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 .
Status of the Application
Claim(s) 1-19 and 21 are pending and under examination
The following Office Action is in response to Applicant's communication dated 06/29/2025.
Drawings
The drawings are objected to because the drawing was labeled “ Figs. 1 A-C”; however, the figure 1C is not included in the drawing file nor mentioned in specification. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
Specific deficiency - Sequences appearing in the specification and claims are not identified by sequence identifiers (i.e., "SEQ ID NO:X" or the like) in accordance with 37 CFR 1.831(c). Specifically, the sequences corresponding to the 30-nucleotide primer binding site [¶0012] in the specification and recited in claim 4 are presented without reference to their respective sequence identifiers. Applicant is required to amend the specification and claim to identify the sequences using the corresponding SEQ ID NO.
Required response – Applicant must provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, 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.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim(s) 1-19, and 21 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1, 8, and 19 recite “biotinylated dNTP (e.g., biotin-dUTP)”, which render the claim indefinite because it is unclear whether “biotin-dUTP” is merely an example of biotinylated dNTP or whether “biotin-dUTP” is a required limitation of the claimed method. Hence the metes and bounds of claimed subject matter is unclear. See MPEP 2173.05(d) " If stated in the claims, examples and preferences may lead to confusion over the intended scope of a claim ".
Claim(s) 2-19 and 21 depend from claim 1 and is/are therefore similarly rejected.
Claims 9 and 15 contains trademark/trade name “Vent® (exo-) DNA Polymerase” and “Hemo KlenTaq® DNA polymerase”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade names are used to identify/describe commercially available photoresists and, accordingly, the identification/description is indefinite.
Given that a trademark or trade name is used to identify a source of goods, and not the goods themselves, it is suggested that Applicant amend the claims to properly define the DNA polymerase that harbors 5' to 3' strand displacement activity (e.g. using generic descriptions).
Claim 12 recites “steps (d) and (e) occur without any exogenous manipulation”, which does not reasonably identify which actions are excluded during the process. The claim does not define whether “exogenous manipulation” include reagent addition, temperature changed, mixing, agitation, or other external intervention. Hence the claim is indefinite and the metes and bounds of the claim are unascertainable.
For purposes of examination only, and to facilitate a complete analysis of the claim, the Examiner interprets the “exogenous manipulation” as requiring after reagents for nicking and extension have been combined, the repeated nicking, primer extension, strand displacement, and probe release cycle proceed without further addition of reagents.
Claim 21 recites “hybridizing the panel of probes of any one of claims 18-20”. However, claim 20 has been canceled. Hence claim 21 is incomplete because the limitations of canceled base claim is necessary to define the claimed subject matter no longer present in the pending claim. See MPEP § 608.01(n)(V).
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 18, 19, and 21 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Makrigiorgos et al. (US20210310061A1, EFD: August 18th 2018).
Regarding claim 18 and 19, Makrigiorgos discloses biotinylated oligonucleotide probes wherein each probe comprises one or more biotin-NMP residues (e.g. Fig 12 (below) shown biotinylated probes used for DNA hybrid capture)
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Regarding claim 21, Makrigiorgos discloses method of sequencing a plurality of nucleic acid molecules comprising: (a) obtaining a sample comprising the plurality of nucleic acid molecules; (b) hybridizing the panel of probes of any one of claims 18-20 to the plurality of nucleic acid molecules; (c) capturing the hybridized probes using streptavidin beads; (d) amplifying the nucleic acid molecules that were bound to the captured hybridized probes; and (e) sequencing the amplified nucleic acid molecules.
(e.g. The capture method comprises incubating sample of DNA suspected to have one or more of the target DNA regions to allow the probes to capture complementary target DNA regions; amplifying the captured target DNA regions; and performing sequencing on the captured target DNA sequences. [0248-0250]. Fig 12 shows target-specific capture using Biotinylated probes attached to streptavidin beads).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Wang et al. and Makrigiorgos et al.
Claim(s) 1-4, 10, and 12-17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20160348142A1, EFD: May 5th 2016) in view of Makrigiorgos et al. (US20210310061A1, EFD: August 18th 2018).
Regarding claim 1, Wang discloses method of preparing oligonucleotide probes, the method comprising: (a) obtaining a set of oligonucleotides, each comprising a target gene binding sequence at its 5' end and a primer binding sequence at its 3' end, wherein each oligonucleotide has the same the primer binding sequence, and wherein the 5' end of the primer binding sequence comprises a nickase target sequence; (b) incubating the set of oligonucleotides with a primer that hybridizes to the primer binding sequence and extension of the primer using the oligonucleotides as a template, thereby producing extended primers complementary to the oligonucleotides, where the extended primers each comprise, from 5' to 3', the primer, the nickase target sequence. (c) nicking the extended primers complementary to the oligonucleotides with a nickase capable of cleaving the extended primers at the nickase target sequence to separate the biotinylated probes and regenerate the primers' 3' end; (d) extending the regenerated primers 3' end using the oligonucleotides as templates
to displace and release the biotinylated probes; and (e) repeating steps (c) and (d). [Fig 7 shown below]
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However, Wang does not disclose amplifying the probes in the presence of biotinylated dNTP (e.g., biotin-dUTP) to generate biotinylated probes.
