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 .
Priority
Instant application does claim the benefit of priority to an earlier application. The benefit of the priority date determined based on provisional application that was filed on 10/11/2021 (application No. 63/254,425) and EFD was considered as 10/11/2021.
Information Disclosure Statement
The IDS filed on 4/12/2023 is considered by the Examiner.
Claim Status
Claims 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 are pending and examined on the merits.
Claims 3-8, 11-13, 18, 19, 23, 24, 33, 35,36, and 38-79 are canceled.
Claims 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 are rejected.
Claim Rejections - 35 USC § 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.
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, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 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 applicant regards as the invention.
Claim 1, 80 and 81 recites “a respective …. splicing events in common with the respective principal mRNA isoform, …. a respective … not in common with the respective principal mRNA isoform” is ambiguous in the context of sequence alignment. Neither the claim nor the specification defines what degree of overlap between splice sites or splicing events constitutes “in common” nor do they establish when an event is considered “not in common”. For example, it is unclear whether “common” requires identical splice donor and acceptor sites, a shared exon, a shared intron, a percentage of overlapping splice junctions, or merely the presence of at least one identical splice event. Likewise, the specification does not provide any quotative threshold, algorithm, by which a person of ordinary skill in the art could consistently determine whether a given splicing event falls within either category.
Consequently, the metes and bounds of the claim cannot be determined with reasonable certainty. Different person of ordinary skill in the art could reasonably reach different conclusions regarding whether a particular splicing event is “in common” or “not in common” with the principal mRNA isoform. Accordingly, the claim fails to particularly point out and distinctly claim the subject matter regarded as invention, rendering the claim indefinite under 35 U.S.C. 112(b)
Claim 10 recites the limitation "unique occurrences" is ambiguous in the context of sequence reads. It is unclear whether "unique" refers to counting distinct reads that contain the coordinate exactly once, or if it refers to counting unique sequences that map to that coordinate. This ambiguity makes the metes and bounds of the claim unclear and it is deemed indefinite. Without defining “unique occurrences,” a person of ordinary skill in the art cannot determine the scope of the invention. (See MPEP § 2173.02 and MPEP § 2173(e)).
Claim 15 is indefinite because it lacks proper antecedent basis, making it impossible to determine the scope of the invention. Specifically, the phrase “wherein the D) identifying further comprises” refers to an element "D) identifying" that has not been previously introduced in independent claim 1. Although it has been introduced in claim 2, but claim 15 refers to claim 1, makes it unclear what step "D) identifying" refers to, or how it relates to the steps of the method making it impossible for a PHOSITA to determine the scope of the claim, satisfying the criteria for an indefinite claim under 35 U.S.C. 112(b). (See MPEP § 2173.05(e)).
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 therefore, subject to the conditions and requirements of this title.
Claim 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract idea without significantly more.
Step 2A, Prong 1
In accordance with MPEP § 2106, the instant claims 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, and 37 are drawn to a (method), claims 80 and 81 are drawn to a CRM, and therefore are found to recite statutory subject matter (Step 1: YES). The instant claims are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). The instant claims recite
the following limitations equate to an abstract idea:
Claims 1, 80 and 81 recite
Comparing, for each respective gene in the first set of one or more genes, the respective plurality of splice site coordinates …… site coordinates (Mental process or mathematical calculation). Comparing data points (coordinates) to sort them into subsets based on matching criteria is a fundamental algorithmic step that can be done in the human mind
Determining, for each respective gene in the set of one or more genes, …. coordinates. (Mental process)
Claim 2 recites
Identifying, for each respective gene in the set of one or more genes, ….. for a respective splice site coordinates. (Mental process)
Identifying the acceptor splice site corresponding to the respective splice site in a genomic construct for the respective gene. (Mental process)
Identifying the donor splice site corresponding to the respective splice site in a genomic construct for the respective gene and searching a region of the genomic construct. (Mental process)
Claim 9 recites aggregation of splice site coordinates across the respective aligned ….to the respective gene. (Mental process).
