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 .
Claim Status
Claims 1-16 are currently pending and under examination herein.
Priority
The present application, filed May 18, 2022 claims benefit of US Provisional Patent Application 63/190,202, filed May 18, 2021. At this point in examination, the effective filing date of claims 1-16 is May 18, 2021.
Information Disclosure Statement
No information disclosure statement has been filed in the instant application. Applicants are reminded of their duty to disclose all information known to them to be material to the patentability as defined in 37 C.F.R. 1.56.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because reference character “130” is designated as “a network” according to the specification [0015], but does not appear within the drawings.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(4) because reference character “120” has been used to designate both “a computer” and “a network”.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Interpretation
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 interpretation of the following claims notifies the applicant of the interpretation of claim language to aid in the understanding of possible objections/rejections.
A limitation of Claims 1 and 9 recite “generating a mutation index file, wherein the mutation index file identifies a location of wild type and mutated nucleotides in the customized reference genome, wherein the mutation index file is used to diagnose a genetic condition”. The element “wherein the mutation index file is used to diagnose a genetic condition” is considered intended use as it does not impart structural limitations onto the mutation index file.
An element in Claims 5 and 12 recite “requesting a new mutation input file” if a certain condition is met. The claim element is considered contingent and therefore not limitation of the claimed invention because the condition being met is not required.
Claim Rejections - 35 USC § 112
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 1, 8, and 9 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.
Claims 1 and 9 recite “…the mutation index file identifies a location of wild type and mutated nucleotides in the customized reference genome" wherein “the customized reference genome” lacks antecedent basis in the claim.
Claim 8 recites the limitation “wherein the data identifying chromosome location, start position, and end position for each gene with a mutation from the mutation input file is in GTF file format”. There is insufficient antecedent basis for the data identifying “end position” in the claim. Applicant may overcome rejection by including data identifying “end position” to the limitation that recites “receiving data” in claim 1, which this claim depends.
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 1-16 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; (b) mathematical concepts; and (c) natural phenomena/laws of nature.
Eligibility Step 1: Subject matter eligibility evaluation in accordance with MPEP § 2106:
Claims 1-8 are directed to a method of genetic analysis (process).
Claims 9-16 are directed to a genetic analysis system (machine).
Therefore claims 1-16 are encompassed by the categories of statutory subject matter and satisfy the subject matter eligibility requirements under step 1.
[Eligibility Step 1: YES]
Eligibility Step 2a : This step determines whether a claim is directed to a judicial exception in accordance with MPEP § 2106.
Eligibility Step 2a - Prong One: Limitations are analyzed to determine if the claims recite any concepts that could equate to a judicial exception (i.e. abstract idea, law of nature, or natural phenomenon).
In the instant application, evidence of claims 1-3, 5, 6, 8-12, and 16 reciting limitations that equate to judicial exceptions are examined below.
Independent claims 1 and 9 recite:
reading a plurality of input parameters, wherein the input parameters comprise a path to a mutation input file wherein the mutation input file is comprised of a mutated genetic sequence
sorting mutations in the input file based on starting positions
receives data identifying chromosome location, start position, and end position for each gene with a mutation in the mutation input file
comparing the mutation input file to the standardized reference genome
Dependent claims 6 and 14 recite:
The method of claim 1, wherein the comparison of the mutation input file to the standardized reference genome comprises matching non-altered nucleotides in the mutation input file against the standardized reference genome.
The limitations of sorting, comparing, and matching mutations or nucleotides can be achieved through making mental observations of a mutation input file, comprising a mutated genetic sequence, and performing analysis using pen and paper to derive secondary data.
Furthermore, claims directed to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind have been found to recite abstract ideas of the mental process grouping, as evidenced by, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016).
As such claims 1, 6, 9, and 14 include limitations that can be categorized under the “mental processes” grouping of abstract ideas.
Dependent claims 2 and 10 recite:
wherein the mutation index file is used to quantify the number of next generation sequencing reads aligned to the wild type allele or mutant allele, wherein the quantification is performed using allelic expression of mutations.
Dependent claims 3 and 11 recite:
wherein the genetic condition is diagnosed using the allelic expression of mutations.
Quantifying the number of reads aligned to different alleles can be executed by applying mathematical calculations to a mental observation. This analysis of allelic expression can also be conducted using a pen and paper.
