DETAILED ACTION
The Applicant’s response, received 17 September 2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
This Office action is a second Non-final action because there are new grounds of rejection under 35 U.S.C. 101 that are not necessitated by the Applicant’s amendment.
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 .
Terminal Disclaimer
The terminal disclaimer filed on 17 September 2025 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of US Patent 10,387,301 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Status of the Claims
Claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are pending.
Claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are rejected.
Priority
Claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are given the benefit of Provisional Application No. 61/654,295, filed 01 June 2012.
The Petition Decision received on 03 July 2023 effectively gives claims 1-3, 5, 9-11, 14-16, 19, and 23-35 the benefit of priority to Provisional Application No. 61/654,295, filed 01 June 2012.
Claim Objections
The objection to claim 1 in the Office action mailed 20 March 2025 is withdrawn in view of the amendment received 17 September 2025.
Claim Rejections - 35 USC § 112
The rejection of claims 1-3, 5, 9-12, 14-16, 18, 19, and 23-35 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 20 March 2025 is withdrawn in view of the amendment received 17 September 2025.
Claim Rejections - 35 USC § 101
The rejection of claims 12, 14-16, 18, 19, and 27-35 under 35 U.S.C. 101 in the Office action mailed 20 March 2025 is withdrawn in view of the amendment received 17 September 2025.
The amendment received 17 September 2025 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 101 that are not necessitated by the Applicant’s amendment.
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mental processes, i.e., concepts performed in the human mind (e.g., observation, evaluation, judgement, opinion); and (b) mathematical concepts (e.g., mathematical relationships, formulas or equations, mathematical calculations).
Claim Interpretation
Claims 15 and 32 recite the term “item of information.” This term is interpreted to reference a data file of encoded binary information, e.g., text, image, audio, or video.
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are directed to a method (i.e., a process) of storing bytes of digital information.
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
converting the digital information into DNA sequence data, wherein the DNA sequence data is split into a plurality of overlapping DNA segment data (i.e., mental processes);
a first one of the plurality of DNA segments includes a first overlapping region (i.e., mental processes);
a second one of the plurality of DNA segments includes a second overlapping region, where the second overlapping region is identical to the first overlapping region (i.e., mental processes); and
decoding the sequence of the plurality of DNA segments into bytes of the digital information (i.e., mental processes and mathematical concepts).
Dependent claims 2-3, 5, 9-11, 14-16, 23-26, 29, 32, 34, and 35 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
the information is in binary form using bit sequences or byte sequences (i.e., mental processes).
Dependent claim 3 further recites:
at least one of the plurality of DNA segment data comprises indexing information configured to identify a source of the digital information (i.e., mental processes).
Dependent claim 5 further recites:
at least one of the plurality of DNA segment data comprises indexing information configured to identify a location of the corresponding one of the DNA segment data in the DNA sequence data (i.e., mental processes).
Dependent claim 9 further recites:
the first overlap region includes at least 75 bases (i.e., mental processes).
Dependent claim 10 further recites:
the information comprises at least 15,646 bytes of binary data (i.e., mental processes).
Dependent claim 11 further recites:
the information comprises at least one of text, images, music, and video (i.e., mental processes).
Dependent claim 14 further recites:
the plurality of DNA segments to be sequenced comprises indexing information (i.e., mental processes).
Dependent claim 15 further recites:
the indexing information is configured to identify a source of the item of information (i.e., mental processes).
Dependent claim 16 further recites:
the indexing information is configured to indicate a position in the DNA sequence data of any one nucleotide datum in any one of the plurality of DNA segments data (i.e., mental processes).
Dependent claim 23 further recites:
shuffling the DNA sequence data prior to splitting the DNA sequence data into the plurality of overlapping DNA segment data (i.e., mental processes).
Dependent claim 24 further recites:
adding a series of random digits to each one of the DNA segment data (i.e., mental processes).
Dependent claim 25 further recites:
the plurality of DNA segments are uniform in length (i.e., mental processes).
Dependent claim 26 further recites:
the plurality of DNA segments do not comprise homopolymers (i.e., mental processes).
Dependent claim 29 further recites:
the paired-end reads comprise 104 base pairs (i.e., mental processes).
Dependent claim 32 further recites:
the item of information is encoded using a base-3 scheme (i.e., mental processes and mathematical concepts).
Dependent claim 34 further recites:
the indexing information comprises an error-detecting component, and the error-detecting component includes a parity-check (i.e., mental processes).