Claim 10 recites for each respective splice site coordinate ……. a respective count of the number of unique occurrences ……sequence reads. (Mental process)
Claim 14 recites for a respective gene in the first set, the principal mRNA isoform is identified as the predominant mRNA isoform. (Mental process)
Claim 15 recites
Identifying the donor splice site corresponding ……for the respective gene. (Mental process)
Searching the region of the genomic construct downstream ……identifying an alternative terminal exon. (Mental process or mathematical concept)
Claim 16 recites the region ….. limited to a first threshold number …. the genomic construct. (Mental process or human organizing activity)
Claim 17 recites the region of the ….. limited to a second threshold number ….. the genomic construct. (Mental process or human organizing activity)
Claim 20 recites when more than one ….. closest to the acceptor splice site is identified as the corresponding donor splice site. (Human organizing activity or mental process)
Claim 21 recites when more than one ……closest to the donor splice site is identified as the corresponding acceptor splice site. (Human organizing activity or mental process)
Claim 22 recites when a respective …. comprising more than a first threshold number of different exons …filtering out respective novel non-canonical exons that are represented in the respective plurality of novel non-canonical exons less than a second threshold number of times. (Mental process or human organizing activity)
Claim 25 recites the second threshold number of times is a measure of central tendency ……. splice site coordinates. (Mathematical concept).
Claim 26 recites about identifying from a first respective splice site ………. respective genes. (Mental process)
Claim 27 recites
Identifying a second respective splice site coordinate …………. a second respective first non- canonical exon identified. (Mental process)
Identifying from the second respective splice site coordinate. (Mental process)
Claim 28 recites identifying from a second respective splice site ….in order, (i) each respective exon of the known mRNA isoform … (ii) the first respective second novel non-canonical exon, and (iii) each respective exon in the respective principal mRNA isoform …splice site. (Mental process or mathematical concept)
Claim 29 recites identifying from a second respective splice site coordinate in the respective fourth subset of splice site coordinates, ……in order, (i) each respective exon of the known mRNA isoform upstream of the predicted acceptor splice site, (ii) the first respective second non-canonical exon, and (iii) each respective exon in the respective principal mRNA isoform ……. acceptor splice site. (Mental process or mathematical concept)
Claim 30 describes a series of conditional steps ("when the predicted acceptor site... is not represented... identifying a third... site") designed to classify or identify genetic structures such as non-canonical exon. (Mental process and mathematical concept)
Claim 31 recites “when the corresponding …. donor splice site for the second respective splice site coordinate is represented in the reference …. corresponding acceptor splice site” describes a method of defining an alternative transcript based on analytical steps (comparing donor splice site coordinates to a reference). (Mental process)
Claim 34 describes of generating a respective isoform library for a respective gene in the set of …. respective non-canonical exon identified. (Mental process)
Claim 37 describes generating a report comprising whether the biological sample included an alternative splicing event for one or more genes in the first set of one or more genes. (Mental process)
As such, claims 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 recite an abstract idea (Step 2A, Prong1: YES).
Step 2A, Prong 2
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Specifically, the claims recite the following additional elements:
Claims 1 recites
A computer system comprising at least one processor and a memory storing at least one program for execution by at least one processor.
Obtaining, for each respective gene in a first set of one or more genes, …. sequence read.
Claim 80 describes a computer system comprising: one or more processors; and a non-transitory computer-readable medium including computer-executable instructions that, when executed by one or more processors, cause the processors to perform a method for mapping splicing events in a test subject.
Claim 81 describes a non-transitory computer-readable medium containing instructions to execute a method for mapping mRNA splicing events in a biological sample.
The limitations about obtaining sequence read (data) serve as being merely an insignificant, routine, or conventional post-solution activity and used an input for the judicial exception. The gathering data does not add any significant practical application.
Therefore, these limitations are mere data gathering or analyzing activities. As set forth in MPEP 2106.05(g), mere data gathering and analyzing activity has been identified by the courts as insignificant extra-solution activity that does not provide a practical application.
The additional element does not provide any details of how specific structures of the computer elements are used to implement the JE. The claims require nothing more than a general-purpose computer to perform the functions that constitute judicial exceptions. The computer elements of the claims do not provide improvements to the functioning of the computer itself (as in DDR Holdings, LLC v. Hotels.com LP); they do not provide improvements to any other technology or technical field (as in Diamond v. Diehr); nor do they utilize a particular machine (as in Eibel Process Co. v. Minn. & Ont. Paper Co.). Hence, these are mere instructions to apply the JE using a computer, and therefore the claim does not integrate that JE into a practical application.
As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d in 1983. See also 573 U.S. at 224, 110 USPQ2d in 1984.
