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 . Applicant’s preliminary amendment filed 9/8/2022. Claim 10 has been amended. Claims 1-10 are pending and under examination.
Drawings
The drawings were received on 9/8/2022. These drawings are found acceptable by the Examiner.
Specification
The disclosure is objected to because of the following informalities: The use of the term “Thruplex (see entire specification) which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction is required.
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.
7. Claim(s) 1-10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Makarov et al., {Makarov, used interchangeably herein}, US 8728737, May 20, 2014) in view of Aigrain et al (BMC Genomics (2016) 17:458, pages 1-11).
Regarding claims 1, 9 and 10, Makarov teaches a method for amplifying free nucleic acids directly from genomic sample, wherein the sample comprises nucleic acid fragments (col. 6, lines 40-45 and col. 17, lines 28-32), the method comprising the sequential steps of: (a) dilution: mixing the sample with a buffer thoroughly to form a mixed solution (col. 5, lines 32-64; col. 10, lines 60-62 and col. 34, lines 60-66),
(b) protein denaturation: adding the mixed solution into a test tube, heating the mixed solution in the test tube to denature proteins in the mixed solution, and then cooling the mixed solution to room temperature (col. 10, lines 60-64, col. 13, lines 55 to col. 14, lines 8 and example 3, first paragraph and Figures 1-3);
(c) end modification of nucleic acid molecules: subjecting the nucleic acid fragments in the mixed solution to a processing reaction required for an adapter-dependent polymerase chain reaction (PCR) (col. 5-9, col. 13, lines 9-20 and col. 14, lines 35);
(d) adapter ligation: performing a ligation reaction between the processed nucleic acid fragments and double-stranded adapters having a single type of sequence, defined as double- stranded homogeneous adapters, in order to form nucleic acid fragments each ligated at each of two ends thereof with one said double-stranded homogeneous adapter, wherein each said double- stranded homogeneous adapter is a complementary double-stranded nucleic acid (dsNA) fragment with one strand being an oligonucleotide carrying a 5'-phosphate group and the other strand being an oligonucleotide carrying a thymine (T) or uracil (U) (col. 4-9, 13-14 and 17-18); and
(e) PCR: adding components required for performing the adapter-dependent PCR on the ligated nucleic acid fragments, and then performing the adapter-dependent PCR on the ligated nucleic acid fragments in the mixed solution (col. 4-9, 13-14 and 17-18, see also Examples) and analyzing a product by sequencing or other diagnostic methods (Examples).
Regarding claim 2, Makarov teaches wherein the nucleic acid fragments in the unpurified sample are dsNA fragments (col. 4, 8-14, col. 6, lines 39-44).
Regarding claim 3, Makarov teaches wherein the unpurified sample is in an amount of 15 mL (example 1).
Regarding claim 4, Makarov teaches wherein the steps (b) to (e) are carried out in the same test tube (col. 5, lines 32 and col. 6, lines 1-20; col.35, lines 55 to col. 36, line 1-4).
Regarding claim 5, Makarov teaches wherein the test tube is provided therein with a filter, and the step (b) comprises adding the mixed solution onto the filter in order for the mixed solution to pass through the filter and then flow to a bottom of the test tube (Example 7).
Regarding claim 6, Makarov teaches wherein the processing reaction in the step (c) is end modification performed on the nucleic acid fragments in the mixed solution in order for the nucleic acid fragments in the mixed solution to form nucleic acid fragments each having a blunt end, wherein the blunt ends are formed by repairing the nucleic acid fragments in the mixed solution or cleaving the nucleic acid fragments in the mixed solution with an enzyme (col. 6-9 and 11-14).
Regarding claim 7, Makarov teaches wherein the adapter-dependent PCR in the step (e) is performed by using the nucleic acid fragments ligated with the double-stranded homogeneous adapters as templates, and by using a single type of bidirectional primer corresponding to the double-stranded homogeneous adapters (col. 4-8, 11-14, and Examples).
Regarding claims 1-10, While Makarov teaches numerous embodiments of the claimed invention, the reference does not expression teach wherein the adapter-dependent PCR assay encompasses performing digital PCR.
Aigrain et al provides a general teaching of using digital droplet PCR (ddPCR) assay with DNA preparation kits for sequencing (abstract). Aigrain teaches that the ddPCR technology to measure the amount of DNA remaining after each step of a protocol, as well as the percentage of fragment bearing adaptors at their ends after ligation steps or after primer extension after amplification (page 2, second paragraph at col. 1). Aigrain teaches where in steps includes a fragmentase step, after fragmenting, the sample can go straight into the end repair and A-tailng steps, improving the DNA recovery and reducing overall preparation time even further. Aigrain teaches combining several steps decreases overall preparation time and DNA recovery (see page 2, line 2 (section “Results). Aigrain teaches that ddPCR allows one to prove the amount DNA remaining in each sample after A-tailing, after adaptor ligation and after OCR (page 3).
In view of the foregoing, it would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have been motivated to have modified the method of Makarov et al to encompass steps of not only fragmentation, A-tailing, adapter ligation, PCR in single tube but include droplet digital PCR as taught by Aigrain because Aigrain teaches the advantages of do so which allows the user to probe the efficiency of most critical steps in library preparations, ligations and allows quantification of not only overall yield but also of the yield of some critical intermediate steps such as adapter ligation as discuss by both Makarov and Aigrain.
Conclusion
8. No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/ Primary Examiner, Art Unit 1681