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 .
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.
Claims 1-3, 6-8, 10, 16-17, 21, 23, 29, 55-56, 66-69, 71 and 87 are rejected under 35 U.S.C. 103 as being unpatentable over Roquet et al. (US 12,236,354), hereinafter Roquet, in view of Bhatia et al. (US 2024/0404593), hereinafter Bhatia.
Regarding claim 1, Roquet teaches a method for encoding data (Roquet, Abstract, Fig. 1), the method comprising: (a) splitting data into a plurality of frames (Roquet, col. 1, lines 64-67 through col. 2, lines 1-2, "the present disclosure provides a method for coding digital information into nucleic acid sequence(s), comprising: (a) coding the digital information into a sequence of symbols and converting the sequence of symbols into codewords using one or more codebooks; (b) parsing the codewords into a coded sequence of symbols..."; the coded sequence of symbols equates to plurality of frames), wherein each frame in the plurality of frames comprises a frame index (Roquet, col. 2, lines 3-5, "mapping the coded sequence of symbols to a plurality of identifiers, wherein an individual identifier of the plurality of identifiers comprises one or more nucleic acid sequences"; col. 7, lines 52-55, "The term "identifier," as used herein, generally refers to a nucleic acid molecule or a nucleic acid sequence that represents the position and value of a bit-string within a larger bit-string"; the identifier equates to a frame index); (b) applying an outer codec to each frame in the plurality of frames, wherein the outer codec comprises an error correction scheme (Roquet, col. 2, lines 40-43, “In some embodiments, a codebook appends one or more error protection symbols to individual codewords of the sequence of codewords”); and (e) applying an inner codec to encode each lane in a corresponding polynucleotide sequence, thereby generating a plurality of corresponding polynucleotide sequences (Roquet, col. 2, lines 3-5, "mapping the coded sequence of symbols to a plurality of identifiers, wherein an individual identifier of the plurality of identifiers comprises one or more nucleic acid sequences").
Roquet fails to teach (c) dividing each frame into a plurality of lanes, wherein each lane in the plurality of lanes comprises a lane index and (d) shuffling each lane based at least in part on the lane index.
However, Bhatia, in an analogous art, teaches (c) dividing each frame into a plurality of lanes, wherein each lane in the plurality of lanes comprises a lane index (Bhatia, para. [0091], lines 3-6, “(a) receiving the digital information as a string of symbols, wherein each symbol in the string of symbols has a symbol value and a symbol position within the string of symbols”; claim 2, lines 1-2, “The method of claim 1, wherein the library of component nucleic acid sequences comprises a plurality of layers”; the layers equate to lanes, and the symbol position equates to a lane index); (d) shuffling each lane based at least in part on the lane index (Bhatia, Figs. 11A-11B, para. [0123], lines 1-4, “FIGS. 11A and 11B schematically illustrate an example method, referred to as the "permutation scheme", for constructing identifiers [e.g., nucleic acid molecules] with permuted components [e.g., nucleic acid sequences]”; para. [0123], line 163, “The components may be concatenated in any order”; permuting components based on position equates to shuffling lanes based on lane index).
Roquet and Bhatia are both considered to be analogous to the claimed invention because both are in the same field of nucleic acid data storage.
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified Roquet to incorporate the teachings of Bhatia by including the functionality of dividing frames into lanes, with each lane having an index, and shuffling each lane based at least in part on the index.
The suggestion/motivation for doing so would be to improve reliability when accessing and reconstructing stored data.
Regarding claim 2, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein the data comprises binary data, including a byte stream or a byte array (Roquet, col. 1, lines 34-40, “Current methods rely on encoding the digital information [e.g., binary code] into base-by-base nucleic acids sequences, such that the base to base relationship in the sequence directly translates into the digital information [e.g., binary code]. Sequencing of digital data stored in base-by-base sequences that can be read into bit-streams or bytes of digitally encoded information…”).