Dependent claim 35 further recites:
the paired end reads comprise 104 base pairs (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., converting the digital information into DNA sequence data), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas regardless of whether or not the limitations are practical to perform in the human mind. The specification shows encoding steps at ¶¶ [0055] - [0067]) with steps requiring mathematical concepts, and ¶ [0068] shows that the decoding process is the reverse of the encoding process. Furthermore, it is noted that the term “DNA segment” is used in reference to DNA sequence data (Specification, ¶¶ [0013], [0015], [0035], [0040], [0041], and [0045]) and also used in reference to synthetic DNA composed of molecules, i.e., nucleotides (Specification, ¶¶ [0016], [0019], and [0046]). Further still, it is noted that the steps described at ¶¶ [0035], [0040], and [0041] are shown to occur prior to the synthesis step in Figure 7.
Therefore, claims 1-3, 5, 9-11, 14-16, 19, and 23-35 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 3, 5, 9, 14-16, 23-26, 29, 32, 34, and 35 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
a computer-controlled DNA synthesis platform;
providing the plurality of overlapping DNA segment data as input to a computer;
synthesizing a plurality of DNA segments, wherein each DNA segment of the plurality of DNA segments is synthesized based on a corresponding one of the DNA segment data of the plurality of overlapping DNA segment data; and
sequencing the plurality of DNA segments.
The additional elements in dependent claims 2, 10, 11, 19, 27, 28, 30, 31, and 33 include:
storing digital data in a computer file (claim 2);
digital data (claims 10 and 11);
the digital file is stored on a hard disk (claim 19);
the sequencing comprises parallel sequencing, in particular sequencing by synthesis (claim 27);
the parallel sequencing comprises generation of paired-end reads (claim 28);
each DNA segment of the plurality of DNA segments comprises an adapter (claim 30);
the adapter comprises SEQ ID NO: 1, SEQ ID NO: 2, a reverse complement of SEQ ID NO: 1, or a reverse complement of SEQ ID NO: 2 (claim 31); and
the parallel sequencing includes paired-end PCR primers, and the paired-end PCR primers comprise SEQ ID NO: 1 and SEQ ID NO: 2 (claim 33).
The additional elements of a computer (claim 1); storing digital data in a computer file (claim 2); digital data (claims 10 and 11); and the digital file is stored on a hard disk (claim 19); invoke a computer and/or computer-related components and/or computer-related processes merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (see MPEP 2106.04(d)(1)).
The additional element of inputting data to a computer (claim 1); is merely a pre-solution activity used in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional elements of a computer-controlled DNA synthesis platform (claim 1); synthesizing a plurality of DNA segments wherein each DNA segment of the plurality of DNA segments is synthesized based on a corresponding one of the DNA segment data of the plurality of overlapping DNA segment data (claim 1); sequencing the plurality of DNA segments (claim 1); the sequencing comprises parallel sequencing, in particular sequencing by synthesis (claim 27); the parallel sequencing comprises generation of paired-end reads (claim 28); each DNA segment of the plurality of DNA segments comprises an adapter (claim 30); the adapter comprises SEQ ID NO: 1, SEQ ID NO: 2, a reverse complement of SEQ ID NO: 1, or a reverse complement of SEQ ID NO: 2 (claim 31); and the parallel sequencing includes paired-end PCR primers, and the paired-end PCR primers comprise SEQ ID NO: 1 and SEQ ID NO: 2 (claim 33); are merely pre-solution activities or elements that are part of the process of gathering data for use in the claimed process – nominal additions to the claims that do not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Furthermore, the additional element of synthesizing a plurality of DNA segments (claim 1) does not effect a transformation or reduction of a particular article to a different state or thing, and therefore does not integrate the judicial exception(s) into a practical application (MPEP 2106.05(c)).
Thus, the additionally recited elements merely invoke a computer and/or computer-related components and/or processes as tools; and/or amount to insignificant extra-solution activities; and as such, when all limitations in claims 1-3, 5, 9-11, 14-16, 19, and 23-35 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 3, 5, 9, 14-16, 23-26, 29, 32, 34, and 35 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claim 1 and dependent claims 2, 10, 11, 19, 27, 28, 30, 31, and 33 are identified above, and carried over from Step 2A Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computer (claim 1); storing digital data in a computer file (claim 2); digital data (claims 10 and 11); the digital file is stored on a hard disk (claim 19); and inputting data to a computer (claim 1); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of a computer-controlled DNA synthesis platform (claim 1); and synthesizing a plurality of DNA segments wherein each DNA segment of the plurality of DNA segments is synthesized based on a corresponding one of the DNA segment data of the plurality of overlapping DNA segment data (claim 1); are conventional.
