DETAILED ACTION
Status of the Claims
1. Claims 1-20 are pending.
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.
2. Claims 1-14 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 recites the limitation "the nucleic acid storage system" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-14 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph for being dependent on claim 1.
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.
3. Claim(s) 1-7 and 11-18 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Polonsky et al. (US 2010/0025249).
Claims 1 and 4. Polonsky et al. teach a nucleic acid digital data storage system that uses nanopore sequencing to read data values chemically embedded in oligonucleotides (polymer position control device to nanopore sequencing by detecting nucleotide [0027][0009][0049][0024] and Fig 1), the nucleic acid storage system comprising:
a membrane having a plurality of nanopores that are stacked upon one another in a multi-nanopore arrangement (membrane 102 having plurality of stacked electrodes to form plurality of nanopores; see Fig 1 and [0027]);
a voltage source that is configured to direct voltage across the plurality of nanopores (control unit applies direct voltage to electrodes/nanopores independently; [0027]); and
a nucleic acid strand including the oligonucleotides that is threaded through each of the plurality of nanopores within the membrane (DNA/RNA strand/linear polymer 112 which inherently is comprised of oligonucleotides is threaded through the nanopores; see Fig 1 and [0030][0033]).
Claim 2. Polonsky et al. teach the nanopores are surrounded by an electrolyte solution within the membrane (nanopores are surrounded by solution from the CIS reservoir to TRANS reservoir [0034]).
Claim 3. Polonsky et al. teach the nucleic acid strand is a DNA strand; and wherein the oligonucleotides include one or more of adenine, guanine, cytosine, and thymine (DNA strand [0033] and inherently is comprised of oligonucleotides such as adenine, cytosine, guanine and thymine).
Claim 5. Polonsky et al. teach the voltage from the voltage source is applied across each of the plurality of nanopores independently of one another to create an electrical field across pore ends of each of the plurality of nanopores; and wherein the electrical field creates an ionic current to pass through each of the plurality of nanopores (independent voltages V1-V3 across each of the nanopore represented by electrodes 106-108 respectively to create electrical field across the nanopores [0027] wherein the electric field is ionic current; [0052]).
Claim 6. Polonsky et al. teach the membrane is usable to capture multiple waveforms for a base sequence when the oligonucleotides are threaded through the plurality of nanopores; and wherein the oligonucleotides being threaded through each of the plurality of nanopores generates a corresponding ionic current (membrane captures multiple waveforms as seen in Fig 2 to obtain base sequence as the DNA threaded across the plurality of nanopores/electrodes to obtain sequence of DNA; [0033]).
Claim 7. Polonsky et al. teach a separate base signal is generated from the nucleic acid strand being threaded through each of the plurality of nanopores (Fig 2 shows signal generated at each of electrodes/nanopores as polymer translocated by one or more monomers; [0013]).
Claim 11. Polonsky et al. teach the plurality of nanopores includes a first nanopore, a second nanopore and a third nanopore that are stacked one on top of another from top to bottom in the multi-nanopore arrangement (plurality of stack electrodes 106-108 which forms respective nanopores are stacked on top of another; see Fig 1); and wherein the membrane further includes a first cavity that is defined between the first nanopore and the second nanopore, and a second cavity that is defined between the second nanopore and the third nanopore (space between each of the stacked nanopores reads on first cavity and second cavity respectively).
Claim 12. Polonsky et al. teach each of the plurality of nanopores is different from each of the other nanopores in translocation speed (the DNA/polymer translocate at different speed in each of the nanopores; see Fig 2).
Claim 13. Polonsky et al. teach the first cavity has a first size, and the second cavity has a second size that is different than the first size (the potential well formed in the different nanopores are of different sizes; see Fig 2).
Claim 14. Polonsky et al. teach the membrane is one of a biological membrane, a solid-state membrane [0006].
Claim 15. Polonsky et al. teach a method for using nanopore sequencing to read data values chemically embedded in oligonucleotides (polymer position control method for nanopore sequencing of a nucleotide [0027][0009][0049][0024] and Fig 1, the method comprising the steps of:
stacking a plurality of nanopores upon one another in a multi-nanopore arrangement within a membrane (membrane 102 having plurality of stacked electrodes to form plurality of nanopores; see Fig 1 and [0027]);
directing voltage across the plurality of nanopores with a voltage source (control unit applies direct voltage to electrodes/nanopores independently; [0027]); and
threading a nucleic acid strand including the oligonucleotides through each of the plurality of nanopores within the membrane (DNA/RNA strand/linear polymer 112 which inherently is comprised of oligonucleotides is threaded through the nanopores; see Fig 1 and [0030][0033]).
Claim 16. Polonsky et al. teach the step of providing an electrolyte solution within the membrane so that the nanopores are surrounded by the electrolyte solution (nanopores are surrounded by solution from the CIS reservoir to TRANS reservoir [0034]).
Claim 17. Polonsky et al. teach the step of directing includes applying the voltage from the voltage source across each of the plurality of nanopores independently of one another to create an electrical field across pore ends of each of the plurality of nanopores; and creating an ionic current with the electrical field to pass through each of the plurality of nanopores (independent voltages V1-V3 across each of the nanopore represented by electrodes 106-108 respectively to create electrical field across the nanopores [0027] wherein the electric field is ionic current; [0052]).
Claim 18. Polonsky et al. teach the steps of capturing multiple waveforms for a base sequence with the membrane when the oligonucleotides are threaded through the plurality of nanopores; and generating a corresponding ionic current from the oligonucleotides being threaded through each of the plurality of nanopores (membrane captures multiple waveforms as seen in Fig 2 to obtain base sequence as the DNA threaded across the plurality of nanopores/electrodes to obtain sequence of DNA; [0033]).
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.
Claim(s) 8-9 and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Polonsky et al. as applied to claims 7 and 18 above, and further in view of Mandell (US 2025/0215487) and Peng et al. (US 2019/0221234).
Claims 8-9 and 19, Polonsky et al. do not teach Recursive Neural Networks are used to estimate a signal shape for each nucleotide or Recurrent Convolutional Neural Networks and noise predictive maximum likelihood data detection algorithms are used based on the estimated signal shapes to sequence the oligonucleotides.
However, Mandell et al. teach system for sequencing polynucleotides using nanopores comprising using recursive neural networks or recurrent convolution neural networks to sequence the nucleotides (abstract and [0183][0184]) and Peng et al. teach use of noise predictive maximum likelihood data detection algorithm (NPMLD) to lower signal to noise ratio (SNR) .
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention in view of Mandell et al. teaching to use recursive neural networks or recurrent convolution neural networks to obtain sequence of nucleotides in Polonsky et al. system because the neural networks are well known algorithms used for sequencing and thus their use would have resulted in same results with reasonable expectation and use of NPMLD to lower signal to noise ratio.
Claim(s) 10 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Polonsky et al. as applied to claim 7 above, and further in view of Conde-Canencia (US 2023/0187024).
Claims 10 and 20. Polonsky et al. do not teach each of the base signals is modified by each of a post-processing system, a joint symbol detection system, and an Error Correction Coding (ECC) decoding system. However, Conde-Canencia teach method of determining sequence of DNA comprising post-processing step of decoding and error correction codes to correct for insertion or deletion errors introduced during the time of encoding (see Fig 2 and [0082][0083].
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention in view of Conde-Canencia et al. teaching to use post-processing step of decoding and error correction codes in Polonsky et al. system because it would correct for any insertion or deletion errors introduced during the time of encoding.
Conclusion
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/GURPREET KAUR/
Primary Examiner
Art Unit 1759