The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 1-81 (excluding the cancelled claims) are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B
Claims found to be directed at a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic computing environment or well-understood, routine and conventional activity. Also, remaining additional elements are routine and conventional in bioinformatic pipelines and merely serve extra solution activity.
As discussed above, there are no additional limitations to indicate that the claimed processor requires anything other than generic computer components to carry out the recited abstract idea in the claims. Claims that amount to nothing more than instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d in 1983. See also 573 U.S. at 224, 110 USPQ2d in 1984.
Furthermore, the additional elements recited in the claims amount to well-understood, routine and conventional activity.
As such, the combination of additional elements recited in the claims is well-understood, routine and conventional. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1, 2, 9, 10, 14-17, 20-22, 25-32, 34, 37, 80 and 81 are not patent eligible.
Claim Rejections - 35 USC § 103
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 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 should not be negated by the way 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 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 is 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.
Claims 1, 9, 10, 14, 20, and 21 rejected under 35 U.S.C. 103 as being unpatentable over Brenner et al. (US 7149631 B2) in view of Au. et al. (Nucleic Acids Research, 2010, Vol. 38, No. 14, 4570–4578)
Regarding claim 1:
Brenner et al. discloses:
“a computational method for systemically identifying alternatives mRNA splice isoforms of known genes.” (Brenner, Claim 1; Description, Section I, col. 2, lines 10-45). The method is expressly performed computationally, with source-code files provided “for implementing this protocol” (Brenner, Description I, Col. 4, lines 1-25; referring to the “/src directory” software); i.e., at a computer system executing stored program instructions – the generic computer-implementation recited in claim 1’s preamble (“at a computer system comprising at least one processor and a memory storing at least one program for execution by the at least one processor”)
Identifying target genes sequences by “mapping mRNA sequences to an mRNA sequence dataset” and “identifying a dataset of alternate mRNA splice isoforms of the target gene sequences by aligning EST sequences from the target gene sequences by aligning EST sequences from an EST sequence dataset to the target sequences” (Brenner, claim 1(a)-(b); Description I). In the working example, “we align EST sequences from dbEST to the genomic sequence and use TAP to infer alternate mRNA splice forms from these alignments,” producing, for each gene, “alternate splice pairs,” which Brenner et al. defines as “splice donor/acceptor sites … inferred from the alignments.” (Brenner, Detailed Description of Fig. 1(c); Exemplary Protocols), “Analysis of canonical and alternative splice pairs” (“2226 canonical RefSeq mRNAs were found to have 4452 alternative splice pairs and 3577 alternative mRNA isoforms). Alternative splice pairs are defined as ESTs (expressed sequence tags) are themselves sequence reads generated from a biological mRNA sample and aligned to the genome—i.e., “aligned sequence reads for mRNA in a biological sample …. mapping to the respective gene,” each read yielding splice site coordinates that correspond to a donor and acceptor site, exactly as recited in step A in claim 1.
Thus, above disclosure suggests the limitation of “obtaining splice site coordinates from aligned sequence reads mapping to a gene, each corresponding to a donor and acceptor splice site.”
Using RefSeq mRNA, — “well-characterized human mRNAs” representing “canonical (RefSeq) splices” – as the reference/principal isoform for each gene, against which EST-derived splice pairs are compared: “Canonical (Refseq) splices are indicated above the exons while alternative splices indicated below the exons,” and “Alternative splice pairs are those indicated by ESTs, but not by a RefSeq mRNA.” (Brenner, Detailed Description of Fig. 1(a), (c)). Brenner et al. further explains: “Whenever a splice in an alternative isoform was not covered by ESTs, it was designated canonical,” i.e., splice pairs matching the reference isoform are classified as canonical/constitutional (claim 1’s first subset), while EST-supported pairs differing from RefSeq are classified as “alternative splice pairs” (claim 1’s second subset). (Brenner, Exemplary Protocols, Col. 6, lines 50-70; “Analysis of canonical and “alternative splice pairs.”)
Thus, the above disclosure suggests the limitation of “comparing the splice site coordinates to reference (principal-isoform) coordinates to identify a first subset representatives of constitutional splicing (in common with the principal isoform) and a second subset representative of alternative splicing.”
