asdfasdfDETAILED 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 .
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Status
Claims 1-12 and 14-21 are pending.
Claims 7-12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 9/10/2025.
Claims 1-6 and 14-21 are being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (see paragraphs [0004, 0068, 0072, 0089, 0113, 0131, 0136, 0157, 0161, 0162, 0180, and 0188]). 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.
Applicant did not respond to this notice in the Remarks of 11/20/2025 and no new IDS has been filed. Therefore, the references noted above remain unconsidered unless cited by the examiner on form PTO-892.
Drawings
The drawings are objected to because Fig. 1B and Fig. 2 contain the phrase “amplified mutant DNA, complimentary single-strand”, which should read “amplified mutant DNA, [[complimentary single-strand]]complementary single strand”. 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.
Response to Remarks
Applicant has indicated in the Remarks of 11/20/2025 (page 8) that the above noted issue in regards to the typos in Fig. 1B and Fig. 2 has been amended. However, the drawings submitted on 11/20/2025 contain the same typographical error (the drawings include the term “complimentary” where the term “complementary” is correct). It is noted that the amended drawings of 11/20/2025 remove the unnecessary hyphen in “single-strand”. Correction is required and the objection to the drawings is maintained.
Specification
In light of Applicant’s amendments to the specification to remove hyperlinks and properly denote trademarks the objection to the specification is withdrawn.
Withdrawn Claim Objections
The objection to claims 15 and 21 are withdrawn in light of Applicant’s amendments to the claims.
Withdrawn Claim Rejections - 35 USC § 112b - Indefiniteness
The rejection of claims 1-5, 6, and 14-21 under 35 U.S.C. 112(b) are withdrawn in light of Applicant’s amendments to the claims.
New Claim Rejections - 35 USC § 112d – Failure to Further Limit
Necessitated by Amendments
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 19 and 20 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, 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. Claims 19 and 20, which depend from claims 1 and 5, respectively, contain the limitation “wherein the capture oligonucleotide comprises a reverse complement of the blocker oligonucleotide”. However, the new amendments to claims 1 and 5 includes the limitation that the capture oligonucleotide “comprises a reverse complement of the blocker oligonucleotide”, therefore meaning that claims 19 and 20 now fail to further limit. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Interpretation
Claims 5 and 20 are directed to “an oligonucleotide set”. The specification does not specify what is meant by a “set”, so given the broadest reasonable interpretation of the term “set”, the examiner is interpreting “set” to mean a combination of elements with no further structural limitations to said claim term.
Maintained Claim Rejections - 35 USC § 103
Modified as Necessitated by Amendments
Claims 1-3, 5-6, and 14-21 are rejected under 35 U.S.C. 103 as being unpatentable over Powell (Powell et al., US 20190330692 A1; cited on IDS of 10/312025) in view of Bailey (Bailey et al., WO 2013/138251 A1), Kutyavin (Kutyavin et al., US 5912340 A; cited on IDS of 10/31/2025), and Albitar (US 20170002427 A1).
Claims 1-3, 6, 14-19, and 21
Regarding claim 1: Powell teaches a method for selective enrichment of a target nucleic acid containing a genetic variation (Abstract). Powell teaches that this method is used to determine if a nucleotide sequence (or variation) is present in a target nucleic acid sequence (paragraph [0003]). Powell teaches that the target nucleic acid comprises a polymorphic site that is characterized by a first nucleotide sequence and a second nucleotide sequence that differ from each other by at least one nucleotide (Figure 1 and paragraph [0004]). Powell teaches contacting the nucleic acid with forward and reverse primers that flank and amplify the target nucleic acid sequence in the presence of a blocker oligonucleotide that is complementary to the first nucleotide sequence (Figure 1 and paragraphs [0003 and 0025]). Powell teaches that if the target nucleotide sequence comprises the first nucleotide sequence (“wildtype polynucleotide sequence”), the blocker oligonucleotide (“xenonucleic acid clamp” (XNA)) will hybridize to this sequence and prevent amplification but will not hybridize to the second nucleotide sequence (“mutant”) which therefore allows the mutant template to be amplified (paragraph [0026]; Figure 1). Powell teaches the inclusion of a modified base (XNA) within an oligonucleotide probe that allows for highly specific and strong binding to exact sequence matches (paragraphs [0042-0043 and 0069] and Figure 1). Powell teaches after combining the primers and XNA clamp with the target nucleic acid sequence, conducting an amplification reaction in the mixture (paragraph [0026]). Powell teaches that mutant specific capture probes immobilized on beads can be used to capture mutant specific amplicons generated by the amplification reaction (paragraph [0047]).
Powell does not teach that capture oligonucleotides comprise one or more second modified bases. However, inclusion of modified bases within capture oligonucleotides is known in the art, as taught by Bailey.
