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 .
Election/Restrictions
Applicant’s election without traverse of group I, claims 16-25 and 33-35 in the reply filed on 05/18/2026 is acknowledged.
Claims 26-32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 05/18/2026.
Claims 16-25 and 33-35 are under examination.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). The sequences on page 30-31 have sequences with SEQ ID NO but are not correct identifiers. For example, the sequence on page 30 lists a sequence with SEQ ID NO 25 and SEQ ID NO 26 however the entire length is a sequence and should be indicated as a sequence not two separate sequence identifiers.
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.
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. Figures 1A, 1B, Figure 3-4
Required response – Applicant must provide:
Amended 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 (i.e., “SEQ ID NO:X” or the like) 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.
Claim Rejections - 35 USC § 112
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.
Claims 16-25 and 33-35 are 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.
Claim 16 recites the limitation "the first and second PCR primers" in step (b)(ii). There is insufficient antecedent basis for this limitation in the claim. The claim recites an upstream and downstream primer in the preceding steps however the claim does not recite or require a first and second primer. It is unclear if the upstream and downstream primer is the first and second primer or if the first and second primer is in addition to the upstream and downstream primer. It is unclear if the claim requires 4 primers or 2 primers. Additionally claim 16 is vague and indefinite for requiring a first and second oligonucleotide probe placed down stream of the first and second PCR primer and within the upstream and downstream primer region. It is unclear where the first and second oligonucleotide probe is placed because the claim does not indicate or require a first and second primer, the claim only requires an upstream and downstream primer and binding region. It is unclear how the probes can be placed downstream of both the first and second primer. If the first and second primer are the upstream and downstream primer, it is unclear how the probes are placed downstream of the upstream primer but within the primer region because the probes will be upstream of the downstream primer. If the first and second primer are different primers than the upstream and downstream primer, it is unclear how these primers will contribute to the amplification and where these primers are located such that the probes are downstream of both the first and second primer. Is it unclear where the probes are placed in relation to the primers and the metes and bound of the claims are unclear.
Regarding claim 16, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 18-19, 21 and 22 recites the limitation "the primer" in lines 1-2 of the claims. There is insufficient antecedent basis for this limitation in the claim. Each of the claims depend from claim 16. Claim 16 recites an upstream primer, downstream primer, the first and second primer and it is unclear which of the primers in claim 16 is “the primer” for claims 18-19, 21-22. It is unclear if the primer is the upstream primer, downstream primer, first or second primer.
Claim 25 contains the trademark/trade name Scorpion. 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 name is used to identify/describe a specific nucleic acid probe and, accordingly, the identification/description is indefinite.
Claims 17-25, 33-35 depend from claim 16 and are indefinite for the reasons applied to claim 16.
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.
Claims 16-25 and 33-35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by White (US20100069250 A1).
With regard to claim 16, 24 and 35, White teaches digital PCR of nucleic acids libraries of amplicon DNA (see fig 4, para 41) . White teaches digital PCR that comprises amplification product using a multiwall plate(see para 52). White teaches examining amplification product by using a forward primer binding to a 5’ adapter and a reverse primer binding to a 3’ adapter, generating a signal by a probe that binds to a sequence defined by the forward primer or reverse primer (See para 64 and para 72). Therefore White teaches providing an amplification product that comprises an upstream and downstream primer region (5’ and 3’ adapter region) and primer binding to the primer binding region (forward and reverse primer), examining the amplification by amplification wherein the forward and reverse primer bind in the upstream and downstream primer region, a first and second oligonucleotide probe are placed downstream of the upstream and downstream primer (first and second primer being the upstream and downstream primer which is the forward and reverse primer, respectively), performing digital PCR and examining the amplified product (probe gives a signal in each reaction area). White teaches probe-binding sequence is appended to PCR primers (See para 65). White teaches a 18-20 nucleotide binding portion in additional to a 8 mer universal template (over 20 nucleotides and under 35 nucleotides) (primer between 10 nucleotides and 22 nucleotides and probe between 8 and 17 nucleotides in length) (claim 18) (see para 65). White teaches the primer with hybridize to the signal generating probe and the universal adapter sequence of the amplicon. It is noted that White teaches two probes by teaching three oligo scorpion format and does not teach a single probe. The claim does not require two different probes or require that the first and second probes are different sequences, the claim only requires a requires a first and second probe. The UT probe of White comprises a first and second probe in addition to White teaches multiple detection including scorpion probes and three oligo scorpion format (see para 83).
With regard to claim 17, White teaches the amplification product comprises an amplified target region between the forward and reverse primer (upstream and downstream primer) (see fig 8B, product of probe binding primer, para 69).
With regard to claims 19-23, White teaches modified nucleotides that are LNA that increases binding (see para 59-60, 66) (claim 19-23).
With regard to claim 25 and 34, White teaches library is a sequencing library (see para 70).
With regard to claim 33, White teaches hydrolysis probes with different labels are used (see para 56). White further teaches TaqMan hydrolysis probes were used but a three oligo scorpion format can be used (see para 83)
With regard to claim 18, 21-23, White teaches the probe is 8 nucleotides in length and replaced with LNA (see para 65). Because White teaches a primer that is 18-20 bases and a UT region that binds the signal generating probe that is 8 nucleotides in length, White teaches primers between 18 to 20 bases and probe 8 nucleotides in length.
Claims 16-17, 24-25, 33-35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Saxonov (WO2013017951A1, cited on IDS)
With regard to claim 16-17, 24-25 and 33-35, Saxonov teaches examining amplification assay to quantify nucleic acid library members (see fig 8 ). Saxonov teaches library characterization before sequencing (see pg. 6) (amplifying a nucleic acid library, library is a sequencing library) Saxonov teaches digital amplification assay relies on amplification of templates (templates provided by library members) in partitions to enable detection of a single library member. Saxonov teaches amplification is conducted by PCR and detection is by a fluorophore. Saxonov teaches dPCR can be multiplex to permit detection of two or more different targets within each partition and can be distinguished by utilizing target specific reporter that are distinguishable including using different target specific reporters (see pg. 10). Saxonov teaches library member are amplified with a primer for each adapter region. One of the primers binding to the first adapter region and the other primer binding to the second adapter region at the other end of the inset. Saxonov teaches amplification is performed in the presence of a labeled reporter and include a first labeled probe and a second labeled probe (see pg. 13, lines 15-32). Saxonov teaches amplification data is created by signals (see pg. 14). Therefore Saxon teaches providing an amplification product, examining the amplification by amplifying and performing digital PCR. Saxon teaches the primers comprise an upstream and downstream binding region and a first and second oligonucleotide probe is placed downstream of the primer and within the binding site (see figure 7 and fig 8). Saxonov teaches adapter regions (primer binding regions) with two probes with amplification spanning each insert. Saxonov teaches using probes for both primer binding regions (see pg. 19). Saxonov teaches two primer binding regions with two primers binding the annealing region see FP and RP of fig 8. Saxonov teaches probe 1 and probe 2 bind downstream of the first PCR primers. It is noted that it is unclear what is encompassed by the first and second PCR primer and it has been intercepted that the upstream binding primer comprises a first and second primer, as such probe 1 and probe 2 are downstream of the forward primer.
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SARAE L BAUSCH whose telephone number is (571)272-2912. The examiner can normally be reached M-F 9a-4p.
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/SARAE L BAUSCH/Primary Examiner, Art Unit 1699
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