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 .
The following is a non-final, first office action on the merits, in response to application filed 7/14/2022. Claims 1-20 have been examined and are currently pending.
Priority
This application discloses and claims a continuation of 15/932287 (now patent 11,393, 558) filed 2/16/2018, and names the inventor or at least one joint inventor named in the prior application. Accordingly, this application constitutes a continuation of 15/932287.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 7/14/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 1-20 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over current allowed co-pending independent claims 1, 14 of U.S. Application 15/932287 (now patent 11,393,558). Although the conflicting claims are not identical, they are not patentably distinct from each other of claim 1, 16, respectively of the instant application. because all the elements of the instant application claims 1, 16 are to be found in patent claims 1, 14. The difference between the instant application claims and the patent claims lies in the fact that the patent claim includes more elements and is thus more specific. Thus, the invention of the claims 1, 14, of the patent is in effect a “species” of the “generic” invention of the instant application claims 1, 16. It has been held that the generic invention is “anticipated” by the “species”. See In re Goodman, 29 USPQ2d 2010 (Fed. Cir. 1993). Since instant application claim 1, 16 are anticipated by the claim 1, 14 of the patent, it is not patentably distinct from the claims of the patent.
For reference, the following table matches the primary limitations of claim 1 of application 15/932287 (now patent 11,393,558) with the similar limitations of claim 1 of the instant application (differences highlighted in bold type).
Allowed Claim 1 in patent Application 15/932287, (now Patent 11,393,558)
Claim 1 in current Application 17/864710 which is Continuation of patent Application 15/932287, (now Patent 11,393,558)
Claim 1
A method of operating a finite state machine …comprising:
determining if a target sequence of characters is included in a string within a reference sequence of characters using states indicated by the finite state machine to indicate a number of character mismatches between the target sequence of characters and the string within the reference sequence of characters, wherein the target sequence of characters and the string within the reference sequence of characters are nucleic acid sequences, wherein the reference sequence of characters comprise a genome, and wherein determining comprises:
comparing, in a first state of the finite state machine, one of the target sequence of characters to a respective one of the reference sequence of characters;
transitioning from the first state to a second state of the finite state machine responsive to a match between the one of the target sequence of characters and the respective one of the reference sequence of characters when in the first state and maintaining a value of the number of character mismatches from the first state to the second state;
and
transitioning from the first state to a third state of the finite state machine, that is different from the second state, responsive to a mismatch between the one of the target sequence of characters and the respective one of the reference sequence of characters when in the first state and increasing the value of the number of character mismatches from the first state to the third state,
wherein the target sequence of characters is determined to be included in a string within the genome if the value of the number of character mismatches is within a specified Hamming distance from the string within the genome.
Claim 1
A method of operating a finite state machine …. comprising:
determining if an off-target site to a target nucleic acid sequence occurs within a reference nucleic acid sequence using states indicated by the finite state machine to indicate a number of nucleobase mismatches between the target nucleic acid sequence and a string within the reference nucleic acid sequence, wherein determining comprises:
comparing, in a first state of the finite state machine, one nucleobase of the target nucleic acid sequence to a respective one nucleobase of the reference nucleic acid sequence;
transitioning from the first state to a second state of the finite state machine responsive to a match between the one nucleobase of the target nucleic acid sequence and the respective one nucleobase of the reference nucleic acid sequence when in the first state; and
transitioning from the first state to a third state of the finite state machine that is different from the second state, responsive to a mismatch between the one nucleobase of the target nucleic acid sequence and the respective one nucleobase of the reference nucleic acid sequence when in the first state,
wherein an off-target nucleic acid sequence is determined to be included in the string within the reference nucleic acid sequence if the number of character mismatches has a value within a specified Hamming distance from the string within the reference nucleic acid sequence, and
wherein the reference nucleic acid sequence comprises a chromosome or a genome.
Therefore, as discussed above, the scope of claim 1, 16 of the present application and allowed claim 1, 14 of U.S. Application No. 15/932287 (now patent 11,393,558) are practically identical.
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims are directed to the same subject matter, perform the same method steps, and a person of ordinary skill in the art would not be free to practice one of the claimed inventions without infringing upon the other invention.