Brenner et al. classifies each alternative splice pair “according to … exon and splice site usage,” recording for each pair, the number of “splice site introduces” – i.e., “the number of splice donor/acceptor sites that were observed in the alternative splice, but were not included in the canonical splice” – versus splice sites that were already present in the canonical isoform. (Brenner, Detailed description of Fig. 1(b)). This “splice sites introduced” count of 0 versus ≥ is precisely the distinction drawn by claim 1’s “first criteria” : where an alternative splice pair introduces zero new sites (both the donor and acceptor were already present, individually, in the canonical isoform—e.g., mutually exclusive exon usage recombining known sites) it falls in claim 1’s third subset; where it introduces one or more new sites (at least one of the donor/acceptor was not present in the canonical isoform) it falls in claim 1’s fourth subset. Brenner expressly reports classifying alternative splice pairs by this introduced/lost-site metric “at various levels of EST coverage” (Brenner, Detailed description of Fig. 1(d), which is the same operation recited in claim 1, part C) and thus, suggesting the limitation of “determining, for the second subset, whether both the donor and acceptor sites are individually represented in the reference isoform (identifying a third subset satisfying that “first criteria,” representative of alternative splicing between donor/acceptor sites each individually known, versus a fourth subset where at least one site itself novel.”
What Brenner et al. does not expressly teach:
Brenner’s exemplary implementation compares mRNA/EST sequences (Sanger-sequenced cDNA fragments, hundreds of nucleotides long) to genomic sequence using the Spidey and sim4 alignment tools (Brenner, Exemplary Protocols, “Aligning EST sequences to genomic sequences”), rather than the short, massively parallel “aligned sequence reads” produced by second generation (“next-generation”) RNA sequencing (RNA-seq) that had become the dominant technology for transcriptome profiling by the relevant time. Brenner does not use the terms “RNA-seq” or describe alignment of short (i.e., 25-100nt) sequencing reads.
Au et al. teaches:
Au et al. discloses SpliceMap, “a computational method … to detect splice junctions from RNA-seq data,” specifically addressing the problem that “tens or hundreds of millions of short sequences (30-100nt) are read randomly from the population of transcripts under study” in “RNA-seq projects,” and that “the first step of the analysis is thus the mapping of each short read to a reference genome.” (Au, Abstract; p. 4570, col.1 (Introduction)). Au et al. further explains that “reads that are most interest for novel isoform discovery are the ones that span across exon-exon junctions” --- “junction reads” and discloses aligning such reads to identify the precise donor/acceptor splice-site coordinates underlying each junction. (Au, p. 4570, col. 2). Au et al.’s method is explicitly annotation-independent, “utilizing merely the reference genomic sequence to find the junction independently of existing exon annotation,” i.e., it produces, for a biological RNA sample, a set of splice site coordinates derived from aligned sequence reads mapping to each gene—the same data structure recited in claim 1, step A. (Au, Abstract)
A PHOSITA would have had ample reason, under MPEP 2143 (I)(B) (“simple substitution of one known element for another to obtain predictable results”) and the KSR “obvious to try”/” predictable use of known technique” rationales, to substitute Au et al.’s RNA-seq short-read junction mapping for Brenner’s EST-alignment step as the source of “aligned sequence reads” feeding into Brenner’s comparison-and-classification pipelines:
Both references solve the identical technical problem, inferring a gene’s actual splice-site usage in a biological sample from sequence reads aligned to the genome, and comparing that usage against a reference/canonical isoform to detect alternative splicing. Brenner et al. already frames its EST alignment as a proxy for “sequence reads” of the transcriptome; Au et al. simply supplies a newer, higher-throughout read type for the same alignment-and-comparison workflow.
Au et al. itself articulates the motivation to replace ESTs with RNA-seq reads, explaining that the increased read length and throughput of “second generation sequencing technology (SGS) make it possible to detect rare alternative splicing events” that EST-based approaches (limited by low -throughput, biased cDNA-library sampling) could not reliably detect. (Au, p. 4570, col.1). Brenner et al. itself acknowledges the corresponding limitation of its own EST-based approach that EST subject a gene’s rarer/fewer stable isoforms to “bias against less stable transcripts’ (Brenner, Exemplary Protocols, “The coupling of alternatives splicing”) providing an independent, in-reference reason for a PHOSITA to seek exactly the kind of deeper, less-biased sequencing data that Au et al. supplies.
