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 .
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 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.
Claim Status
Claims 16-34 are pending.
Claims 1-15 are canceled.
Claims 16-34 are rejected.
Priority
This application is a CON of 16/057,357 filed Aug 7 2018 (now USP 11,894,106), which claims priority to provisional application 62/542,203, filed Aug 7 2017.
Accordingly, each of claims 16-34 are afforded the effective filing date of Aug 7 2017.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Dec 18 2023 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Drawings
The Drawings submitted Dec 18 2023 are accepted.
Claim Rejections - 35 USC § 112
35 U.S.C. 112(b)
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.
Claims 16-34 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 16, limitations 2 and 4, recites “receiving a variant list… the variant list… being generated based on a comparison between the at least a first portion of the unaligned genomic sequence read data and the at least a portion of the first reference sequence and a comparison between the at least a second portion of the unaligned genomic sequence read data and the at least a portion of the second reference sequence”. It is unclear whether the generation of the variant list is intended to be performed within the metes and bounds of the claimed invention, or if it is only further limiting the variant list which was received, such that performing the generation is not required within the metes and bounds of the invention. Limitation 4 is not clear because the claim only previously actively recites “receiving a variant list”. As the claim does not recite an active performance of the generation, but recites the active verb of “being” generated in a limitation which limits the received variant list, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the generation is not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed. Claims 17-34 are rejected based on their dependency from claim 16.
Claim 18 recites “wherein the quality score curve parameter information is generated based on a quality score curve”. It is unclear whether the generation of the quality score curve parameter information is intended to be performed within the metes and bounds of the claimed invention, or if it is only further limiting the quality score curve parameter information which was received in claim 17, such that performing the generation is not required within the metes and bounds of the invention. Claim 18 is not clear because the claim only previously actively recites “receiving… quality score curve parameter information”. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claim does not recite an active performance of the generation, but recites the active verb of “is” generated in a limitation which limits the received variant list, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the generation is not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed. Claims 19-24 are rejected based on their dependency from claim 18.
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 16-34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) are as follows:
Independent claim 16: reconstructing… the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication.
Dependent claim 20: reconstructing… at least an approximation of the quality score curve based on the quality score parameter information.
Dependent claims 26-34 recite further steps that limit the judicial exception of reconstructing the unaligned genomic sequence read data in independent claim 16 and, as such, also are directed to those abstract ideas.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually reconstruct sequence read data based on a reference sequence and a variant list. Without further detail as to the methodology involved in “reconstructing”, under the BRI, one may simply, for example, use pen and paper to perform such an action.
Therefore, claim 16 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 16: receiving, by the first computing system from a second computing system, an initiation of a transfer of unaligned genomic sequence read data;
receiving, by the first system from the second computing system, a variant list representative of the unaligned genomic sequence read data, a first indication of a first reference motif included in the unaligned genomic sequence read data, and a second indication of a second reference motif included in the unaligned genomic sequence read data, the variant list: indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence, the first reference sequence being different than the second reference sequence, and being generated based on a comparison between the at least a first portion of the unaligned genomic sequence read data and the at least a portion of the first reference sequence and a comparison between the at least a second portion of the unaligned genomic sequence read data and the at least a portion of the second reference sequence, wherein the first reference sequence is associated with the first reference motif and the second reference sequence is associated with the second reference motif.
Dependent claim 17: receiving, by the first computing system from the second computing system, quality score curve parameter information.
Dependent claims 18-19 and 21-25 recite steps that further limit the recited additional elements in the claims. For example, claims 18-19 and 21-24 further limits the received quality score curve parameter information; and claim 25 further limits the received first indication.
The claims also include non-abstract computing elements. For example, independent claim 16 includes a first computing system comprising a processor and a non-transitory computer-readable medium storing instructions that, when executed by the processor, cause the first computing system to perform the method and a second computing system.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “receiving” data, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computing elements do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The specification as published discloses that the instant invention allows for the communication of unaligned sequence read data to a system with greater computational resources to perform the alignment process without communicating all of the unaligned sequence read data at [0006-0007], but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 16 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification as published also notes that computer processors and systems, as example, are commercially available or widely used at [0035]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 16 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Hahm et al. (US 2018/0121601 A1; priority Oct 28 2016; cited on the Dec 18 2023 IDS).
