) wherein the distinct barcode sequence includes 5-35 bases (Applicant Remarks, pg. 14 through pg. 15).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). Moreover, it is noted that none of the references has to teach each and every claim limitation. If they did, this would have been anticipation and not an obviousness-type rejection. One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). As noted in MPEP 2112.01(I),
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Applicant’s assertion that Eltoukhy is silent regarding the limitations: (i) a surface comprising an initiator species; (ii) wherein the initiator species comprises an organosilane with at least two surface bonding groups; (iii) wherein each surface bonding group of the at least two surface bonding groups differs; (iv) wherein a size of each feature of the plurality of features is smaller than 0.5 μm, and (v) wherein the distinct barcode sequence includes 5-35 bases, is not found persuasive.
Initiator Species (i)-(iii): as an initial matter, instant claims 1 and 63 do not recite:
Any function or use for the initiator species.
There is no recitation that the initiator species are bound to the surface of the substrate surface.
There is no recitation that the initiator species are bound to any other group.
There is no indication that the surface bonding groups of the initiator species have been hydrolyzed to hydroxy groups such that they can be to the surface.
As noted supra, the instant rejection is based on the combination of Eltoukhy and Rajasekaran.
Rajasekaran teaches that the wafer surface is derivatized using aminopropyl triethoxysilane (APTES) (interpreted as comprising an initiator species comprising at least two surface bonding groups that differ; and the initiator species (EtO)3Si, claims 1 and 63), where it is known that APTES comprises the structure of (EtO)3Si as evidenced by Strem Catalog (pg. 1) and Acres (Abstract).
Size of Each Feature (IV): as an initial matter, there is no definition for the term “feature” in the instant as-filed Specification.
Eltoukhy teaches:
The substrate can be a bead or planar surface including a surface of a bead for an Illumina flow cell; beads comprising probes; and that a sample is digested, precipitated, captured, and selected using SPRI magnetic bead capture, wherein SPRI beads are coated with carboxy molecules and have a size of 1 mm as evidenced by Beckman Coulter (interpreting that the size of each feature is smaller than 0.5 μm).
The polynucleotides can be amplified including by PCR, and sequenced by massively parallel sequencing to simultaneously sequence any of at least 100, 1000, 10,000, 100,000, 1 million, 100 million, or 1 billion polynucleotide molecules;
wherein sequencing methods include high-throughput sequencing, pyrosequencing, sequencing-by-synthesis, single-molecule sequencing, nanopore sequencing, semiconductor sequencing, sequencing-by-ligation, sequencing-by-hybridization, RNA-Seq (Illumina), Digital Gene Expression (Helicos), Next Generation Sequencing, Single Molecule Sequencing by Synthesis (SMSS) (Helicos), massively-parallel sequencing, Clonal Single Molecule Array (Solexa), shotgun sequencing, Maxam-Gilbert or Sanger sequencing, primer walking, sequencing using PacBio, SOLiD, Ion Torrent, or Nanopore platforms (interpreted as encompassing oligonucleotides on an array located in a feature size less than 0.5 microns, claims 1 and 63);
wherein the feature size for Solexa sequencing is 1.0 microns to submicron levels as evidenced by Illumina (interpreting that the size of each feature is smaller than 0.5 μm).
wherein it is known that the 454 flow cell comprises a fiber optic slide with ~1.6 million 75-piocliter wells; and that in the Illumina system, templates are applied at high density to the flow cells, while Helicos applies templates at very high density as evidenced by Holt (interpreting that the size of each feature is smaller than 0.5 μm).
where it is known that the number of features within a microarray includes about 5,000,000 templates/cm2 or higher as evidenced by Gunderson (interpreting that the size of each feature is smaller than 0.5 μm).
Additionally, Rajasekaran teaches:
The plurality of pillars are present at a density of greater than 10,000/cm2; and that the surface area of each pillar is 1 mm2, or at least 10,000 peptides molecules per square centimeter (interpreted as encompassing oligonucleotides on an array located in a feature size less than 0.5 microns, claims 1 and 63).
Number of Bases in a Barcode Sequence (v): Eltoukhy teaches that the strand-identification barcode includes at least 4 nucleotide bases; and that each of the library adaptors comprises a molecular barcode that is at least 5, 6, 7, 8, 9, and 10 nucleotide bases in length (interpreted as encompassing 5-35 bases, claims 1 and 63).
The combined references of Eltoukhy and Rajasekaran teach all of the limitations of the claims. Thus, the claims remain rejected.
Conclusion
Claims 1, 7, 11, 13, 55, 60-63, 67 and 69-72 are rejected.
THIS ACTION IS MADE FINAL. 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.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684