Both EST alignment and RNA-seq junction reads output the same data type needed by Brenner’s comparison step, a set of splice-donor/acceptor coordinate pairs per gene, so substituting one-read-alignment technology for the other requires no more than ordinary skill and predictably yields the same downstream classification (canonical vs. alternative; sites-introduced vs. not) that Brenner already performs. (MPEP 2143 (I)(A) -(B); KSR, 550 U.S. at 416 (“if a person of ordinary skill can implement a predictable variation, 103 likely bars its patentability”)
Combining Brenner et al.’s principal-isoform comparison/classification logic (steps B and C of claim 1) with Au et al.’s RNA-seq short-read alignment (as the source of the :aligned sequence reads” of step A) results in a method that: (a) obtains, for each gene, splice site coordinates from RNA-seq reads aligned to the gene (Au) , each corresponding to a donor and acceptor site; (b) compares those coordinates to the reference/principal isoform’s splice sites to identify constitutional (first subset) vs. alternative (second subset) splice pairs (Brenner); and (c) further classifies the alternative pairs by whether they introduce a wholly new donor or acceptor site not otherwise present in the reference isoform (Brenner’ “splice sites introduces” metric), yielding third and fourth subsets exactly as recited in claim 1.
Regarding claim 9:
The limitation of claim 9 (splice site coordinate set “aggregates splice site coordinates across the respective aligned sequence reads… mapping to the respective gene”) is taught by the combination of Brenner et al.’s splice pairs are, by construction, aggregated across all EST/read alignments supporting a given gene (Brenner, Detailed Description of Fig. 1(c) : “The exon composition of an isoform was determined from EST-demonstrated splice pairs which may be covered by multiple ESTs”) and Au et al.’s junction detection likewise aggregates evidence across all reads mapping to a locus (Au, p 4570 (paired-end filtering combines evidence from multiple reads at a locus)).
Regarding claim 10:
The limitation of claim 10 (“count of the number of unique occurrences of the respective splice site coordinate”) is taught by Brenner et al.’s EST-coverage metric: Coverage of splice pairs is indicated in each” and “we assign higher confidence in splicing events with coverage by multiple ESTs.” (Brenner, Detailed description of Fig. 1(c); Exemplary Protocols), Au et al. likewise reports and thresholds junction “read counts” supporting each junction (Au, p. 4570 et seq., junction filtering by supporting-read count).
Regarding claim 14:
The limitation of claim 14 (“principal mRNA isoform is identified as the predominant mRNA isoform in the respective plurality of sequence reads aligned to the respective gene”) taught by Brenner et al.’s use of RefSeq as the reference/canonical isoform, selected as “the mRNA sequence containing the largest number of exons” when multiple candidates align to a locus (Brenner, description I), in combination with the general knowledge (reflected in Au’s read-count-based confidence weighting) of using expression-level (read count) evidence to identify a locus’s predominant isoform, renders obvious selecting the isoform best supported by the aligned-read data as the “principal” isoform, a straightforward application of Brenner’s coverage-based confidence metric to isoform (rather than splice-pair) selection, a predictable variation under MPEP 2143(I)(A).
Regarding claims 20 and 21:
The limitation of claims 20 and 21 (selecting, where multiple candidate donor/acceptor sites are found, the one closest to the known counterpart site) reflect the well-understood, field standard process reflected in Au et al.’s own splice-boundary-refinement procedure, which locates “the approximate location of a junction: from half-read mapping and then resolves the precise boundary by scanning the flanking sequence for the nearest valid splice-site dinucleotide (Au, p. 4570, col. 2, “Detection of splice junctions …based on the idea of using the mapping of half-reads … to identify the approximate location of a junction”;( Au, Materials and Methods, splice-boundary refinement by canonical dinucleotide search outward from the approximate junction location) a “closest-candidate” resolution rule that a PHOSITA would apply as an obvious design choice, predictably narrowing ambiguous multi-coordinate splice-site calls (MPEP 2144.04 and KSR’s “obvious to try” rationale (a finite, easily-traversed set of predictable solutions, nearest, second nearest, etc. from which “closest” is the PHOSITA’s default choice).
Claims 2, 15, 16, 17, 22, and 25 rejected under 35 U.S.C. 103 as being unpatentable over Brenner et al. in view of Au et al. as applied to claims 1, 9, 10, 14, 20 and 21 above and further in view of Rogers et al. (Genome Biology 2012, 13: R4)
Brenner et al. in view of Au et al. are applied to claims 1, 9, 10, 14, 20 and 21 above.