Makrigiorgos discloses isothermal methods to amplify biotinylated DNA capture probes for sequencing workflows. The approach involves incorporation of labeled dNTPs (e.g., biotinylated dUTP) during PCR amplification to generate biotinylated probes [¶0146, ¶0169-0170].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to modify Wang’s probe amplification method by incorporating biotinylated dNTPs (e.g., biotinylated dUTP) during probe synthesis, taught by Makrigiorgos. Wang already recognizes the benefit of biotinylating probes to enable affinity capture and separation of probes from reaction intermediates and byproducts [¶0007], but accomplishes this through post synthesis terminal-transferase end-labeling [¶0080]. Makrigiorgos teaches that incorporation biotinylated dNTPs during isothermal amplification generate biotinylated probes directly, eliminating the need for an extra end labeling step while producing efficient and low-cost probes for hybridizing capture [¶0146]. A skilled artisan would be motivated to substitute Wang’s post synthesis labeling techniques with Makrigiorgos’s in process nucleotide incorporation because both techniques achieve similar purpose of generating biotinylated capture probes, and Makrigiorgos provides recognized advantages of simplifying workflow and reducing cost without thermal cycling. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (MPEP § 2143)
Regarding claim 2, Wang discloses oligonucleotide in the set is about 60 to 150 nucleotides long. (e.g. The length of individual probes within the pool may vary depending on precursor probes and tags included. Examples provides probe with length between 100 and 150 or between 110 and 121 bases [¶0102 and ¶0129]).
Regarding claim 3, Wang discloses each oligonucleotide in the set comprises a 30 to 120-nucleotide sequence at its 5' end that is capable of hybridizing to a target gene (e.g. 5′ target homology region, i.e. H1, may have length between 18 and 30 bases [¶0082 and ¶0102]). Wang further discloses and the length of the primer, in any given case (3’ or 5’), depends on, for example, the intended use of the primer, and generally ranges from 15 to 30 nucleotides [¶0072]. As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to optimize the primer to be 30 nucleotide in length because Wang already discloses that primer lengths may vary between 15 and 30 nucleotides provide the ideal balance for routine optimization, ensuring target specificity, and achieving proper melting temperatures through routine experimentation. See MPEP § 2144.05 (II) "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Regarding claim 4, Wang discloses using universal primer and nickase targeting sequence in amplifying the probes. Wang especially teaches nicking enzymes used may include N.AlwI, N.BstNBI, Nb. BsmI, N. BbvCIA and/or N. BbvCIB [¶0092]. However, Wang does not disclose the specific primers discloses in claim 4. However, as of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to select/design an appropriate universal primer sequence containing the recognition sequence for the chosen nickase as the primer sequence and nickase must be designed to function together. The particular nucleotide sequence outside the nickase recognition site represents routine primer design choice generated/selected to provide suitable primer annealing and amplification efficiency, while minimizing non-specific hybridization and unintended cleavage. Hence, selection of the claimed primer sequence would have been an obvious matter of design choice yielding predictable operation of Wang’s probe amplification system.
Regarding claims 10, Wang discloses a nickase to the reaction and incubating at a temperature between 20°C and 37°C. (e.g. probes are nicked with Nb.BtsI at 37°C [¶0129])
Regarding claims 12, Wang discloses the nicking, extension, strand-displacement, and probe release steps are repeatedly performed in the same reaction system. As shown in Fig 7 (shown above), following step 751 nicking, the polymerase extends and regenerated 3’ end, displaces the probe at steps 752-753, after which the nickase target sequence is regenerated and cycle reapeat without additional reagents or external intervention. Hence, Wang teaches that steps (d) and (e) occur without any exogenous manipulation.
Regarding claims 13, Wang discloses isolating and/or purifying the biotinylated probes. (e.g. All ends of the double stranded product are labeled with an affinity selection reagent such as biotin so that the processed probe can be separated from the intermediates and byproducts [0007].)
Regarding claims 14, Wang discloses nickase can include, but are not limited to Nt.BspQI, Nt.BstNBI, Nb.Alwl, or Nt.BsmAI.[¶0068]
Regarding claims 15, Wang and Makrigiorgos discloses the extension is performed by a DNA polymerase that harbors 5' to 3' strand displacement activity including, but not limited to Klenow Fragment (3'-----+5' exo-) DNA polymerase; Hemo KlenTaq DNA polymerase; Bst DNA Polymerase, Large Fragment; Bst DNA Polymerase; Bsu DNA Polymerase, Large Fragment; phi29 DNA Polymerase; and Vent (exo-) DNA Polymerase. [Wang ¶0074 and Makrigiorgos ¶0162-0166]
Regarding claims 16, Wang and Makrigiorgos discloses the method is an isothermal reaction [Wang ¶0041, 0073, 0108 and Makrigiorgos Abstract, ¶ 0004, 0053, 0056-0058, 0167].
