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 .
Drawings
The drawings are objected to because figures 7-9 are blurry and not legible. 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.
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 1-8, 11-13, and 15-17 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 1 is indefinite because it appears to be missing some steps. In part (3) of the claim is recited “wherein the hybridization system comprises the probes” and then instructions to hybridize, however there is no indication what the probes are hybridizing as they are the only thing added to the reaction.
Part (5) is also indefinite because it is unclear what “separately washing” means. Is each captured product washed by itself or is captured target intended to include the entire population of targets. There is also an extra space between separately and washing. It is also unclear is the elution buffers are different, if the numbers are to indicate a specific buffer, or if the numbers are to indicate an order. The specification recites a preferable formula but does not define the terms.
Claim 1 recites the limitation "oligonucleotide" in part (1). There is insufficient antecedent basis for this limitation in the claim.
Claims 2-8 and 11-13 are included in this rejection as they do not overcome all of the issues recited above
Claim 16 is indefinite because it does not recite any active method steps. It is not clear how it can be used in genomic target region capture. Claim 17 depends from claim 16 and does not remedy this rejection.
Claims 7, 8, and 11 contains the trademark/trade names: HyB Buffer, Enhance, Human Cot-1, Blocker, HiFi PCR Master Mix, and Index Primer Mix. 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 components used in hybridization assays and, accordingly, the identification/description is indefinite because it is not known what the components are. Claim 8 is included in this rejection as it depends from claim 7.
Claim 13 recites the limitation "formula" when describing the elution buffers. There is insufficient antecedent basis for this limitation in claim 1 from which claim 13 depends.
Claim 15 recites a PCR premix and it is not clear from the claim of the specification what a PCR premix is or what it contains.
Claim 15 recites a DNA blocker and it is not clear from the claim or the specification what the DNA blocker is. It is not defined in the specification.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claims 1-6, 12, 14, 16, and 17 are rejected under 35 U.S.C. 103 as being unpatentable over CN111926066A (Methods and Kits for rapid hybridization of probes to libraries, 2020) in view of Eder et al. (US 8,877,436 B2).
CN111926066A teach contacting a probe with a library in a hybridization buffer, capturing the complex with streptavidin, cleaning the complex, amplification with PCR, and high throughput sequencing. (Claim 1).
CN111926066A teach that the probe is a nucleic acid with a 5’ biotin label. (page 3 of translation).
CN111926066A teach the use of a DNA library building kit to construct the pre-library used in the method. (page 4 of the translation).
CN111926066A teach that after capture is complete, the captured product is washed three times. (page 7 of the translation).
CN111926066A teach purification with magnetic beads after the PCR reaction is complete. (page 8 of the translation).
CN111926066A does not teach wherein the probe comprises a sequence complimentary to another probe, or the hybridization conditions in part ii of claim 1.
Eder et al. teach a fast results hybrid capture assay. Eder et al. teach library construction comprising the steps of suspending the sample in a collection medium (Col. 3, lines 17-18). Eder et al. teach contacting one or more probes with target nucleic acid molecules under conditions that allow the probes and the target nucleic acid molecules to hybridize. (Col. 2, line 12-16). Eder et al. teach capturing the probe-target hybrids (Col 2., line 17) and separating the hybrids from unbound target nucleic acids (Col 2., lines 18-19). Eder et al. teach that capture is achieved with biotin-streptavidin on a magnetic bead. (Col. 16, line 28-49). Eder et al. teach washing the captured product with a wash buffer one to ten times. (col. 18, lines 11-12).
Eder et al. teach that the probe can be full length, truncated or synthetic DNA (or RNA). (Col. 14, lines 23-25). Probes are designed to match the sequence they are detecting and can be short or long. (see section titled polynucleotide probes starting in Col 20).
Both CN111926066A and Eder et al. are interested in hybridization of a target for further analysis. Both teach methods of hybridization of specific targets and analysis of those targets after several capture and elution steps. Therefore, it would have been obvious to one of ordinary skill in the art to create probes that bind to each other to increase the stability of the probes hybridized to the target in order to maintain that hybridization through the remaining steps of the method.
Furthermore, Eder et al. teaches that one of skill in the art would understand the incubation time and temperature are conditions that one of skill in the art would vary to achieve alternative capture kinetics. (Col. 17, lines 8-10). One of skill in the art would appreciate that the hybridization step would need to proceed under certain conditions to accommodate both binding to the target and binding to adjacent probes. Eder et al. teaches up to 1 hr of incubation at 67° and one of skill in the art would optimize those conditions for the specific method. Therefore, a temperature between 57-63° for 1-2 hr is sufficiently close to the parameters taught by Eder et al. that one of skill in the art would be motivated to try those conditions.
Regarding claims 2 and 3, as stated above, it would have been obvious to one of ordinary skill in the art to create probes that bind to each other to increase the stability of the probes hybridized to the target in order to maintain that hybridization through the remaining steps of the method.
Regarding claim 4, Eder et al. teach the sample can come from a variety of sources including tissue, fluids, biological, and environmental samples. (Col. 6, lines 19-48).
Regarding claim 5, Eder et al. teach the sample are whole cells and cells contain genomic DNA.
Regarding claim 6, CN111926066A teach the library fragment size is between 200-600 bp. (page 8 of the translation).
Regarding claim 12, CN111926066A teach the library is prepared with a Rapid DNALib Prep Kit and the kit has enzymes and buffers for end-preparation and adapter ligation. (see PDF of website description).
Regarding claim 14, both CN111926066A and Eder et al. teach a kit to carry out the methods described.
Regarding claim 16, Eder et al. teach the sample are whole cells and cells contain genomic DNA.
Regarding claim 17, CN111926066A teaches that the method can be used with high-throughput sequencing which is next generation sequencing. (for example, claim 1).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MINDY G BROWN whose telephone number is (571)270-5605. The examiner can normally be reached Monday -Friday, 9:00 am - 5:00 pm EST.
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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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/MINDY G BROWN/Patent Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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