Evidence for the conventionality is shown by Hughes et al. (Gene Synthesis: Methods and Applications, 2011, In Christopher Voigt (Ed.), Methods in Enzymology, Vol. 498, pp. 277-309, as cited in the Office action mailed 20 March 2025). Hughes et al. reviews DNA synthesis techniques and technologies (Abstract) and briefly review automated synthesizer platforms for oligonucleotide synthesis (page 280, para. 2; and page 281, para. 1). Hughes et al. further discusses methods to assemble relatively short synthetic oligonucleotides into longer sequences (page 282, Section 3.1; and page 284, Section 3.2). Hughes et al. further discusses gene design software for designing over-lapping oligonucleotides for gene synthesis (page 291, Section 4, through page 293, para. 3). Hughes et al. further discusses an example of high-throughput gene synthesis using protein fabrication automation (page 300, Section 7) and shows that the first step in most synthetic methods is to break down the target sequence into a set of overlapping primers compatible with the general assembly strategy (page 300, para. 3) and then using software (GeneFab) that will render a DNA sequence as overlapping fragments and oligonucleotide pairs based on user-provided overlaps and oligonucleotide length constraints (page 301, para. 2). Hughes et al. further shows that the software has a graphical user interface that provides a view of the sequence, its translation, the location of each primer, and a mispriming graph to aid in manually adjusting derived assembly schemes, and that is also capable of limited point-and-click DNA editing and of filtering of sequences (Ibid.). Hughes et al. further shows a different software (FabMgr) that is used to manage the variant sequences and that maintains a database to enable efficient reuse of shared oligonucleotides, and that the combination of these two computer programs ultimately produces scripts for TECAN robotic workstations (Ibid.). Hughes et al. further discusses using the automated TECAN robotic workstation for a synthesis operation to construct single chain antibodies (page 301, para. 5, through page 302, 4).
The additional elements of sequencing the plurality of DNA segments (claim 1); the sequencing comprises parallel sequencing, in particular sequencing by synthesis (claim 27); the parallel sequencing comprises generation of paired-end reads (claim 28); each DNA segment of the plurality of DNA segments comprises an adapter (claim 30); and the parallel sequencing includes paired-end PCR primers (claim 33); are conventional.
Evidence for the conventionality is shown by Ansorge (New Biotechnology, 2009, Vol. 25, No. 4, pp. 195-203, as cited in the Office action mailed 06 May 2024). Ansorge shows next-generation sequencing technologies (Abstract; and page 196, column, para. 4, through page 201, column 2, para. 1). Ansorge further shows a sequencing platform based on sequencing-by-synthesis chemistry; using adapters with DNA fragments; the adapters act as primers for PCR amplification (page 197, column 1, para. 2); and the sequencer system upgraded with a paired-end sequencing module (page 197, column 2, para. 2).
The additional elements of SEQ ID NO: 1 and SEQ ID NO: 2 (claims 31 and 33) are conventional.
Evidence for the conventionality is shown by May et al. (United States Patent Application Publication No.: US 2010/0273219, as cited in the Office action mailed 05 November 2024), Rigatti et al. (United States Patent Application Publication No.: US 2009/0176662, as cited in the Office action mailed 05 November 2024), Peters et al. (United States Patent Application Publication No.: US 2012/0065076, as cited in the Office action mailed 05 November 2024), Igartua et al. (Current Protocols in Human Genetics, 2010, Supplement 66, pp. 18.3.1-18.3.14, as cited in the Office action mailed 05 November 2024), Jiang et al. (Virology Journal, 2011, Vol. 8:194, pp. 1-8, as cited in the Office action mailed 05 November 2024). Specific examples demonstrating evidence of conventionality include the following:
May et al. shows using SEQ ID NO. 1 (page 130, SEQ ID NO. 440);
Rigatti et al. shows using SEQ ID NO. 1 (page 33, SEQ ID NO. 7);
Peters et al. shows using SEQ ID NO. 1 (page 65, SEQ ID NO. 69);
Igartua et al. shows using both SEQ ID NO. 1 and SEQ ID NO. 2 (Table 18.3.1) with SEQ ID NO. 2 shown at line 8 (EXOME_BLOCK_R_rev) and both SEQ ID NO. 1 and SEQ ID NO. 2 shown at the bottom of the table (EXOME_ADAPT_HI and EXOME_ADAPT_LO); and
Jiang et al. shows using both SEQ ID NO. 1 and SEQ ID NO. 2 (page 2, column 1, para. 3).
Therefore, when taken alone, all additional elements in claims 1-3, 5, 9-11, 14-16, 19, and 23-35 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-3, 5, 9-11, 14-16, 19, and 23-35 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exceptions (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 17 September 2025 have been fully considered, and are persuasive.