Therefore, the limitations in claims 2, 3, 10, and 11 can be categorized under the “mathematical concepts” and/or “mental processes” groupings of abstract ideas.
Independent Claims 1 and 9 recite:
generating a mutation index file, wherein the mutation index file identifies a location of wild type and mutated nucleotides in the customized reference genome, wherein the mutation index file is used to diagnose a genetic condition.
The analysis of gene sequences and allelic expression can further lead to diagnoses, prognoses, and understanding of genetic conditions, including cancer. Therefore, limiting the identification of mutant nucleotides to a means of diagnosing a genetic condition simply correlates information of a known natural phenomenon/law of nature.
This classification is evidenced by the correlation between variations in non-coding regions of DNA and allele presence in coding regions of DNA, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1375, 118 USPQ2d 1541, 1545 (Fed. Cir. 2016) being drawn to a natural phenomenon/law of nature.
Therefore claims 1 and 9 contain limitations that can be categorized as “natural phenomena”.
As such, claims 1-3, 5, 6, 8-12, and 16 contain limitations that recite judicial exceptions in the form of abstract ideas and/or natural phenomena.
[Eligibility 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 analyzed if the claim recited additional elements that when examined as a whole integrate the judicial exception into 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 claim elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III).
The following claim elements are analyzed to determine if they integrate the judicial exception of their claim into practical applications.
Independent Claim 1 recites:
storing the mutation input file
loading a standardized reference genome
Independent Claim 9 recites wherein a computer:
stores the mutation input file
loads a standardized reference genome.
The claims do not recite an additional element that reflects an improvement to technology or application of the recited judicial exception to a particular computer or genome. Rather, the instant claims recite additional elements that amount to instructions to implement the abstract idea in a generic computing environment.
Therefore, the additional elements in claims 1 and 9 do not integrate the judicial exceptions into practical application.
Claims 2-3, 5-6, 8-12, and 14, and 16 do not recite any elements in addition to the judicial exception.
As such, claims 1-3, 5, 6, 8-12, and 16 when considered as a whole are directed to a judicial exception (abstract idea, natural phenomena).
[Eligibility Step 2A - Prong Two: YES].
Eligibility Step 2B: Claims are further analyzed as a whole to determine if they provide inventive concept, equating to significantly more than the exception itself (MPEP 2106.04(II)).
Dependent claims 4 and 13 recite:
wherein the genetic condition is a cancer.
Dependent claims 7 and 15 recite:
wherein the customized reference genome is comprised of a separate mutated gene sequence for each mutation in the mutation input file or a merged gene sequence that includes all of the mutations from the mutation input file.
These elements describe the field of use in which to apply a judicial exception. Limiting cancer to the genetic condition diagnosed through an analysis of mutations merely informs the relevant audience that the law of nature can be applied in this manner and does not equate to inventive concept, as established in Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1379, 118 USPQ2d 1541, 1549 (Fed. Cir. 2016).
Furthermore, diagnosing cancer and other genetic conditions by quantifying and evaluating the allelic expression of mutations is a well understood technique in the art. This is evidenced by the presentation of a computational tool that identified differential allelic expression of mutations, revealing associations to cancer and other genetic conditions in Yang et al. (Bioinformatics; Vol. 19 (8), 2003).
Additionally, the elements that store and load data equate to data gathering activities necessary to the claimed invention. Though necessary, storing and retrieving information in memory was also established as routine and conventional during Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
Therefore, the additional elements within the claims are conventional and merely apply judicial exceptions resulting in use of a well-understood method of genetic analysis.
As such, claims 1-16 do not include any elements, when evaluated separately or as a whole claimed invention, that amount to an inventive concept according to MPEP 2106.05(II) and are rejected.
[Eligibility Step 2B : NO]
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 1-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Grant et al(Scientific Reports Vol. 9, 2019), as evidenced by Thorvaldsdóttir et al (Briefings in Bioinfo; Vol. 14 (2), 2012) and Adglink (GitHub; “MAXX: Mutant Allele EXpression EXtractor”, 2018).
Thorvaldsdóttir et al. (Briefings in Bioinfo; Vol. 14 (2), 2012) describes features of the data visualization tool, Integrative Genomic Viewer (IGV).