Regarding claim 3, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein the shuffling in (d) comprises a rotation scheme within each lane (Bhatia, Figs. 11A-11B, para. [0123], lines 1-4, “FIGS. 11A and 11B schematically illustrate an example method, referred to as the "permutation scheme", for constructing identifiers [e.g., nucleic acid molecules] with permuted components [e.g., nucleic acid sequences]”), comprises a pseudorandom process within each lane (Bhatia, para. [0335]-[0341] teaches various algorithms for converting a source bitstream into encoded data; para. [0123], line 163, “The components may be concatenated in any order”), and/or provides resistance against errors.
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified Roquet to incorporate the teachings of Bhatia by including the functionality of a shuffling operation comprising a rotation scheme and pseudorandom process in each lane.
The suggestion/motivation for doing so would be to encode and retrieved data in a way that is less costly and easier to commercially implement (Bhatia, para. [0004], lines 8-11, “Opportunities for new methods of performing nucleic acid digital data storage may provide approaches for encoding and retrieving data that are less costly and easier to commercially implement”).
Regarding claim 6, the combination of Roquet in view of Bhatia teaches the method of claim 3, wherein the shuffling in (d) provides resistance against errors, and the errors are nucleotide synthesis errors or sequencing errors (Roquet, col. 1, lines 38-45, “Sequencing of digital data stored in base-by-base sequences that can be read into bit-streams or bytes of digitally encoded information can be error prone and costly to encode since the cost of de nova base-by-base nucleic acid synthesis can be expensive. Opportunities for new methods of performing nucleic acid digital data storage may provide approaches for encoding and retrieving data that are less costly and easier to commercially implement”).
Regarding claim 7, the combination of Roquet in view of Bhatia teaches the method of claim 6, wherein the errors comprise a deletion, an insertion, or a substitution (Roquet, col. 1, lines 38-45, “Sequencing of digital data stored in base-by-base sequences that can be read into bit-streams or bytes of digitally encoded information can be error prone and costly to encode since the cost of de nova base-by-base nucleic acid synthesis can be expensive. Opportunities for new methods of performing nucleic acid digital data storage may provide approaches for encoding and retrieving data that are less costly and easier to commercially implement”). While the reference does not explicitly teach the limitation, the reference teaches encoding digital information from nucleic acid molecules despite errors that are introduced during synthesis and sequencing, which inherently includes insertion , deletion, and substitution errors.
Regarding claim 8, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein the error correction scheme comprises a Reed-Solomon (RS) code, a low-density parity-check (LDPC) code, a Turbo-code, a polar code, or any combination thereof (Bhatia, para. [0337], lines 1-9, “The codec may apply one or more error detection and correction algorithms to each block and compute one or more error protection bytes. The codec may then combine the original block with the error protection information to obtain an error-protected block. For example, the codec may apply convolution coding to bits in the block and Reed Solomon or erasure coding to chunks of bytes in the block and append the Reed-Solomon or erasure error protection bytes to each chunk of the block”).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified Roquet to incorporate the teachings of Bhatia by including an error correction scheme comprising a Reed-Solomon (RS) code, a low-density parity-check (LDPC) code, a Turbo-code, a polar code, or any combination thereof.
The suggestion/motivation for doing so would be that selecting a known ECC scheme of well-known schemes, represent a routine and predictable design choice.
Regarding claim 10, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein: the plurality of frames comprises about 100 to about 10,000 frames; each frame comprises less than or equal to about 5000 lanes; each lane comprises about 100 to about 300 bits; each frame index comprises about 16 to about 20 bits; the lane index comprises about 12 bits or about 16 bits; and/or each corresponding polynucleotide sequence of the plurality of corresponding polynucleotide sequences has a length of about 100 to about 300 bases. The claimed numerical ranges represent routing and predictable parameters for DNA storage systems.
Regarding claim 16, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein the frame index and/or the lane index are prepended to each lane prior to (d) (Roquet, Fig. 2A, col. 6, lines 20-24, “FIGS. 2A and 2B schematically illustrate a method of encoding digital data, referred to as "data at address", using objects or identifiers [e.g., nucleic acid molecules]; FIG. 2 illustrates combining a rank object (or address object) with a byte-value object (or data object) to create an identifier”). The reference teaches constructing each encoded data unit by combining a rank object with a data object, such that the positional index information is added to each lane before further processing steps.