The Applicant states on page 7 of the Remarks that claims 12 and 18 have been deleted, and the dependencies of claims 14, 19, 27, 30, 32, and 33 have been correspondingly adapted, and accordingly, the rejection of claims 12, 14-16, 18, 19, and 27-35 under 35 U.S.C. 101 in the Office action mailed 20 March 2025 should be withdrawn.
This argument is persuasive, in view of the cancellation of independent claim 12.
The Applicant’s arguments/remarks received 05 February 2025 regarding the rejection of claims 1-3, 5, 9-12, 14-16, 18, 19, and 23-35 in the Office action mailed 05 November 2024 are determined to be unpersuasive in view of further consideration and review of the aforementioned arguments/remarks (received 05 February 2025), Office actions (mailings on 05 November 2024 and 20 March 2025), and US Patent No. 10,387,301, resulting in the new grounds of rejection under 35 U.S.C. 101 that are not necessitated by the Applicant’s amendment, as noted and discussed above.
In the arguments/remarks received 05 February 2025, the Applicant states on page 13 (para. 2) that amended claim 1 is not directed to an abstract idea, and further states on page 14 (para. 1) that claims 1 and 12 recite a practical application of the alleged judicial exceptions. The Applicant further states (para. 2) that amended claim 1 recites a practical application similar to the ‘301 patent, and also recites a synthesizing step that transforms nucleotides into a polynucleotide that is a different state or thing, and thus, amended claim 1 is patent-eligible for at least the same reasons as claim 1 of the ’301 patent.
These arguments/remarks are not persuasive in view of further consideration of the instant claims, the Applicant’s foregoing arguments, and the ‘301 patent, because first, claim 1 of the ‘301 patent embodies a different fact pattern than instant claim 1, not least in that claim 1 of the ‘301 patent ends with an additional element (i.e., synthesizing a plurality of DNA segments) that appears to apply, rely on, or use the earlier recited judicial exception(s) in a manner that imposes a meaningful limit on the judicial exception, and therefore appears to integrate the judicial exception(s) into a practical application of the judicial exception(s). Second, the Applicant’s argument that the synthesizing step transforms nucleotides into a polynucleotide that is a different state or thing, is not persuasive in view of further consideration, because the additional element of synthesizing a plurality of DNA segments in instant claim 1 does not effect a transformation or reduction of a particular article to a different state or thing (MPEP 2106.05(c), as noted in the rejection above, because as noted at MPEP 2106.05(c), an “article” includes a physical object or substance, and the physical object or substance must be particular, meaning it can be specifically identified, and that “transformation” of an article means that the “article” has changed to a different state or thing. With regard to the instant application, the claims do not specifically identify any DNA segments, i.e., the DNA segments are merely a generically recited article, and furthermore, a synthesis step that incorporates a nucleotide monomer into a polynucleotide does not effect a particular transformation of a nucleotide itself into a different state or thing, because the polynucleotide is merely composed of nucleotide monomers that are linked together in a sequence, and thus, the nucleotide monomer itself is still the same nucleotide, i.e., it did not transform into something else.
In the arguments/remarks received 05 February 2025, the Applicant states on page 14 (para. 2) that converting digital information into DNA sequence data, as well as synthesizing, sequencing, and decoding DNA segments, is beyond what is well-understood, routine, and conventional in the field of digital information storage in DNA, and therefore, even if sequencing or synthesizing DNA may have been known, the claimed methods integrate sequencing and synthesizing DNA in a manner that provides improved technical features compared to what was known in the art. The Applicant points to paragraphs [0075] – [0082] in the Specification, and states that these technical features include indexing information and overlapping DNA segments, which are not well-understood, routine, or conventional as applied to DNA to store information and as claimed, and therefore, these features of the amended claims integrate any alleged judicial exceptions into a practical application.
These arguments are not persuasive in view of further consideration of the instant claims, the Applicant’s foregoing arguments, and the ‘301 patent, because first, multiple elements presented in the foregoing argument are identified as data (i.e., information) as recited in the instant claims, and therefore are judicial exceptions, e.g., converting digital information into DNA sequence data, decoding DNA segments, indexing information, and overlapping DNA segments, as noted and discussed in the above rejection. Further, the limitations reciting synthesizing and sequencing are identified as conventional additional elements that are part of the data gathering process, as noted and discussed in the above rejection.
Double Patenting
The rejection of claims 1, 2, 3, 5, 10, and 11 on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 10,387,301 in view of Hughes et al. in view of Wei et al. in the Office action mailed 20 March 2025 is withdrawn in view of the Terminal Disclaimer received 17 September 2025, as noted above.
Conclusion
No claims are allowed.
This Office action is a Non-final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
Inquiry
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687