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 .
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
See Figs 13A, 14A and 17.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
See paragraph 0094.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1, 2, 16, 19, 23-25 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Merriman (US 2020/0242482).
Regarding claim 1, Merriman disclosed:
A method for creating an oligonucleotide sequence to represent digital data,
Para 0008: “converting the information into one or more nucleotides using an encoding scheme, the nucleotides predetermined to generate distinguishable signals relating to the information in a measurable electrical parameter of a molecular electronics sensor; assembling the one or more nucleotides into a nucleotide sequence”.
Para 0009: “the information comprises a string of binary data”.
See also Fig. 4-6.
the method comprising: selecting from a first set of multiple oligonucleotide sequences one oligonucleotide sequence for each of multiple parts of the data,
the multiple oligonucleotide sequences being configured to generate an electric time-domain signal from one oligonucleotide sequence that is distinguishable from the electric time-domain signal from another oligonucleotide sequence, the electric time-domain signal being indicative of an electric characteristic of one or more nucleotides present in an electric sensor at any one point in time;
See, e.g., Fig 16 (and para 0038, 0154) which illustrates different oligonucleotide sequences (20A, 3C) producing distinguishable electric time-domain signals.
and combining the one oligonucleotide sequence for each of multiple parts of the data into a single oligonucleotide sequence that represents a single oligonucleotide molecule to encode the digital data.
See para 0154 in connection with Fig 16: “…0 encoded by the poly-A tract and read from the high peak signals having several seconds duration, and 1 encoded by the CCC tract and read from the low trough features having several seconds duration…”.
Regarding claim 2, see para 0180 and Fig 24: “As the polymerase processes a DNA template, the ionic current through the pore is modulated by this activity, producing distinguishable signal features that correspond to distinct sequence features. Aside from a different geometry of the nano-electrical measurement, the considerations are otherwise identical to those already reviewed herein. That is, nano-pore current sensor versions of the polymerase-based DNS digital data reader are of similar use herein.”
Regarding claim 16, see para 0075: “Information is encoded as DNA sequences, synthesized into DNA molecules, stored, and then read, decoded and output.”
Regarding claim 19, see para 0086: “In other embodiments, there may be “punctuation” sequence segments inserted between the distinguishable signal features, which do not alter the distinguishable features…to provide spacers for added time separation between signal features…”. It is intuitive that the signal would be “split” by the spacer.
Regarding claims 23 and 24, see para 0075:
As illustrated in FIG. 1, an amplification-free DNA storage system comprises an information encoder/decoder algorithm, a DNA writing device (synthesizer), a DNA reading device (sequencer), and a library management subsystem for managing physical DNA molecules in the library physical storage to support archival operations. This example shows the major elements of a DNA storage system, including the physical system used to handle and maintain the DNA material during storage, and which carries out operations on the stored archive, such as copying. An external computer provides a high level control of the system, supplying information for storage, and receiving extracted information. Information is encoded as DNA sequences, synthesized into DNA molecules, stored, and then read, decoded and output. In addition, such a system is capable of physical I/O of the DNA archive material samples as well.
The external computer controlling the system would necessarily require “non-transitory computer-readable medium with program code stored thereon” as recited in claim 23, and memory and a processor as recited in claim 24.
Regarding claim 25, e.g., Fig 16 (and para 0038, 0154) which illustrates such an oligonucleotide.
Claim Rejections - 35 USC § 103
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.
Claim(s) 9 and 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merriman (US 2020/0242482). The teachings of Merriman have been discussed. In addition, Merriman disclosed (para 0086): “In other embodiments, there may be “punctuation” sequence segments inserted between the distinguishable signal features, which do not alter the distinguishable features…to provide spacers for added time separation between signal features…”.
Merriman did not explicitly disclose wherein the spacer sequence is of sufficient length to generate, for a second oligonucleotide sequence from the first set, a predictable interference from the spacer sequence and not a preceding first oligonucleotide sequence, which is construed to mean that the spacer is of sufficient length to separate the signals from the first and second oligonucleotides, and such that the spacer signal would be distinguishable from the signals of each of the first and second oligonucleotides.