The prior art to Hahm discloses a system, method and apparatus for executing a bioinformatics analysis on genetic sequence data (abstract) (abstract). Hahm, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 16 discloses a method for efficiently communicating genomic information performed by a first computing system comprising a processor and a non-transitory computer-readable medium storing instructions that, when executed by the processor, cause the first computing system to perform the method, the method comprising:
receiving, by the first computing system from a second computing system, an initiation of a transfer of unaligned genomic sequence read data;
Hahm teaches receiving a plurality of reads of genomic data (i.e., unaligned sequence genomic sequence read data) directly from the sequencer or from an associated memory (i.e., unaligned sequence genomic sequence read data) [0007] for analysis. Hahm teaches requests to process data in shared memory, where data is passed from one or more software threads from one or more CPU cores to a hardware engine, or vice versa, may be continuously and/or seamlessly updated in the shared memory, or a cache and/or layer thereof, which is visible to each device [0546].
receiving, by the first system from the second computing system, a variant list representative of the unaligned genomic sequence read data, a first indication of a first reference motif included in the unaligned genomic sequence read data, and a second indication of a second reference motif included in the unaligned genomic sequence read data, the variant list: indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence, the first reference sequence being different than the second reference sequence, and being generated based on a comparison between the at least a first portion of the unaligned genomic sequence read data and the at least a portion of the first reference sequence and a comparison between the at least a second portion of the unaligned genomic sequence read data and the at least a portion of the second reference sequence, wherein the first reference sequence is associated with the first reference motif and the second reference sequence is associated with the second reference motif; and
Hahm teaches a mapping module so as to map one of a plurality of reads to one or more segments of the one or more genetic reference sequences (i.e., portions of reference sequences) based on the index [0009], where the indexes (i.e., reference motifs) are built from one or more reference genomes [0012]. Hahm teaches employing a hash table that contains indexes of known alternative haplotype sequences for mapping purposes [0157]. Hahm teaches a hash table based mapper that employs such a hash table index [0014]. Hahm teaches receiving one or more of the mapped positions for the read data and retrieving a segment of the reference sequence/genome corresponding to the mapped position so that an alignment of the read to each retrieved reference segment may be calculated [0014]. The mapped position is known from the index, as the index is associated with an address which represents position information in the genetic reference sequence [0012-0013]. Hahm teaches a variant call module for processing the mapped, aligned, and/or sorted reads with respect to a reference genome to thereby produce a variant call file (i.e., a variant list generated based on the comparison between the first and second portions of the unaligned sequence genomic sequence read data and the at least a portion of the first and second reference sequences) [0010] detailing how the mapped, aligned, and/or sorted reads vary from that of one or more reference sequences [0018]. It is considered that Hahm fairly teaches first and second reference sequences which are different, as instantly claimed, because Hahm teaches identifying variants in both multiple haplotypes and locations in the genome, as described above.
reconstructing, by the first computing system, the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication.
Hahm teaches that one or more of the plurality of physical electrical interconnects may include an output from the integrated circuit for communicating result data from the mapping module and/or the alignment and/or sorting and/or variant call modules [0010]. Hahm teaches a second mapping and/or aligning and/or sorting and/or variant calling instrument, e.g., a cloud based instrument, with the proper authorities, may also be connected with the genomics dropbox, so as to access the files, e.g., compressed files, stored thereby the local computing resource, and may then decompress those files to make the results available for further, e.g., secondary or tertiary, processing [0700]. Hahm teaches performing compression and decompression steps on digitized genetic data files [0169] which are performed when storing and/or retrieving the requested data [0633]. Hahm teaches that a user may access a compressed results file and convert it to an original version of the generated BCL (i.e., unaligned sequence reads) [0710]. Hahm teaches interfaces for accessing genetic references sequences and indexes [0886]. However, Hahm teaches conversion of a BCL file to a FASTQ file, and then the conversion of a FASTQ file to a SAM or BAM file, and then the conversion of a BAM file to a CRAM and/or VCF file, and back again [0621], where conversion from a variant call file (VCF) back to a BCL or FASTQ file reads on reconstructing the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication).
Regarding claim 25, Hahm teaches the method of claim 16 as described above. Claim 25 further adds that the first indication comprises a first pointer to the at least a portion of the first reference sequence and a second pointer to the at least a portion of the second reference sequence.
Hahm teaches that even if a data unit is large at the desired software/hardware boundary, it can still be efficiently handed off to a hardware engine for processing, just by passing a pointer to the particular data unit [0559]. Hahm does not particularly teach that the indication of the at least one reference motif comprises a pointer to the at least a portion of the reference sequence.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the embodiments taught by Hahm to include, in the output of the aligning module, a pointer indicating the reference sequence in order to select, very precisely, the low-complexity/high-compute-load portions of a genomic data processing operation for implementation in custom logic, with optimized software/hardware boundaries with efficient small accesses, as taught by Hahm [0559].