Bailey teaches a method of using capture probes to detect an analyte of interest (Abstract and paragraphs [0124-0126]). Bailey teaches the inclusion of modified bases in said capture probes (paragraphs 0128, 0135, and 0138]).
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 Powell to include modified bases in the capture oligonucleotides as well, as taught by Bailey. One would be motivated to do so given the assertion by Bailey that capture oligonucleotides that comprise modified bases such as LNA “increase the sensitivity and specificity of conventional oligonucleotides…for hybridization to short target sequences” (paragraph [0138]). One would have a reasonable expectation of success given that Bailey successfully demonstrates use of modified oligonucleotide included in capture probes to increase capture efficiency (Table 2 and Example 1).
Powell in view of Bailey does not teach that one of the first modified bases in the blocker oligonucleotide is complementary to one of the second modified bases in the capture oligonucleotide, wherein the modified bases preferentially pair with unmodified forms of the their complementary baes, as compared to pairing between the modified complementary bases, or that the presence of the one or more modified bases in the blocker oligonucleotide and in the capture oligonucleotide destabilizes hybridization between the blocker and the capture oligonucleotides. However, inclusion of modified bases in complementary nucleotide sequences to destabilize hybridization between the two sequences is known in the art, as taught by Kutyavin.
Kutyavin teaches a matched pair of oligonucleotides (ODNs) that are complementary to each strand of a target duplex (col 1, ln 39-43). Kutyavin teaches inclusion within the ODNs modified bases that form stable hydrogen bonded base pairs with the natural partner base, but not with its modified partner (this reads on the capture oligonucleotide comprises a reverse complement to the blocker oligonucleotide; Abstract; col 24, ln 52-58). The oligonucleotides can contain one or more modified bases (col 9, ln 39-53). Kutyavin teaches that the inclusion of the modified bases destabilizes hybridization between the two reverse complementary oligonucleotides by ensuring that two hydrogen bonds are formed between the modified base and its unmodified partner, while only one hydrogen bond is formed between two complementary modified bases (Abstract; col 24, ln 52-58).
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 Powell in view of Bailey with the modified bases in complementary sequences as taught by Kutyavin. One would be motivated to do so given that preventing hybridization between capture probes and complementary oligonucleotides that serve as blockers of wild-type sequences is a known problem in the art as taught by Albitar (paragraph [0026]). Modifying Powell with the teachings of Bailey allows inclusion of modified bases in both the blocker oligonucleotide and the capture oligonucleotide to allow for stronger hybridization to their respective target sequences. Modifying Powell in view of Bailey with the teachings of Kutyavin allows for this enhancement to occur while additionally preventing aberrant hybridization between the blocker oligonucleotides and capture oligonucleotides while still enabling strong hybridization to their respective target sequences, thus solving the problem as posed by Albitar. One would have a reasonable expectation of success given that Kutyavin presents several forms of oligonucleotides with complementary modified bases that have significantly disrupted hybridization when compared to their respective hybridization to their natural base complements (col 24, ln 52-58). Furthermore, the principles of hybridization would yield predictable results when employed in the methodology of Powell in view of Bailey.
Regarding claim 2: Kutyavin teaches oligonucleotides with multiple complementary modified bases (col 24, Table 2).
Regarding claim 3: Powell teaches quantifying specific hybridization to the capture oligonucleotide following amplification with a blocker oligonucleotide (Example 4, paragraphs [0107-0108]).
Regarding claim 6: Powell teaches that mutant specific capture probes immobilized on beads can be used to capture mutant specific amplicons (paragraph [0047]). The specification of the instant application teaches that a “support” can be “any substrate, typically one to which oligonucleotides can be attached”, which reads on a bead/microbead (paragraphs [0091 and 0109] of instant specification).
Regarding claim 14: Kutyavin teaches that the modified complementary bases form fewer hydrogen bonds with each other than with unmodified complementary bases (Abstract).
Regarding claim 15: Kutyavin teaches that the base pair with two complementary modified bases lack stable hydrogen-bonded base pairing and therefore has a Tm of less than 40 ºC (Abstract; col 1, 55-56; col 4, ln 39-45).
Regarding claim 16-17: Kutyavin teaches that at least one complementary pair of modified bases comprises modified forms of adenine and thymine (claim 16; col 24, Table 2). Kutyavin teaches that at least one complementary pair of modified bases comprises modified forms of guanine and cytosine (claim 17; col 2, ln 63-67 and claim 1).
Regarding claim 18: Powell teaches use of a blocking oligonucleotide that binds to a wild-type sequence and prevents amplification of said sequence (as cited above in the rejection of claim 1). Powell does not teach that the blocking oligonucleotide is blocked to 3’ extension. However, use of blocking oligonucleotides that are blocked to 3’ extension is known in the art, as taught by Albitar.