Regarding claim 2:
Claim 2 adds step 2 D): for a splice site coordinate in the fourth subset (i.e., where at least one of the donor/acceptor sites is not present in the reference isoform), identifying a “novel non-canonical exon” by: (i) if the acceptor site is not represented in the reference, searching a region of the ‘genomic construct” upstream of the acceptor site to find a predicted donor site, the sequence spanning the predicted donor to the (known) acceptor defining a first novel exon; and (ii) if the donor site is not represented in the reference, searching a region downstream of the donor site to find a predicted acceptor site, the sequence spanning the (known) donor to the predicted acceptor defining a second novel exon.
Rogers et al. disclose a method, that, working from RNA-seq reads aligned to a reference genome together with gene-model annotation, distinguishes “known” junctions that are derived from gene model annotations; ‘recombined’ junctions constructed from novel combinations of known splice sites; and ‘predicted’ junctions in which one or both splice sites are novel.” (Rogers, Methods, “Splice junction prediction” (p. 11). Critically, for junctions with a novel (non-annotated) site, Rogers et al. “performs spliced alignment by first constructing a database of splice junction sequences that are formed by concatenating the sequence directly upstream of a donor site with the sequence directly downstream pf an acceptor site” i.e., Rogers et al. constructs a genomic sequence spanning candidate donor/acceptor pairs (a ”genomic construct” in claim 2’s terminology) and searches it to identify and validate the novel splice boundary. (Rogers, Methods, “Splice junction prediction.”) Rogers et al. further explains that genomic regions “flanked by a splice acceptor and a splice donor are candidate internal exons” that are searched and validated against read-coverage evidence (Rogers, Results, “Splice graph construction’), i.e., the region between a known site and a searched-for novel site defines a candidate (“novel”) exon exactly as recited in claim 2.
A PHOSITA combining Brenner et al.’s principal-isoform comparison (as described in claim 1 rejection) with Au et al.’s RNA-seq junction mapping would, upon identifying (per Brenner’s own “splice site introduced” classification) a splice pair in which one site is novel relative to the reference isoform, naturally turn to Rogers’s specific technique for resolving what exon that novel site defines because:
Rogers et al. addresses the exact next problem left open by Brenner/Au. Brenner et al.’s classification (as in claim 1 rejection) flags a splice pair as containing a novel donor or acceptor site but does not locate the exon boundary created by that novel site. Rogers et al. supplies the missing technique, searching the genomic sequence flanking the known site for the pair candidate site that a PHOSITA would need to complete the analysis Brenner et al. starts. This is a textbook “combining prior art elements according to known methods to yield predictable results” scenario under MPEP 2143 (I)(A): each reference performs its known function (Brenner/Au: detect and flag a novel splice pair; Rogers: resolve the novel exon boundary from a known anchor site) and the combination yields nothing more than the predictable sum of those functions.
Rogers et al. itself teaches integrating annotation-based comparison with RNA-seq evidence, expressly designing SpliceGrapher “to integrate RNA-seq reads into splice graph predictions” built on top of “curated gene models” (Rogers, Abstract; Background), i.e., Rogers et al. already contemplates exactly the RNA-seq-plus-reference-annotation combination that was described in claim 1, 9, 10, 14, 20 and 21 rejection render obvious, reinforcing that a PHOSITA implementing Brenner/Au would look to Roger’s junction-classification and exon-construction methodology as a compatible, purpose-built extension.
Applying Rogers et al. donor / acceptor search technique to a fourth-subset splice pair identified by Brenner / Au: where the acceptor site is not representative in the reference isoform(Brenner’s “site introduced” at the acceptor), Rogers et al.’s technique or searching genomic sequence upstream of the (known or itself-searched) acceptor for a compatible donor dinucleotide / splice-site motif identifies the predicted donor site, and spanned genomic sequence defines the first novel exon; systemically for a novel donor site, searching downstream for a predicted acceptor defines the second novel exon precisely claimed 2 step D).