Regarding claim 17, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein applying the inner codec comprises adding redundancy across the plurality of corresponding polynucleotide sequences, wherein the redundancy is about 5% to about 10% (Roquet, col. 12, lines 19-22, “The identifiers may be rationally designed and selected for ease of read, write, access, copy, and deletion operations. The identifiers may be designed and selected to minimize write errors, mutations, degradation, and read errors”). While the reference does not explicitly teach the limitation, it does teach minimizing errors which inherently require some sort of redundancy.
Regarding claim 21, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein applying the inner codec comprises: (a) combining symbols from a lane, a symbol history, and a symbol position (Roquet, col. 12, lines 26-29, “FIG. 2A illustrates encoding a bit stream into an identifier library wherein the individual identifiers are constructed by concatenating a single component that specifies an identifier rank with a single component that specifies a byte-value”); and (b) generating a base candidate using a lookup table, a hash, or both (Roquet, col. 15, lines 62-66, “Writing information into nucleic acid sequences may comprise parsing the information into strings of symbols, mapping the string of symbols to unique identifiers, and generating an identifier library that comprises identifiers corresponding to the string of symbols”; col. 16, lines 15-21, “The set of identifiers (e.g., identifier library) may include, or have appended to it, information related to the one or more codebooks, data structure, and combinatorial space. The formal data structure may include a tree, a trie, a table, set, a key-value dictionary, or a set of multidimensional vectors”).
Regarding claim 23, the combination of Roquet in view of Bhatia teaches the method of claim 21, further comprising performing a base repetition check, updating the symbol history, incrementing the lane index, incrementing the frame index, or any combination thereof (Roquet, col. 1, lines 29-35, “In general, the data at address method uses identifiers that encode information modularly by comprising two objects: one object, the "byte-value object" (or "data object"), that identifies a byte-value and one object, the "rank object" (or "address object"), that identifies the identifier rank ( or the relative position of the byte in the original bit-stream)”). While the reference does not explicitly teach the limitation, it teaches identifying the relative position of a byte in a bit stream, which involves sequential processing. Sequential processing of indexed symbols requires incrementing index values.
Regarding claim 29, the combination of Roquet in view of Bhatia teaches the method of claim 1, wherein each lane comprises a plurality of symbols, and applying the inner codec comprises: (a) generating a base candidate for each symbol within a lane using a lookup table (Roquet, col. 12, lines 37-39, “each rank object is combinatorially constructed from a set of components and each byte-value object may be combinatorially constructed from a set of components”); and (b) selecting a next lookup table based at least in part on the previously encoded symbol (Bhatia, para. [0030], lines 10-13, “FIG. 11D shows an example of how the implementation from FIG. 11C may be modified to construct identifiers with permuted and repeated components”; the use of repeated components to construct identifiers that are used in mapping equates in step (b)).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified Roquet to incorporate the teachings of Bhatia by including the functionality of selecting a next lookup table based in part on a previously encoded symbol.
The suggestion/motivation for doing so would be to address DNA storage constraints.
Regarding claim 55, Roquet teaches a method for encoding data, the method comprising: (a) generating an inner codec comprising a codebook (Roquet, col. 1, lines 66-67 through col. 2, line 1, “the present disclosure provides a method for coding digital information into nucleic acid sequence(s), comprising: (a) coding the digital information into a sequence of symbols and converting the sequence of symbols into codewords using one or more codebooks”); and (b) applying the inner codec to encode the data as a plurality of polynucleotide sequences (Roquet, col. 2, lines 3-5, “mapping the coded sequence of symbols to a plurality of identifiers, wherein an individual identifier of the plurality of identifiers comprises one or more nucleic acid sequences”).
Roquet fails to explicitly teach wherein the codebook is optimized for one or more constraints.
However, Bhatia, in an analogous art, teaches wherein the codebook is optimized for one or more constraints (Bhatia, para. [0339], lines 3-6, “The codec may map each word in an error protected block to a new codeword. The codec may use a search algorithm to generate a set of codewords with a specific set of properties”; para. [0340], lines 1-3, “The codec may choose a specific set of codewords to ensure optimized chemical conditions during encoding or decoding”).
Roquet and Bhatia are both considered to be analogous to the claimed invention because both are in the same field of nucleic acid data storage.
