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 .
OBJECTIONS
2. The specification is objected to because of the following informality: the continuation information must be updated to indicate the issue of the parent ‘230 application as US 11,913,063.
3. Claim 28 is objected to because of the following informality: ‘the adaptor molecule are’. Correction is required.
4. Claim 39 is objected to because of the following informality: ‘the adaptor molecules comprises’. Correction is required.
NON-PRIOR ART REJECTIONS
5. 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 22-23 and 39 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.
A) Claims 22-23 are indefinite because ‘the mixture’ and ‘the reverse transcriptase’ in claim 22 lack proper antecedent basis in independent claim 19. Correction is required.
B) Claim 39 is indefinite because it cannot be determined what is encompassed by adaptor molecules that comprise ‘sequences for interaction with the sequencer’. Such sequences have not been defined in the specification, and one of ordinary skill in the art would not be apprised of the meaning. Clarification is required.
PRIOR ART REJECTIONS
6. 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.
7. 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.
8. 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.
9. 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.
10. Claims 1-27 and 29-41 are rejected under 35 U.S.C. 103 as being unpatentable over Talasaz (US 2014/0066317).
Initially, it is noted that the claims are directed to a system which is a type of product, and as well settled in U.S. patent practice product claims are examined only based on the required components or elements, and ‘intended use’ language is not given patentable weight. Thus, any proper motivation found in the prior art to make and use a claimed product is appropriate in showing obviousness, even if that prior art motivation differs from that disclosed in an application.
In light of the above, regarding independent claim 19, Talasaz discloses a plurality of molecular barcode nucleic acids comprising an RNA tag sequence and a molecular barcode sequence that is configured to selectively interact with ssRNA. Talasaz also discloses a plurality of adaptor molecules comprising an adaptor molecular barcode sequence which is configured to label dsDNA and double-stranded derivatives of ssRNA, namely reverse-transcribed ds-cDNA. See paragraphs 0003-0016, 0034-0036, 0042-0043, 0056-0060, 0078-0080, 0094-0095, 0102-0103, and 0107-0115.
Talasaz does not explicitly disclose a system comprising the disclosed molecular barcode nucleic acids targeting RNA and adaptor molecules targeting dsDNA or ds-cDNA.
One of ordinary skill in the art would have been motivated to combine the molecular barcode nucleic acids targeting RNA and the adaptor molecules targeting dsDNA or ds-cDNA of Talasaz into a system because such a system would have clearly been useful in practicing the methods of Talasaz and clearly provided the expected benefit of providing valuable genetic information regarding both RNA and DNA. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to make and use the claimed system.
For the sake of completeness, it is noted that the point of patentability in the patented methods of the parent applications relies on two-layered barcoding of both RNA and DNA in a mixed sample, wherein RNA is labeled with a first barcode during reverse transcription to produce a barcoded ds-cDNA, and then the mixture of first-barcoded ds-cDNA and unbarcoded dsDNA is labeled with a second barcode, such that the RNA-derived ds-cDNA comprises both the first and second barcodes, whereas the dsDNA from the sample only comprises the second barcode. This point of patentability is not applicable to the claimed system, which can be used in another way(s) as suggested by Talasaz.
Regarding claim 20, Talasaz discloses that molecular barcode nucleic acids comprise sequences complementary to ssRNA.
Regarding claims 21-23, Talasaz discloses the use of reverse transcriptase to generate ss-cDNA from RNA which is then converted to ds-cDNA via a polymerase.
Regarding claims 24-25, Talasaz discloses the use of a ligase.
Regarding claim 26, Talasaz discloses the use of different first barcode sequences.
Regarding claim 27, Talasaz discloses the use of common or non-unique tag sequences.
Regarding claims 29-30, Talasaz discloses that the RNA and DNA comprise a genetic alteration.
Regarding claim 31, Talasaz discloses the use of a sample comprising ssRNA and dsDNA.
Regarding claims 32-37, Talasaz discloses the use of a sample which is a cell-free sample of a biofluid including blood, plasma, and urine.
Regarding claims 38-39, Talasaz discloses the use of a nucleic acid sequencer.
Regarding claims 40-41, Talasaz discloses using a sample derived from a subject, which subject is suspected of having cancer.
11. Claim 28 is rejected under 35 U.S.C. 103 as being unpatentable over Talasaz (US 2014/0066317) in view of Eltoukhy et al. (US 2016/0046986).
The teachings of Talasaz are discussed above.
Talasaz does not disclose adaptors that are Y-shaped or forked.
Eltoukhy discloses, in the same sequencing context as Talasaz, the use of Y-shaped or forked adaptors (see paragraphs 0006 and 0258).
One of ordinary skill in the art would have been motivated to modify the suggested system of Talasaz by using as adaptors those that are Y-shaped or forked because Eltoukhy disclosed that Y-shaped or forked adaptors were useful in sequencing applications. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to make and use the claimed system.
CONCLUSION
12. No claims are free of the prior art.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENNETH R HORLICK whose telephone number is (571)272-0784. The examiner can normally be reached Mon. - Thurs. 8:30 - 6:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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08/04/26
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681
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