Regarding claim 16 and 17:
The limitation of claim 16 and 17 (limiting the upstream / downstream search To a threshold number of nucleotides) are taught by Rogers et al.’s practice a bounding the candidate-junction search region rather than scanning the entire genomic sequence, Rogers et al. constrains its junction-sequence database construction to sequence “directly upstream”/ “directly downstream” of the known site (Rogers, Methods, “Splice junction prediction”), and more generally, bounding a sequence search to a fixed flanking window (e.g., typical intron/ exon length limits) to control false-positive rate and competition time is a well-known, obvious design choice for a PHOSITA implementing any splice-site search (MPEP 2144.04, “Optimization / Routine parameter selection”).
Regarding claim 15:
Claim 15 adds limitation of defining an “alternative terminal exon” when no corresponding acceptor is found downstream of a novel donor, using the RefSeq/principal -isoform exon that terminates at the (represented) acceptor, or the first novel exon otherwise) is an obvious variant of the same Rogers et al./ Brenner et al. search-and-compare logic applied to the terminal-exon case, which Brenner et al.’s own framework already accommodates through its principal isoform exon boundaries (Brenner, Description I; , FIG. 1a).
Regarding claim 22:
Claim 22 adds limitation of “filtering out low-recurrence novel exon sharing a donor / acceptor site” is taught by Brenner et al.’s coverage- based confidence filtering, "we assign higher confidence in splicing events with coverage by multiple ESTs” and, correspondingly, in the working example, “rejecting putative alternative splice pairs found less than 7 base pair from a canonical splice pair” as a reliability filter (Brenner , Exemplary Protocols) combined with the Rogers et al.’s own machine-learning-based filtering of “spurious splice sites” to “improve the reliability of detection of alternative splicing” (Rogers, Abstract), which a PHOSITA would apply, as a predictable variation, to filter low -recurrence novel exons sharing a splice site .
Regarding claim 25:
Claim 25 adds limitation of “second threshold= a measure of central tendency of recurrence counts” is an obvious, routine statistical implementation of the coverage- threshold filtering already taught by Brenner et al. and Rogers et al. (MPEP 2144.04).
Claim 26-32 and 34 rejected under 35 U.S.C. 103 as unpatentable over Brenner et al. in view of Au et al. and Rogers et al. as applied to claims 1, 2, 9, 10, 14, 15, 16, 17, 20, 21, 22, and 25 above and further in view of Brenner et al.’s transcript assembly (TAP) teaching.
Brenner et al. in view of Au et al. and Rogers et al. are applied to claims 1, 2, 9, 10, 14, 15, 16, 17, 20, 21, 22, and 25 above.
Regarding claims 26-32 and 34:
Claims 26-31 recite defining a complete “alternative transcript” by splicing together (i) principal-isoform exons upstream of a first novel exon, (ii) the novel exons identified per claim 2’s step D), and (iii) exons of a “known mRNA isoform” (which, per claim 32, maybe the principal isoform itself) downstream of the second is splice site i.e., assembling a full-length alternative mRNA sequence form a mixture of known reference exons and newly-identified novel exons. Claim 34 recites a compiling such alternative transcript, together with known isoforms, into an “isoform library.”
Brenner et al. already teaches this transcript-assembly step directly: Brenner et al.’s method uses “a transcript assembly protocol “(TAP, Kan et al., Genome Research 11:889-900 (2001), cited at Brenner, Description I ) specifically “to infer alternate mRNA splice forms form read alignments,” and states that “a given alternative isoform may be described in terms of a defined splice junction at a defined position, in terms of a particular truncation or excision (e.g., excision of exon X); in terms of a defined exon-exon splice junction, in terms of a recited nucleotide sequence, etc.” (Brenner, Description II). This is the assembly, from a mixture of canonical (RefSeq) exons and EST-supported novel splice junction, of a complete alternative-transcript sequence precisely the operation of claim 26-31. Brenner et al.’s compact-disk submitted “isoforms.altspl.fa” file, containing “sequence and splice site information for all alternative isoforms for the full set of 2226 genes analyzed (Brenner, Compact Disk Inventory), is Brenner et al.’s disclosed embodiment of claims 34’s “isoform library” --- “comprising one or more known mRNA isoforms and one or more alternative transcript defined from a novel exon.”
A PHOSITA combining Brenner et al.’s TAP- based transcript assembly with the novel-exon identification shown in claim 2, 15, 16, 17, 22, and 25 rejection (Brenner/Au/Rogers would apply TAP’s known assembly logic (splice known exons to newly identified exons at their shared boundary to Rogers- identified novel exons in exactly the manner claimed, for the same reason articulated in claim 2, 15, 16, 17, 22, and 25 rejection, the combination performs each element’s known function to yield the predictable result of a spliced full length alternative transcript sequence. (MPEP 2143(I)(A).