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified Roquet to incorporate the teachings of Bhatia by including the functionality of having a codebook that is optimized for one or more constraints.
The suggestion/motivation for doing so to improve write or read performance (Bhatia, para. [0339], lines 1-3, “The codec may further apply another encoding step to an error protected block to improve writing or reading performance”), and ensure optimized chemical conditions (Bhatia, para. [0340], lines 1-3, “The codec may choose a specific set of codewords to ensure optimized chemical conditions during encoding or decoding”).
Regarding claim 56, the combination of Roquet in view of Bhatia teaches the method of claim 55, wherein the one or more constraints are related to nucleic acid synthesis, post-processing, storage, sequencing, or any combination thereof (Roquet, col. 12, lines 19-22, “The identifiers may be rationally designed and selected for ease of read, write, access, copy, and deletion operations. The identifiers may be designed and selected to minimize write errors, mutations, degradation, and read errors”).
Regarding claim 66, the combination of Roquet in view of Bhatia teaches the method of claim 55, further comprising synthesizing a plurality of polynucleotides comprising the plurality of polynucleotide sequences (Roquet, col. 4, lines 31-33, “In some embodiments, the system further comprises a nucleic acid synthesis unit configured to synthesize the one or more nucleic acid sequences”).
Regarding claim 67, the combination of Roquet in view of Bhatia teaches the method of claim 55, wherein the codebook comprises codewords that are generated based at least in part on a base order (Roquet, col. 4, lines 56-58, “a data encoding unit configured to write digital information in one or more nucleic acid sequences”).
Regarding claim 68, the combination of Roquet in view of Bhatia teaches the method of claim 67, wherein the base order comprises predetermined base transitions (Roquet, col. 12, lines 19-20, “The identifiers may be rationally designed and selected for ease of read, write, access, copy, and deletion operations”; the identifiers being rationally designed implies that the identifiers are deliberately designed to avoid errors).
Regarding claim 69, the combination of Roquet in view of Bhatia teaches the method of claim 55, wherein the inner codec comprises two or more codebooks (Roquet, col. 3, lines 63-64, “some embodiments, the assembly unit comprises…one or more layers of components”; col. 4, lines 1-3, “In some embodiments, the assembly unit is configured to output the identifier library”), and wherein each of the two or more codebooks encodes a layer (Roquet, col. 12, lines 37-39, “each rank object is combinatorially constructed from a set of components and each byte-value object may be combinatorially constructed from a set of components”; a set of components equates to a codebook) during synthesis of the plurality of polynucleotides (Roquet, col. 4, lines 31-33, “In some embodiments, the system further comprises a nucleic acid synthesis unit configured to synthesize the one or more nucleic acid sequences”). Roquet teaches a set of components with different objects or layers using different sets of components, equating to two or more codebooks.
Regarding claim 71, the combination of Roquet in view of Bhatia teaches the method of claim 69, wherein the layer comprises extension of each polynucleotide of the plurality of polynucleotides by at least one base (Roquet, col. 4, lines 33-35, “In some embodiments, the one or more nucleic acid sequences are constructed with base-by-base synthesis”).
Regarding claim 87, the combination of Roquet in view of Bhatia teaches the method of claim 66, wherein (c) comprises synthesizing the plurality of polynucleotides on a solid support. While the reference does not explicitly teach the limitation, it teaches nucleic acid sequences being generated. It is well-known in the art of DNA chemistry that sequences are typically synthesized on solid supports. A person of ordinary skill in the art would implement the synthesis step on a solid support as a routine design choice.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Roquet et al. (US 11,227,219) teaches encoding digital data into nucleic acid sequences using layers, component based schemes.
Varadarajalu et al. (WO 2023/168085) teaches state-dependent encoding of digital information into nucleic acid sequences.
Leake et al. (US 2021/0210165) teaches DNA data storage systems that encode digital data into sequences using error correction and shuffling.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GRACE V BRADEN whose telephone number is (703)756-5381. The examiner can normally be reached Mon-Fri: 9AM-5:30 PM ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Albert Decady can be reached at (571) 272-3819. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/G.V.B./Examiner, Art Unit 2112
/ALBERT DECADY/Supervisory Patent Examiner, Art Unit 2112