Albitar teaches a blocking oligonucleotide that is blocked to 3’ extension by a DNA polymerase in the selective enrichment of mutant sequences (paragraph [0040]).
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 Powell in view of Bailey and Kutyavin with the blocker oligonucleotide blocked to 3’ extension as taught by Albitar. One would be motivated to do so both to prevent the blocker oligonucleotide from being used as a primer for non-specific amplification and for prevention of degradation of said blocking oligonucleotide by exonucleases (as taught by Albitar, paragraph [0040]). One would have a reasonable expectation of success given that Albitar successfully demonstrates usage of a blocking oligonucleotide with modified bases and 3’ blockage to perform selective amplification of mutant sequences.
Regarding claim 19: Kutyavin teaches that one oligonucleotide (capture oligonucleotide) is the reverse complement of the other nucleotide (blocker oligonucleotide; col 1, ln 39-43).
Regarding claim 21: Kutyavin teaches that the modified bases form stable hydrogen bonds with the unmodified forms of their complementary bases (Abstract).
Claims 5 and 20
Regarding claim 5: The preamble of this claim recites a “set”. The specification, however, does not define this term, and so it is being interpreted to encompass any collection of reagents that includes all of the elements of the claims. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation of on the claimed subject matter.
Powell in view of Bailey, Kutyavin, and Albitar, according to the citations and rationales provided above, teaches all components of the oligonucleotide set as claimed in claim 5.
Regarding claim 20: Kutyavin teaches that one oligonucleotide (capture oligonucleotide) is the reverse complement of the other nucleotide (blocker oligonucleotide; col 1, ln 39-43).
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Powell (Powell et al., US 20190330692 A1; cited on IDS of 10/312025) in view of Bailey (Bailey et al., WO 2013/138251 A1), Kutyavin (Kutyavin et al., US 5912340 A; cited on IDS of 10/31/2025), and Albitar (US 20170002427 A1) as applied to claims 1-3, 5-6, and 14-21 above, and further in view of Paguirigan (Paguirigan et al., Science Translational Medicine, 2015).
The teachings of Powell in view of Bailey, Kutyavin, and Albitar are detailed above. Relevant to the instantly rejected claim, Powell in view of Bailey, Kutyavin, and Albitar teach selective amplification of mutant target sequences through the use of blocker oligonucleotides and capture oligonucleotides that contain modified bases. Powell in view of Bailey, Kutyavin, and Albitar teach performing this methodology on cell samples (Powell, paragraph [0044]).
Powell in view of Bailey, Kutyavin, and Albitar do not teach performing this methodology in single cells. However, amplification of target sequences via PCR in single cells is known in the art, as taught by Paguirigan.
Paguirigan teaches multiplex, single-cell PCR for detection of mutations at two different loci in cancer cells (Results - Approach for identifying individual genotypes of single cells).
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 Powell in view of Bailey, Kutyavin, and Albitar with that of Paguirigan. One would be motivated to perform the method with nucleic acids from a single cell given the assertion by Paguirigan that this allows for accurate detection of clonal heterogeneity of cancer cells (Results - Approach for identifying individual genotypes of single cells). One would have a reasonable expectation of success given that Paguirigan successfully performs PCR on genetic loci from single cells (Figure 2).
Response to Remarks
Applicant's arguments filed 11/20/2025 have been fully considered but they are not deemed persuasive for the following reasons.
Applicant argues on page 11 of Remarks that “Modifying Powell’s clamp or probe so they are reverse compliments would cause them to compete with the amplified mutant DNA for hybridization. This would lower the sensitivity of Powell’s system and method”. In response to applicant's arguments against the references individually, 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). Additionally, this problem of competition between a blocker oligonucleotide and a probe oligonucleotide for binding to amplified jutant DNA is a known prolem in the art, and one which is addressed in the 103 rejection above. Powell would be motivated to make the capture probe the reverse complement of the blocker oligonucleotide, with inclusion of modified bases in both, to increase the sensitivity of detection of specifically amplified mutant sequences, as taught by the combination of Powell with Bailey, Kutyavin, and Albitar. As noted above, modifying Powell with the teachings of Bailey allows inclusion of modified bases in both the blocker oligonucleotide and the capture oligonucleotide to allow for stronger hybridization to their respective target sequences. Modifying Powell in view of Bailey with the teachings of Kutyavin allows for this enhancement to occur while additionally preventing aberrant hybridization between the blocker oligonucleotides and capture oligonucleotides while still enabling strong hybridization to their respective target sequences, thus solving the problem as posed by Albitar.
For these reasons, the rejection of all claims under 35 USC 103 is maintained.
Conclusion
No claims are allowed.
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
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683