Claim 37 rejected under 35 U.S.C. 103 as unpatentable over Brenner et al. in view of Au et al. and Rogers et al. as applied to claims 1, 2, 9, 10, 14, 15, 16, 17, 20, 21, 22, and 25 and further in view of the general knowledge of a PHOSITA (MPEP 2144.04)
Brenner et al. in view of Au et al. and Rogers et al. are applied to claims 1, 2, 9, 10, 14, 15, 16, 17, 20, 21, 22, and 25 above.
Regarding claim 37:
Claim 37 adds limitation “generating a report comprising whether the biological sample included an alternative splicing event” for one or more genes.
Brenner et al.’s disclosed output already constitutes such a report in substance, a per-gene, per-sample tabulation of whether alternative splice pairs/isoforms were detected, presented in Brenner’s Figure 1 panel (b), (d), (e), (f) and the accompanying “Alt_and_NMD _isoform_list.txt” deliverable file, which lists, for the analyzed sample set, which genes exhibited alternative splicing. (Brenner, Description II, IV; Compact Disk Inventory). Formatting that same determination into an output “report” for a given biological sample is the automation of conventional data-presentation activity that a PHOSITA would find obvious as a matter of common sense and routine engineering, particularly where the underlying determination (does the sample show an alternative splicing event for a gene) is already computed by the combined method of Brenner/Au/Rogers (MPEP 2144.04(III) (automating a manual activity is generally obvious; KSR, 550 U.S. at 417 (“A person of ordinary skill is also a person of ordinary creativity, not an automation.”)
Claims 80 and 81 rejected under 35 U.S.C. 103 as unpatentable over Brenner et al. in view of Au et al. and Rogers et al. as applied to claims 1, 2, 9, 10, 14, 15, 16, 17, 20, 21, 22, and 25 and further in view of the general knowledge of a PHOSITA regarding generic computer implementation.
Claims 80 and 81 recite, respectively, a “computer system comprising one or more processors, and a non-transitory computer readable medium including computer executable instructions and a non-transitory computer readable storage medium having stored thereon program code instructions” each configured to cause a processor to perform the method of claim 1 (as amended to recite steps A-C in full. These claims had no limitation beyond claim 1’s method steps (addressed in combined rejections above other than reciting that the method is carried out by a generic computer system comprising a processor and non-transitory memory storage storing executable instructions.
Brenner et al.’s method is itself computer-implemented: the specification discloses source code “provided on compact disk… incorporated herein” specifically for “implementing this protocol” (Brenner, Description I, III; Compact Disk Inventory, col. 13, “src/” directory), confirming that Brenner et al.’s disclosed method is executed by a general purpose computer system loaded with storage program instructions i.e., “at least one processor and a memory storing at least one program for execution by the… processor,” as recited in claim 1’s preamble, and equally, “one or more processors” and a “non-transitory computer-readable medium including computer-executable instructions” as recited in claim 80 and 81.
To the extent Brenner et al. does not use the verbatim “non-transitory computer-readable medium” claim boilerplate, that generic system/medium framing for a bioinformatics splice-analysis algorithm was well- known and routine well before the relevant filing date, as reflected, for example, in contemporaneous bioinformatics patents claiming the same computational splice classification methods in parallel method/system/non-transitory computer readable medium claim sets (US 11, 488,009 B2, Cols, (reciting, for a splice site classification method, parallel claims to “a non-transitory computer readable storage medium storing instructions executable by a processor to perform the method, and a system including memory and one or more processors operable to execute instruction, is stored in the memory, to perform the method”. Reciting a known method (here, the Brenner/Au/Rogers combination) as a system claim or a computer readable medium claim, without any further limitation, is the obvious routine transposition of a method claim into a “means”/ “medium” claim form, using only conventional, genetic computer hardware elements (processors, non-transitory memory/storage) an obvious application of a known technique to a known method to yield the predictable result of a functionally equivalent system/medium claim. 2143 (I)(A), (B), KSR, 550 U.S. at 421 (“When a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”) (Here, substituting no new element at all, only reciting the environment in which the already-obvious method is carried out.
Conclusion
No claims are allowed.
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/A.H.K./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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