Adglink (GitHub; “Adglink/MAXX: Mutant Allele EXpression EXtractor”, 2018) describes computational pipeline, MAXX, which performs a method of genetic analysis.
The claims are directed to a method in which mutations are received in a file and sorted by starting position. Each mutation is further identified by chromosomal location start position, reference and mutated alleles. The mutation file is compared to a reference genome to create an index file that identifies the location of the wildtype and mutant nucleotides. This comparison is quantified using the allelic expression of mutations.
Grant et al. teaches a method of genetic analysis using Mutation Allelic Expression Extractor (MAXX) software to delineate the allelic expression of genetic mutations [Results: The approach of MAXX enables the calculation of precise RNA mutant allele frequencies…allowing a comprehensive and unbiased analysis of mutation allelic expression](page 2, column 1).
Grant et al. teaches reading a plurality of input parameters, wherein the input parameters comprise a path to a mutation input file [Methods: The mutation files, GRCh38 v21 reference genome and GTF file were then used to generate tumor specific genomes via MAXX (page 12, column 1)]. MAXX inherently requires a path to a path to the input file, as evidenced by Adglink (Github; MAXX, 2018);
Grant et al. teaches storing the mutation input file, wherein the mutation input file is comprised of a mutated genetic sequence [Methods: Next, the mutated sequence and its header are generated. The mutation sequence is created based on the information from the mutation file, while the header is the gene’s name with a _Mut tag] (page 11, column 1);
Grant et al. teaches sorting the mutations in the input file based on starting position [Methods: Bam files derived from exome or RNA sequencing alignment were uploaded into the Integrative Genomic Viewer software] (page 12, column 1). IGV inherently requires that BAM files be sorted by position and indexed, as evidenced by (Thorvaldsdóttir et al. page 180, column 2). Furthermore, Figure 2a displays the mapped mutations from the input file, sorted by their starting position (Grant et al. page 3, figure 2);
Grant et al. teaches receiving data identifying chromosome location, start position, reference allele and mutated allele for each mutation in the mutation input file [Figure 2a shows data identifying chromosome location, start position, and end position, and chromosome location] (page 3, figure 2).
Grant et al. teaches loading a standardized reference genome[Methods: As input MAXX requires… a reference genome and the reference genome’s corresponding GTF file] (page 11, column 1);
Grant et al. teaches comparing the mutation input file to the standardized reference genome [Methods: MAXX is designed to only output the wild type and mutant sequence of genes presented in the mutation file] so, [the mutation files, GRCh38 v21 reference genome and GTF file were then used (compared) to generate tumor specific genomes] (page 11, column 1).
Grant et al. teaches generating a mutation index file, wherein the mutation index file identifies a location of wild type and mutated nucleotides in the customized reference genome [Methods: In addition to the custom-made reference genome, MAXX also outputs an index file that identifies the new positions of the mutations in both the wild type and mutant sequence], wherein the mutation index file is used to diagnose a genetic condition] (page 11, column 1).
Regarding claims 2 and 10, Grant et al. further teaches the mutation index file is used to quantify the number of next generation sequencing reads aligned to the wild type allele or mutant allele [Methods: The filtered bam file, tumor specific reference genome, and tumor mutation index file were then used as input for Bam-Read count which identified the number of reads that aligned to the mutant and wild type sequences] (page 11, column 1).
Grant et al. teaches wherein the quantification is performed using allelic expression of mutations [MAXX enables the calculation of precise RNA mutant allele frequencies… allowing a comprehensive and unbiased analysis of mutation allelic expression] (page 2, column 1).
Regarding claims 3 and 11, Grant et al. teaches the method of claim 2, wherein the genetic condition is diagnosed using the allelic expression of mutations [Abstract: Thus, differentiating mutations based on their mutant allele expression via MAXX represents a means to parse somatic variants in tumor genomes, helping to elucidate a gene’s respective role in cancer (a genetic condition)] (page 1, column 1).
Regarding claims 4 and 13, Grant et al. teaches the genetic condition is a cancer [Introduction: Mutation expression groups also assisted in the identification of pancreatic adenocarcinoma subtypes that have prognostic relevance] (page 2, column 1).