However, this would have been obvious to one of ordinary skill in the art as a matter of common sense, since this is the purpose of the spacer disclosed by Merriman (i.e. to separate the signal features). Regarding claim 11, it would have been within the skill of the ordinary worker to determine the optimal length of such a spacer.
Claim(s) 21, 28, 30 and 32 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merriman (US 2020/0242482) in view of Nilsson (US 2018/0039997, cited on IDS).
The teachings of Merriman have been discussed. Merriman did not suggest using his encoded sequences to mark a product for verification.
Nilsson disclosed (abstract):
In various embodiments, genetic material such as plasmids may be incorporated into and/or otherwise persistently associated with a product. The genetic material may be encoded with, among other things, information that may uniquely identify the product, provide details relating to the origins of the product, the handling, distribution, and/or chain of custody of the product, intellectual property rights and/or other rights associated with the product, and/or the like. By extracting and analyzing the genetic material from the product, information encoded in the genetic material may be obtained by an interested party.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to use the encoding, sequence synthesis, and decoding methods of Merriman to encode nucleic acid sequences with which to make the marked products, and verifying the products based on the encoded sequences as disclosed by Nilsson. This represents nothing more than combining prior art elements according to known methods to yield predictable results (MPEP 2143(I)). It also represents nothing more than selection of a known material based on its suitability for its intended purpose (MPEP 2144.07). Here, Merriman disclosed the purpose of his invention was to encode information in the form of nucleic acid sequences, which would have been recognized as suitable according to the purpose of Nilsson, which was to use encoded nucleic acid to mark a product for later verification.
Claim(s) 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merriman (US 2020/0242482) in view of Nilsson (US 2018/0039997, cited on IDS) as applied to claims 21, 28, 30 and 32 above, and further in view of Polansky (US 2004/0023207).
The teachings of Merriman and Nilsson have been discussed. These references did not teach or suggest putting the encoded nucleic acid molecules into “kits”.
Polansky taught (paragraph [0919]): “Well known advantages of commercial kits include convenience and reproducibility due to manufacturing standardization, quality control and validation procedures.”
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to put the encoded nucleic acids produced by the method of Merriman for the purpose of marking products according to the teachings of Nilsson into “kits” to obtain the advantages of kits described by Polansky.
Claim(s) 3, 6 and 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Merriman (US 2020/0242482) in view of Paegel (US 2020/0190507).
The teachings of Merriman have been discussed. Merriman did not disclose the limitations of claims 3, 6 and 17.
Paegel disclosed methods of encoding chemical libraries using polynucleotides (abstract). Paegel disclosed (para 0045): “Matched sequencing reads were next corrected for sequencing errors and decoded to numeric identifier strings. The genetic language design distributed the sequences in set 1 and set 2 such that all members were maximally genetically distinct (Hamming distance >2). Thus, sequence analysis could tolerate one sequencing error in each coding region and still assign a correct coding sequence.” Thus, Paegel disclosed decoding based on matching the observed sequences to sequences used in the encoding process, and further disclosed selecting encoding sequences based on their “distance” such that the sequences were identifiable and distinguishable taking into account errors in the measurement process.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the application to select the oligos used for encoding in Merriman’s method such that the different sequences in the set of sequences used for encoding were selected based on the “distance” between the predicted (simulated) electric time-domain signals, where such distance was beyond the error of the measurement. Just as Paegel chose sequences having a distance that would be beyond the error of the measurement method in his technique (which was sequencing), it would have been obvious to one of ordinary skill to choose sequences beyond the error of measurement in Merriman’s method, which was based on an electric time-domain measurement. One would have been motivated to do so in order to end up with the correct information upon decoding, even if there had been an error in either synthesizing the nucleic acid molecule, or in “reading” the nucleic acid molecules.
Conclusion
Claims 13-15, 26 and 35 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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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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/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681