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 .
Status
The after final amendment is entered, but it compels that the Quayle be withdrawn. Prosecution should remain closed. Yet, this action is being made non-final as a courtesy.
Specification Objection(s)
Prophetic and working examples generally are distinguished by verb tense. However, applicant uses a hybrid phrase. Please consider adding labels.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a particular machine, does not reasonably provide enablement for, inter alia, assisting (protein) production1 without certain actions by a computer. The specification does not enable a person skilled in the art to which it pertains, or with which it is most nearly connected, to practice the invention commensurate in scope with these claims.
Claim 1 was broadened to fairly encompass inoperable instructions after prosecution was closed.2 Equally, claim 12 does not use a computer for any step whatsoever. The repeated “configured” and “instructions” language remains problematic, including in claims 4, 7, and 11, which endeavor to correspond to 15, 17 and 20, which do not recite a computer either.
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.
Claims 1-20 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.
The terms alternative and same in the claims renders the claims indefinite. The terms are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
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 directed to an abstract idea without significantly more.
The claims recite the abstract idea of obtaining sequence information, analyzing or identifying alternative nucleotide orders, and generating and transmitting corresponding synthesis instructions. These operations are directed to the collection, analysis, and communication of information, which are mental processes and methods of organizing human activity, and thus fall within a judicial exception. Facilitating synthesis is not found to be a practical application since the broad recitation could encompass merely presenting the sequence, generating synthesis instructions, or transmitting the sequence to a synthesizer or vendor. The inoperable instructions, even if construed to be an ordered combination of steps, do not weigh in favor of there being significantly more than the idea. Again, the method does not use a particular machine for any step, and the different formats must stand or fall together for abstract idea analyses, and cannot be separately parsed / saved.3
Claim Rejections - 35 USC § 102
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 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.
Claims 1-11 are rejected under 35 U.S.C. 102 as being anticipated by Applicant’s Admitted Prior Art.
Applicant describes that the concept of using programs and processors to modify genomic sequences / enhance protein production is well known. As detailed above, the inoperable instructions / steps that follow that preamble and (the statutory component) following the transitional phrase are being given no patentable weight.4
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 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claim 12 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 11 of copending Application No. 17/701,531 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because:
17/701,531
18/150,404
Obtain genomic information / nucleic acid sequence
Obtain genomic information / nucleic acid sequence
Identify phenomena in the sequence, including CpG island, hairpin segment, rare nucleotide triplet
Identify promoter regions; detect CpG islands
Receive user-defined priority information
Determine methylation probabilities based on context information
Generate multiple alternative orders by modifying nucleotides
Identify alternative orders of nucleotides for CpG pairs by modification/replacement
Alternatives preserve same compound output
Alternatives result in synthesis of same compounds
Analyze alternatives by re-identifying phenomena
Analyze alternatives by determining methylation probabilities
Determine numerical degrees of compliance with priority information
Select CpG islands for modification based on probabilities/context
Output/present ranked alternatives to user
Present alternative orders of nucleotides
Claim 12 of the ’404 application would have been obvious over claim 11 of the ’531 application because the ’531 claim already teaches obtaining genomic information, identifying sequence features to be addressed, generating modified alternative nucleic acid sequences that preserve the encoded compound, analyzing the alternatives, and presenting ranked alternatives to the user. The ’404 claim merely applies that same general sequence-optimization framework to a narrower set of sequence features, namely promoter regions and CpG islands, and substitutes methylation-probability-based evaluation for the broader priority/compliance scoring of the ’531 claim. Under KSR, a person of ordinary skill in the art would have recognized that using a known optimization workflow on a different but analogous sequence feature, and using a predictable scoring criterion to rank candidate alternatives, amounts to no more than the application of familiar techniques to a known problem with predictable results.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Allowable Subject Matter
To the extent that objections and rejections can be overcome, and the above-described terminal disclaimer is provided, the art of record does not appear to disclose this ordered combination: after certain obtaining, identifying and detecting, determining, by a processor and based on context information and real-world measurements, a methylation probability for a CpG island, and then after certain selecting, generating and analyzing, ranking and presenting modified nucleotide order(s) to a user of the processor.
Conclusion
Horvath describes the CMAPS algorithm as a method for identifying highly conserved methylation probes, ranking candidate human genomic sequences based on conservation across non-human mammalian genomes, and selecting probes for coupling to a matrix to form a DNA methylation array.
No applicant invention disclosure statements are of record in this field; accordingly, no such statements are relied upon in this action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL FUELLING whose telephone number is (571)270-1367.
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.
/MICHAEL FUELLING/ Supervisory Patent Examiner
1 In view of claim differentiation, claims 1-10 and 12-19 must do something different than facilitate synthesis.
2 C.f., 'stored machine-readable instructions that, when executed, cause.'
3 In the past, having one statutory component in a system and/or using a machine/processor in the inventive step might suffice, individually / separately, but the US Supreme Court has instructed that the claim set must be looked at as a whole.
4 C.f., printed matter.
Prosecution Insights