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
A. Claims 17-19 are rejected under 35 U.S.C. 103 as being unpatentable over Hahm, as applied to claim 16 in the above 35 USC 102 rejection, in view of Huang et al. (GigaScience, 2017, 6(5), pages 1–9; cited on the Dec 18 2023 IDS).
Regarding claims 17-19, Hahm teaches the method of claim 16. Claim 17 further adds receiving, by the first computing system from the second computing system, quality score curve parameter information. Claim 18 further adds that the quality score curve parameter information is generated based on a quality score curve, the quality score curve parameter information characterizing the quality score curve. Claim 19 further adds that the quality score curve is associated with the unaligned genomic sequence read data. Hahm does not teach these claims.
However, the prior art to Huang teaches analysis of a whole-genome sequencing dataset generated by the sequencer BGISEQ-500 (abstract). Huang teaches generating a binary file with bases and quality scores (page 2, column 2, paragraph 4). Huang teaches analyzing the read quality by plotting the distributions of base quality scores (page 3, column 2, paragraph 1 and Fig. 3A-B). Huang teaches comparing the distribution plots of base quality scores of sequences generated by two sequencers, the BGISEQ-500 and the HiSeq2500, finding differences in the proportion of low-quality reads, more stable base quality distribution along the reads, and lower overall single base quality scores (i.e., quality score curve parameter information) (page 3, column 2, paragraph 1 and page 6, column 1, paragraph 1).
Regarding claims 17-19, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the method of Hahm for mapping and aligning sequencing reads to an indexed genome with the method of Huang for quality score distribution analysis. The motivation would have been to compare data generated by new sequencing platforms to other sequencers for reference by the community during development of bioinformatics methods and sequencing-based applications for new platforms, as taught by Huang (page 2, column 1, paragraph 1).
B. Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Hahm, as applied to claim 16 in the above 35 USC 102 rejection, and in further view of the features of Hahm.
Regarding claim 25, Hahm teaches the method of claim 16 as described above. Claim 25 further adds that the first indication comprises a first pointer to the at least a portion of the first reference sequence and a second pointer to the at least a portion of the second reference sequence.
Hahm teaches that even if a data unit is large at the desired software/hardware boundary, it can still be efficiently handed off to a hardware engine for processing, just by passing a pointer to the particular data unit [0559]. Hahm does not particularly teach that the indication of the at least one reference motif comprises a pointer to the at least a portion of the reference sequence.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the embodiments taught by Hahm to include, in the output of the aligning module, a pointer indicating the reference sequence in order to select, very precisely, the low-complexity/high-compute-load portions of a genomic data processing operation for implementation in custom logic, with optimized software/hardware boundaries with efficient small accesses, as taught by Hahm [0559].
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success,
The motivation would have been to
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.
Claims 16-25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-6, and 8-9 of of U.S. Patent No. 11894106. Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
Regarding instant claim 16, reference claim 1 discloses the limitations of claim 16.
Regarding instant claims 17-19, reference claim 1, limitations 2 and 7-8 disclose the limitations of claims 17-19.
Regarding instant claim 20, reference claim 1, final limitation, discloses the limitations of claim 20.
Regarding instant claim 21, reference claim 5 discloses the limitations of claim 21.
Regarding instant claim 22, reference claim 6 discloses the limitations of claim 22.
Regarding instant claim 23, reference claim 8 discloses the limitations of claim 23.
Regarding instant claim 24, reference claim 9 discloses the limitations of claim 24.
Regarding instant claim 25, reference claim 4 discloses the limitations of claim 25.
Conclusion
No claims are allowed.
Claims 20-24 and 26-34 appear to be free of the prior art. Although Huang et al. (GigaScience, 2017, 6(5), pages 1–9) is considered to teach quality score curve parameter information as recited in claims 17-19, neither Huang or any other identified references fairly teach reconstructing at least an approximation of the quality score curve based on the quality score parameter information as recited in claim 20 and dependent claims 21-24. Although Hahm et al. (US 2018/0121601 A1; priority Oct 28 2016) is considered to teach reconstructing, by the first computing system, the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication as recited in claim 16 and accessing at least a portion of one or more reference sequences as recited in claim 26, neither Hahm or any other identified references fairly teach accessing the at least a portion of one or more reference sequences in order to reconstruct unaligned genomic sequence read data as recited in claim 26 and dependent claims 27-34.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685