Regarding claims 5 and 12, Grant et al. teaches requesting a new mutation input file if mutations in the mutation input file are duplicated or overlap[Methods: First, the PCR duplicates were removed, using the Picard Tools…MarkDuplicates command where the input parameter REMOVE_DUPLICATES was set to “true”. Second, SAMtools v. 1.4 was used to keep the uniquely aligned reads via the command “samtools view -q 50 -b input.bam >output.bam. Finally, because our data was paired-end, the additional step of singleton removal using the SAMtools v. 1.4 command “samtools view -F 8 -b input.bam >output.bam” was performed] (page 11, column 1). In all, the filtering commands request and produce a new mutation input file (output.bam) when mutations duplicate or overlap.
Regarding claims 6 and 14, Grant et al. teaches the comparison of the mutation input file to the standardized reference genome comprises matching non-altered nucleotides in the mutation input file against the standardized reference genome [Results: We compared RNA mutant allele frequencies established from an Hg19 reference genome with the appended MAXX mutant genome to a MAXX generated reference genome] (page 4, column 1). This matching of non-altered nucleotides is displayed in Figure 1a (page 2, Figure 1).
Regarding claims 7 and 15, Grant et al. teaches the customized reference genome is comprised of a separate mutated gene sequence for each mutation in the mutation input file or a merged gene sequence that includes all of the mutations from the mutation input file. [Discussion: MAXX is also capable of generating customizable gene specific reference genomes..] (page 10, column 1) the software [is designed to only output the wild type and mutant sequence of genes presented in the mutation file. This approach dramatically decreases the size of the fasta] (page 11, column 1).
Regarding claim 8 and 16, Grant et al. teaches the data identifying chromosome location, start position, and end position for each gene with a mutation from the mutation input file is in a GTF file format[Methods: MAXX uses information from the GTF file to identify the sequence of the input genes within the fasta file…MAXX also outputs an index file that identifies the new positions of the mutations in both the wild type and mutant sequence] (page 11, column 1).
Claims 1-16 are rejected under 35 U.S.C. 102(a)(1) based upon a public use or sale or other public availability of the invention within a GitHub repository, Adglink (GitHub; “MAXX: Mutant Allele EXpression EXtractor”, 2018).
Adglink anticipates the claimed invention, as examined below.
Regarding claims 1 and 9, Adglink teaches a method of genetic analysis comprising:
Adglink teaches reading a plurality of input parameters, wherein the input parameters comprise a path to a mutation input file [The path to the mutation list file] (page 2, Required input parameters);
Adglink teaches storing the mutation input file, wherein the mutation input file is comprised of a mutated genetic sequence [The path to the mutation list file. This file contains a list of mutations that will be used to generate the tumor specific reference genome] (page 2, Required Input Parameters);
Adglink teaches sorting the mutations in the input file based on starting position [A file containing the new positions of all input mutations, relative to the tumor specific reference genome. This index file is required by softwares such as Bam Read Count and Sam Tools](page 3, Output files), as evidenced by;
Adglink teaches receiving data identifying chromosome location, start position, reference allele and mutated allele for each mutation in the mutation input file [Figure 1 displays all location identifying data required by limitation, for each mutation in the input file] (page 2, Required Input Parameters).
Adglink teaches loading a standardized reference genome [The path to the reference genome file, most likely will be Hg19 or GRCh38] (page 2, Required Input Parameters);
Adglink teaches comparing the mutation input file to the standardized reference genome [MAXX uses the input reference genome to obtain the genetic sequence of genes presented in the mutation list] (page 2, Required Input Parameters);
Adglink teaches generating a mutation index file, wherein the mutation index file identifies a location of wild type and mutated nucleotides in the customized reference genome [A file containing the new positions of all input mutations, relative to the tumor specific reference genome. This index file is required by softwares such as Bam Read Count and Sam Tools to identify how many reads aligned to that particular nucleotide, providing the information to calculate the RNA allele frequency] (page 3, Output files), wherein the mutation index file is used to diagnose a genetic condition.
Regarding claims 2 and 10, Adglink teaches:
the method of claim 1, wherein the mutation index file is used to quantify the number of next generation sequencing reads aligned to the wild type allele or mutant allele, wherein the quantification is performed using allelic expression of mutations [This index file is required by softwares such as Bam Read Count and Sam Tools to identify how many reads aligned to that particular nucleotide, providing the information to calculate the RNA allele frequency] (page 3, Output Files)…[Since sequencing methods and mutation detection software are dramatically improving, the ability to detect indel mutations within RNA-sequencing data will continue to be an important aspect in performing mutation allelic expression analyses] (page 1, para. 1).
