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 .
Applicants Amendments
Applicants’ amendment filed 3/23/2026 has been received and entered. Claims 1-49 have been cancelled, and claims 50-51, 53-59, 62-64, 66-67, 70-72, 74-75, 78-80 have been amended.
Claims 50-81 are pending.
Election/Restriction
Applicant’s election of Group II in the reply filed on 8/15/2025 was acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). It was noted that in upon initial search and review of the required claim limitations, it does not appear to be a burden to examiner all groups 1-4 together. Accordingly, the restriction requirement was withdrawn.
Claims 50-81 drawn to method of compressing sequence data and a system, hardware and medium which can be used to perform the data manipulation are currently under examination.
Priority
This application filed 3/11/2022 is a 371 National stage filing of PCT/US2020/050586 filed 9/11/2020 which is a continuation of US Application 16/567211 filed 9/11/2019 (now ABN); and through a claim of priority, listed inventors and disclosure the instant application appears related to 18/540814 filed 12/14/2023 (allowance mailed 10/15/2025).
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
Response to Applicants Comments
Applicants indicate they do not concede the appropriateness of interpreting any claims and note the amendments to the claims.
In response, the amendments are noted however the amendment from ‘module’ versus ‘mapping and aligning stage’ still raises a claim interpretation issues as provided below.
The issues provided in the previous action are provided below for completeness of the record. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) are generally a ‘system’ and ‘medium’ and also the ‘mapping and aligning module’ used to implement the analysis (see independent claims). In view of the specification, no unique system or computer appears to be described or required and appears to encompass a general purpose computer. With respect to ‘module’ one interpretation could be a physical device, however the specification does not appear to provide for more than a general purpose computer, and module appears to refer to a portion of instruction or code capable of performing the analysis of aligning and mapping, one sequence to another.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
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 50-81 rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more is withdrawn.
Claim analysis
Claim 50 has been amended and still is generally directed to a method for processing genomic sequence data to assess read data as compared to a reference sequence and to provide mismatches to the imperfectly mapped comparison; wherein at a ‘threshold’ number of differences the sequence is compressed and stored based on the differences and for a plurality of reads. Other independent claims have been amended consistently as in claim 50. Remaining dependent claims provide for additional information be added to the compressed read records such as starting position of the comparison, read length, mismatches, N in a sequence, … and other common features found in read and reference data. Independent claim 58 sets forth a system and provides the same analysis steps performed by one or more computers, and independent claim 66 provides for the CRM with the same instructions for analysis of read data and a reference.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a process and product.
For step 2A of the 101 analysis, broadly comprise the judicial exception of steps of assessing and comparing sequence read data as compared to reference sequences, and to note differences between the two. The step of aligning and comparing sequence to arrive at the identification of differences between the sequences are instructional steps. However, as amended, the claims provide for output and ‘encoding’ that produces a ‘compressed record’ of a specified size which is tied to the technical field of computer processing and data storage which can only be provided in a computer environment. In view of the claim as a whole, while some scope of the claims comprise a judicial exception that can be interpreted as a set of instructions for analysis of sequence data and appears to fall into the category of Mental Processes, the claims as a whole clearly are not directed to a judicial exception.
Accordingly, the claims are found patent eligible, and the rejection is withdrawn.
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).
Response to Applicants comments
Applicants indicate that a terminal disclaimer would be considered upon indication that it is the only remaining issue.
As provided above, the 101 rejection is withdrawn and the claim interpretation under 112f is provided but does not rise to an issue meriting a rejection. No specific arguments that the claims are not obvious are provided, and upon review they two applications claims appear to be obvious over each other in view of the amendments. Accordingly, the rejection is maintained.
Claims 50-81 stand provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 18-22, 24-28, 30-36, 38-48 of copending Application No. 18/540814 (notice of allowance mailed 10/15/2025-no Patent number assigned yet). Although the claims at issue are not identical, they are not patentably distinct from each other because both methods rely on the same provisional application and provide a computer implemented method of compressing sequence read data. More specifically, compression in both methods relies on assessing differences between a new read sequence and a reference and determining mismatches which are encoded into a value. The claim of ‘814 has been amended to delete reference to the match portions and focus on processing ‘imperfectly mapped to the reference’ read sequences; but both require compressing mismatch of the imperfectly mapped read into a compressed record and storing the compressed data. Claim 18 of ‘814 provides that the information is 1 byte (seemingly dependent on the data which is analyzed), however dependent claim 52 also indicates that the data can be 1 byte, providing overlapping claim limitations in the dependent claims.
Independent claim 18 drawn to the method of 18/540814 is provided for completeness of the record and to more easily map claim amendments in both applications.
Claim 18. A method for compressing genomic sequence data, the method comprising:
obtaining, by one or more computers, a read record;
determining, by the one or more computers, whether that the read record corresponds to a read that is perfectly mapped to a reference sequence or imperfectly mapped to the reference sequence;
based on determining, by the one or more computers, that the read record corresponds to a read that is imperfectly mapped to the reference sequence,
determining, by the one or more computers, whether that a number of mismatches of the imperfectly mapped read does not exceed a predetermined threshold number of mismatches; and
based on determining that the number of mismatches does not exceed the predetermined threshold number of mismatches,
(i) obtaining, by the one or more computers, an offset from a previous mismatch that is lower than a maximum encodable offset value, wherein the maximum encodable offset value corresponds to a size of a portion of a field of a compressed read record that is to be allocated for storing the obtained off seti and
(ii) encoding, by the one or more computers, each mismatch of the imperfectly mapped read and the offset from the previous mismatch of the read into a compressed read record having a size of 1 byte.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
As noted in prosecution, 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.
Conclusion
Claims 50-81 are rejected.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
In prosecution the art of record provides for steps of compressing sequence data by obtaining reads, mapping mismatches relative to reference and recording the mismatch in a compressed format, all within a computer environment as exemplified by Sheinin et al (US 2015/227686 A1-of record) for example. It is noted that similarities and differences between sequences for comparison and for assembly were also known, for example Joes et al. provide method for the compression of next-generation sequencing reads aided by highly efficient de novo assembly. Jones et al use a reference based comparison using SAM and BAM formats and store information in a FASTA format. However, the art does not teach or motivate providing differences based on a threshold or providing potentially informative complex or large differences and preserving an order to the reads in a 1 byte size as required of the instant claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
Prosecution Insights