DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. 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
2. Applicant’s election of Group II (claims 8-16), with the species recited in claim 10 as the elected species (thus claim 12 is withdrawn as being drawn to a non-elected species), in the reply filed on 6/25/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
3. Claims 1-16 are pending in the application. Claims 1-7 and 12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 8-11 and 13-16 are currently under examination.
Claim Rejections - 35 USC § 102
4. 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 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.
5. 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.
6. Claims 8 and 15 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tourlousse et al. (Nucleic Acids Res. 2017, 45(4):e23, published online 15 December 2016).
Regarding claim 8
Tourlousse et al. teach a method for identifying contamination associated with at least one of sequencing library preparation and high throughput sequencing, the method comprising: generating a set of quality control template (QCT) molecules (e.g., spike-in standards), each QCT molecule (e.g., spike-in standard) comprising: a target-associated region (e.g., conserved region) with sequence similarity to a target sequence region (e.g., natural 16S rRNA sequence region) of a biological target, and a variation region (e.g., artificial variable region) with sequence dissimilarity to a sequence region of the biological target; and computationally determining a set of QCT sequence read clusters based on the variation regions of the set of QCT molecules, wherein the set of QCT sequence read clusters comprises QCT molecule sequence reads derived from the high throughput sequencing corresponding to a set of QCT mixtures generated based on the set of QCT molecules and a set of samples comprising the biological target, and wherein the sequencing library preparation comprises co-amplification, of the set of QCT molecules and nucleic acid molecules comprising the biological target, based on the sequence similarity of the target-associated region and the target sequence region of the biological target; and based on the set of QCT sequence read clusters, determining a contamination parameter describing the contamination associated with the at least one of the sequencing library preparation and the high throughput sequencing (see the whole document, particularly Abstract; page 2, column 1, paragraphs 2-3; page 4, paragraph spanning columns 1-2; paragraph bridging pages 4-5; page 5, column 2, paragraphs 1-3; page 7, column 1, paragraph 2 – page 8, column 1, paragraph 4; page 8, column 2, paragraphs 2-4; page 11, column 1, paragraph 3 – column 2, paragraph 2; page 12, column 2, paragraph 2; Figure 1).
Regarding claim 15
The method according to Tourlousse et al., further comprising generating a single QCT library comprising the set of QCT molecules, wherein the single QCT library is adapted for deployment, at a single stage of the at least one of the sequencing library preparation and the high throughput sequencing, of less than 0.00001 nanograms of amplifiable QCT molecules for each sample of the set of samples (see page 2, column 2, last paragraph, where 7.6[Symbol font/0xB4]101 copies/PCR reaction would translate to less than 0.00001 nanograms of amplifiable QCT molecules, as evidenced by paragraph [0047] of the specification as filed).
Allowable Subject Matter
7. Claims 9-11, 13-14 and 16 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
8. No claim is currently allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAIJIANG ZHANG whose telephone number is (571)272-5207. The examiner can normally be reached Monday - Friday, 8:30 am - 5 pm.
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/KAIJIANG ZHANG/Primary Examiner, Art Unit 1684
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