Regarding claims 17, Wang and Makrigiorgos disclose the use of strand displacing polymerase, e.g. phi29 DNA Polymerase, which has strand displacement activity at temperature within the claimed range of 20°C - 37°C for initial primer extension. [Wang ¶0075, 0123 and Makrigiorgos ¶0162-¶0163].
Wang et al., Makrigiorgos et al., and Rodesch et al.
Claim(s) 5-7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20160348142A1, EFD: May 5th 2016) in view of Rodesch et al. (US20090105081A1, EFD: August 20th 2008)
Regarding claims 5, Wang and Makrigiorgos do not disclose set of oligonucleotides are tiled across the sequence of each target gene.
Rodesch discloses plurality of overlapping capture probes that span target genomic regions, including individual gene exon regions. Rodesch position successive probes across each target region so hat the probes collectively tile the target sequence [¶0051 and ¶0098].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to apply Rodesch’s tiled probe design to Wang and Makrigiorgos’s probe production method to improves sequence capture uniformity, enhances detection of mutations or variants, and successfully recovers damaged or fragmented DNA. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (MPEP § 2143).
Regarding claims 6, Rodesch discloses the oligonucleotides are tiled at about or greater than a density of 0.5x, lx, or 2x across the sequence of each target gene. (e.g. overlapping microarray probes of more than 60 bases each on the array spanned each target genome region, with a probe positioned each 10 bases for the forward strand of the genome. Such arrangement is denser than 2x coverage. [¶0098])
Regarding claims 7, Rodesch discloses oligonucleotides are tiled across the targeted gene sequence regions, including, but not limited to genomic DNA or RNA sequences of target genes including the exon sequences, or/and the intronic sequences. (e.g. oligonucleotide microarrays that capture short segments that correspond to 6,726 individual gene exon regions of at least 500 base pairs were chosen from 660 genes distributed about the human genome [¶0098])
Wang et al., Makrigiorgos et al., Lebofsky et al., and Rapley et al.
Claim(s) 8 and 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20160348142A1, EFD: May 5th 2016) in view of Makrigiorgos et al. (US20210310061A1, EFD: August 18th 2018), Lebofsky et al.(US20200385791A1, EFD: June 14th 2019), and Rapley et al. (Mol Biotechnol. 1994;2(3):295-298)
Regarding claims 8, Makrigiorgos discloses step (b) comprises (i) combining the set of oligonucleotides, the primer, deoxynucleotides, and biotinylated dNTP (e.g., biotindUTP) and incubating the mixture at 95°C for 2 min [“BST - DSN reaction WITH B - DUTP labeling” on page 78],
(ii) Wang disclose adding into conducting prob synthesis using phi29 DNA Polymerase which is active at temperature 20°C - 37°C [¶0075, 0123]. Makrigiorgos also teaches the use of strand displacing polymerase, e.g. phi29 DNA Polymerase, which has strand displacement activity at temperature within the claimed range of 20°C - 37°C for initial primer extension [¶0162-¶0163].
Wang and Makrigiorgos do not disclose cooling the mixture from 95°C to 4 °C at rate of -0.1 °C/s and adding a single-stranded DNA binding protein.
Lebofsky discloses nucleic acid library preparation involving oligonucleotide and enzymatic processing, cooling the reaction down to 4° C. at 0.1 C/s [¶0221]. As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to use this known controlled colling protocol in Wang and Makrigiorgos method because gradually cooling after denaturation rather than dropping abruptly improves primer-template specificity and enables the successful amplification, especially for GC-rich or structurally complex targets.
Rapley discloses that using single-stranded DNA-binding protein (SSB) in amplification and sequencing improve the yield and quality of a number of templates [abstract]. As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to add Rapley’s SSB to Wang and Makrigiorgos method because Wang’s reaction generates and uses single single-stranded DNA regions during strand displacement synthesis and Rapley teaches that adding SSB in such reaction helps stabilize single strand template and reduce secondary structure formation, thus, improve efficiency of probe production.
Regarding claims 9, Makrigiorgos discloses using phi29 DNA Polymerase [¶0162-¶0163]. Wang also teaches using phi29 DNA Polymerase [¶0123].
Wang et al., Makrigiorgos et al.,and Cann et al.
Claim(s) 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (US20160348142A1, EFD: May 5th 2016) in view of Makrigiorgos et al. (US20210310061A1, EFD: August 18th 2018) and Cann et al. (US10457969B2, EFD: July 20th 2015)
Regarding claims 11, Wang does not disclose the incubating occurs for between 30 min and 24h.
Cann discloses incubating DNA substrate containing Nb.BtsI nicking sequence with Nb.BtsI nicking endonuclease for one hour at 37°C [Example 5]. As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to employ the disclosed one hour incubation condition for achieving efficient Nb.BtsI nicking at 37°C, with predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (MPEP § 2143).
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KHAI QUYNH TIEN PHAM/ Examiner, Art Unit 1684
/JEREMY C FLINDERS/ Primary Examiner, Art Unit 1684
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