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 .
Applicants Amendment
Applicant’s amendment filed 7/13/2026 has been received and entered. Claims 1 and 15 have been amended and claims 2 and 4 have been cancelled.
Claims 1, 3, 5-15 are pending.
Election/Restriction
Applicant’s election without traverse of Group I, claims 1-6, in the reply filed on 6/2/2022 was acknowledged.
Claims 1, 3, 5-15 are pending.
Claims 7-14 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 1, 3, 5, 6, 15 drawn to a method of tagging a nucleic acid to create an ID number are currently under examination.
Priority
This application filed 4/20/2020 is a 371 National stage filing of PCT/EP2018/078810 filed 10/19/2018 and claims benefit to foreign application EP17197597.2 filed 10/20/2017 in the EP.
No comments on the summary of priority are provided in the instant response.
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.
Claim 15 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn.
The amendment makes it consistent with the present disclosure of having one watermark sequence and not another.
Claims 1, 3, 5, 6, 15 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention is withdrawn.
The deletion of ‘pre-defined codebook’ and addition of description of tags and values associated with the tag is consistent with the general disclosure.
Claim 15 recites the limitation "any additional watermark sequence" in reference to the tag of claim 1, however there is no requirement that the tag or code of the tag has a watermark. There is insufficient antecedent basis for this limitation in the claim.
Amending claim 1 to more clearly indicate that there is a watermark or more clearly providing in claim 15 the basis of a tag having a watermark as well as acting as a code would address the basis of the rejection.
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.
Claims 1, 3, 5, 6 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Levy et al. (2015).
Claim 1 has been amended to set forth that a codebook is generated and given the specification it provides the basis of what the each of the bases and subsequent numberical codes represent for any given tag. The limitation is broad and generic, and appears descriptive of what is accomplished in the final step of attributing each base a numerical value. In view of the preamble and guidance of the specification, the codebook with values associated with each tag provides the basis of the tag being a predetermined ID. The ID number is generated based on sequence data which is then ‘translated’ into a representative number ID, and more specifically as set forth in the claim that each of the bases A, G, T or C represents 0-3 and are obtained from a ‘pre-defined codebook’ but still appears to provide for any combination that could be designed for a given length. Broadly, the claim requires representing the AGTC bases as numbers instead of simply using the sequence itself as the tag information. Given the breadth of the claim and guidance of the specification, the tags are different and provide a ‘code’ which can be associated with an ID number. Claim 3 encompasses a tag is 8. The three active steps of claim 1 require that a nucleic acid sequence is attached to another to provide the attached nucleic acid represents the ID number and then amplification and sequencing the nucleic acid to obtain a read for analysis. Claim 15 has been amended to indicate that the tag does not contain an additional watermark, and can interpreted to represent an ID number for a given tag.
The addition of using a codebook, where apparently the sequences and represented ID number is provided is also acknowledged. In review of the specification, the limitations of the tag appear to be descriptive of what the tag sequence could represent, but do not appear to change, affect or limit the ATG or C of a given sequence tag in any specific way. In review of the dependent claims and the specification, it appears that the nucleic acid tag attached to another nucleic acid molecule (claim 5) can also be modified by a detectable label but does not appear to affect or limit the nucleic acid sequence provided in the wherein clause in a way to differentiate the tag from any random sequence or any designed barcode sequence or UMI attached to a nucleic acid of interest. In view of the claim amendments, the scope of the claims do appear to have distinguished any specific design requirements, and thus broadly provides for any sequence or barcode sequence as a tag. Levy does not indicate a ‘codebook’ but the artisan would readily appreciate and know that a tag would have to be informative for use, and that guidance for the association of a given sequence with a given ID would be required and is considered obvious.
As In review of the teachings of Levy et al., there is clearly steps to attach and use barcodes to track alterations in yeast sequences. Given the breadth of the claims a tag encompasses a barcode as both are informative extra sequences attached to another sequence. M Levy et al. generated yeast lineages by inserting a 20-nucleotide barcode sequences at a single location in the genome noting Figure 1B and supplemental data in SM 1.3. The tagged yeast cultures are allowed to replicate and the barcode is amplified and after selection the genomes are subject to whole genome sequencing for analysis.
It is acknowledged that Levy et al. do not specifically state that the barcodes are decoded or converted into numerical values, but these appear to be descriptive of the nucleic acid barcodes and do not appear to distinguish with any specificity the use of tagging with any barcode and thus is obvious given the general teaching to use the barcode as an ID provided in Levy et al. Further, Levy et al teach that the 20mer tags were random, however it is clear that each provide informative information and are used to attribute and ID to each of the associated yeast sequences and thus the sample being analyzed.
Response to Applicants Arguments
Applicant provides a summary of Levy et al a adding barcodes to track yeast and argue that Levy do not provide a codebook. Applicants argue that using non-random tags in a codebook are intentionally designed and provide the basis of a finite number of codes, which addresses a problem of having to synthesize large sets of tags and addresses issues of scalability for use of barcode tagging without indicating size or they are composed of tags and not random like that provided by Levy et al.
In response, it is generally agreed that Levy et al do not recite a ‘codebook’ but the skilled artisan would readily recognize that barcodes are used to tag sequences as Levy et al. did, and that each barcode is a means to ID the sequence that it is attached to. While the specific term codebook of the claims are not provided by Levy et al and it is clear that they are used to ID and track the sequences in yeast as a form of ID.
There does not appear to be a problem in the art as asserted for providing barcodes and using barcodes as IDs. In view of the evidence of record, the teaching of the specification and the art as a whole for the knowledge of the skilled artisan for expectation of success and interpretation of what type of tag is used and how it can be associated with an ID number as used by Levy et al to track the yeast. The limitations of the claims have been evaluated and appear to indicate how one can interpret any given tag sequence and not specifically define any specific design requirements of the tag in a physical way.
With respect to claim 15, it has been included because while watermark is not taught by Levy et al., it is not clear what this limitation includes or excludes beyond a barcode, and it does not appear to exclude the tags of Levy et al because the tags are not indicated to be watermarks and thus a plain reading of Levy et al supports that claim 15 is also anticipated by the tags provided in Levy. The claims as amended do not appear to provide any specific requirement, in particular since description of a Hamming relationship suggests that it is simple a measure of difference between regions, and thus would encompass any sequence tag which is 8 or more.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
In prosecution additional art of record as evidenced by Bystrykh et al., Buschmann et al. and Church et al. demonstrates that the design and method of attaching barcodes to a sequence for further analysis was known. Each of Bystrykh et al., Buschmann et al. and Church et al. provide for the design and use of barcodes. Each Bystrykh et al., Buschmann et al. and Church et al. provide for 0, 1 and 2 for instruction for what a given sequence could represent and the means to use and decode a sequence. Each Bystrykh et al., Buschmann et al. and Church et al. provide for a variety of methodologies and considerations in the design sequences that provide a means to detect and correct for errors would have been an element of the design and use of a tag sequence.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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