Regarding claims 3, 4 , 11, and 13, Adglink teaches:
The method of claim 1, wherein the genetic condition is a cancer [Tumor specific reference genomes have been demonstrated to dramatically enhance alignment of RNA-sequencing reads containing indel mutations, providing an unbiased analysis of mutation allelic expression] (page 1, para. 1).
Regarding claims 5 and 12, Adglink teaches :
The method of claim 1, further comprising requesting a new mutation input file if mutations in the mutation input file are duplicated or overlap[A file containing the new positions of all input mutations, relative to the tumor specific reference genome. This index file is required by softwares such as Bam Read Count and Sam Tools](page 2, Output files).
Regarding claims 6 and 14, Adglink teaches:
The method of claim 1, wherein the comparison of the mutation input file to the standardized reference genome comprises matching non-altered nucleotides in the mutation input file against the standardized reference genome [This reference genome is ideally used in conjunction with a RNA-sequencing aligner to increase alignment accuracy of mutant RNA-sequencing reads] (page 2, Output files). The reads are obtained using information from the mutation input file.
Regarding claims 7 and 15, Adglink teaches:
The method of claim 1, wherein the customized reference genome is comprised of a separate mutated gene sequence for each mutation in the mutation input file or a merged gene sequence that includes all of the mutations from the mutation input file [A tumor specific reference genome in the fasta format. The new reference genome contains the wild type and mutant sequence for all mutated genes present in the mutation list] (page 2, Output files).
Regarding claim 8 and 16, Adglink teaches:
The method of claim 1, wherein the data identifying chromosome location, start position, and end position for each gene with a mutation from the mutation input file is in a GTF file format [The path to the GTF file that corresponds to the input reference genome. MAXX uses the GTF file to identify the start and end positions for each mutated gene, these positions are then used to obtain the genetic sequence from the reference genome] (page 2, Required Input Parameters).
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 claims because the examined application claim is either anticipated by, or would have been obvious over, the reference claims. 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.
The following nonstatutory double patenting rejections are provisional because the patentably indistinct claims have not in fact been patented.
Claims 1-16 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of copending Application No. 17/747,817 (reference), in view of Edwards et al (Brst Cancer Rsrch; Vol. 14 (303), 2012), as evidenced by Iseli et al (PLoS ONE; 2(6), 2007) and Hampton et al. (Genome Res; Vol. 19, 2009).
Edwards et al. (Brst Cancer Rsrch; 14: 303, 2012) explores the role of gene fusion mutations in breast cancers.
Neckles et al. (Wiley Interdiscip Rev RNA; 11 (1), 2019) explores the oncogenic properties of gene fusion mutations.
Iseli et al. (PLoS ONE; 2(6), 2007) describes genome indexing strategies.
Hampton et al. (Genome Res; Vol. 19, 2009) explores the genetic insights derived from breakpoint analysis of gene fusion mutations.
Independent claims 1 and 9 (instant) present an analogous technique to independent claims 1 and 8 (reference). They differ by the addition of the following limitations:
Sorting mutations in the mutation input file based on starting position
Receiving data identifying end position, strand, and break points of two genes for mutations in the input file
Using an index file to identify the location of wild type and mutated nucleotides in the customized reference genome
While accessing relevant data sequences via location is inherent to common indexing strategies within the art (Iseli et al. page 4, column 1), the remainder of differences slightly alter the scope of the claimed inventions. Their function represents the design perspectives behind a genetic analysis system that evaluates “mutations” vs “gene fusion events”. However, “gene fusion” is known in the art to be a species of genetic mutation, as evidenced by Edwards et al. (page 1, column 1), Neckles et al. (page 1, column 1). Therefore, all claims limited to genetic mutation are interpreted as being inclusive of gene fusion events.
Receiving and processing additional mutation data merely uses a known technique to account for the studied breakpoint analysis relevant to gene fusions mutations (Hampton et al. page 168, column 1). As such, the claimed inventions equate to obvious variations of known work in one field (genetic analysis of mutations) based on the design incentives of the slightly narrower field (genetic analysis of gene fusions), in accordance with MPEP § 2143(I)(F).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are currently allowed.
Correspondence
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/M.K.T./
Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687