It would have been obvious to the person having ordinary skill in the art before the effective filing date of the application to include “off-target site”, “one nucleobase” claimed in this application as taught or suggested by claims 1, 14, of patent “558” because instant application claims 1-20 would have been obvious over the reference claims 1-18 in Patent.”558”
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claim Rejections - 35 USC § 101
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 1-20 are NOT rejected under the Alice/Mayo styled 35 U.S.C. 101 because the claimed invention is NOT found to be directed to an abstract idea. The invention uses a finite state machine to determine if a target sequence occurs in a set of reference characters within a specified Hamming distance using states of a finite state machine to indicate the number of mismatches and matches with different states corresponding to comparing nucleic acid sequences and genomic sequences, transitioning between the first and second state and determine a value of the number of character mismatches from the first state to the third state, to detect a match or a mismatch.
Examiner further finds, under Step 2A Prong 2, the additional elements recite a specific way of comparing of a target sequence to a reference genome sequence, in addition to
determining if a target sequence occurs within a specified Hamming distance in a set of characters in a reference genome to indicate the number of matches/mismatches, which is too complex to be practical to be performed in the human mind. Consequently, the claims do not recite the mental process grouping of abstract ideas.
When considered in combination with the rest of the limitations of the claims, reflects a practical application (i.e. an improvement in searching for target sequences within a reference genome while also allowing for a specified number of mis-matches between the target sequence and the reference genome to identify off-target sites within the reference genome), see MPEP 2106.05(a).
The steps are being performed go beyond the limitations and simple implementation of an abstract idea, as such, the claims go far beyond mental processes and methods of organizing human activity or performed in the human mind and are directed to improvement in genome editing/modification centric problems and solutions. Thus, it is integrated in a practical application in computer-related technology. Accordingly, there are no Alice 101 issues.
This statement is simply made to inform the record that the claims were considered under the Alice/Mayo analysis.
Allowable Subject Matter
The instant continuation application has the allowable features presented in 15/932287 (now Patent 11,393,558), filed 2/16/2022. In interpreting the claims, in light of the specification, upon further search and consideration, and for the reasons presented by the claims, the Examiner finds the claimed invention to be patentably distinct from the prior art of records. It is found that claims 1-20 are allowable subject to outstanding double patenting issues. An approved terminal disclaimer is required.
As allowable subject matter has been indicated, applicant's reply must either comply with all formal requirements or specifically traverse each requirement not complied with, and pending remedy to outstanding issues cited above. See 37 CFR 1.111(b) and MPEP § 707.07(a).
The closest prior art of record is:
Liu et al. (US 2018/0075186),
Shdema et al. (US 2018/0011870),
Greenfield et al. (US 2019/0121942),
Bermeister (US 2017/0270240),
Bermeister (WO 2015/175602 A1), and
NPL1---Rasool et al. String Matching Methodologies: A Comparative Analysis International Journal of Computer Science and Information Technologies vol. 3, pages 3394-3397 (Year: 2012)
NPL2— Thomas et al. Denominator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine Bioinformatics vol. 29, pages 542-550 (Year: 2013)
NPL3-- Junager NP, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. Sensors (Basel). 2016 Jul 27;16(8):1173. doi: 10.3390/s16081173. PMID: 27472344; PMCID: PMC5017339. (Year: 2016)
NPL4-- Wright EP, Huppert JL, Waller ZAE. Identification of multiple genomic DNA sequences which form i-motif structures at neutral pH. Nucleic Acids Res. 2017 Apr 7;45(6):2951-2959. doi: 10.1093/nar/gkx090. Erratum in: Nucleic Acids Res. 2017 Dec 15;45(22):13095-13096. doi:10.1093/nar/gkx1178. PMID: 2818027 (Year: 2017), and
are cited or referenced because they are pertinent to applicant's disclosure.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SUN M LI whose telephone number is (571)270-5489. The examiner can normally be reached on Mon-Thurs, 8:30am--5pm. Fax is 571-270-6489.
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/SUN M LI/Primary Examiner, Art Unit 3685