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 .
Status of the Claims
Claims 1-21 are pending and under consideration in this action.
Priority
The instant application is CON of PCT/US2021/047025, filed 8/20/2021, which claims priority to U.S. Provisional Application number 63/166,803, filed 3/26/2021 and U.S. Provisional Application number 63/166,829, filed 3/26/2021, as reflected in the filing receipt mailed 5/18/2022. The claim for domestic benefit for claims 1-21 is acknowledged. As such, the effective filing date of claims 1-21 is 3/26/2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 6/17/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: “470” in Fig. 4B is not described in the specification. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) 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.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
The sequences in Fig. 8A appear to correspond to SEQ IDs 34-51, however, the SEQ ID labels are missing in the figure. Applicant may remedy the deficiency by filing a replacement drawing for figure 8A or by amending the short description of the drawings for figure 8A to include the appropriate SEQ ID NO’s.
Claim Objections
Claims 5-7, 13-14 and 17 are objected to because of the following informalities:
Claim 5 recites the phrase “further comprises” in line 1 of the claim, which should be corrected to “further comprising” for clarity.
Claims 6 and 7 ends with a semicolon, which should be corrected to a period for clarity.
Claim 13 recites the phrase “by calculating a similarity score…” in line 5 of the claim, which should be corrected to “calculating a similarity score…” for clarity.
Claim 14 recites the phrase “comprises a combination of a promoter elements” in line 2 of the claim, which should be corrected to “comprises a combination of promoter elements” for clarity.
Claim 17 recites the phrase “by calculating a similarity score using…” in line 4 of the claim, which should be corrected to “calculating a similarity score using…” for clarity
Appropriate correction is required.
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 2-4, 6, 8-9, and 12-16, 18-19, and 21 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.
Claim 2 recites the limitation “the terminator codon for the gene” in line 11 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. This rejection can be overcome by amendment of claim 2 to recite “a terminator codon for the gene”.
Claim 3 recites the limitation “associated with the splicing site of the nucleotide string” in line 4 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. This rejection can be overcome by amendment of claim 3 to recite “associated with a splicing site of the nucleotide string”.
Regarding claims 4, 12-16, 18-19, and 21, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 6 recites the limitation “identifying…the splice silencer site comprising” in lines 6-7 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. This rejection can be overcome by amendment of claim 6 to recite “identifying…a splice silencer site comprising”.
Claim 8 recites the limitation “or cryptic versions thereof in the gene” in line 3 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. This rejection can be overcome by amendment of claim 8 to recite “or cryptic versions thereof in a gene”.
Claim 9 recites the limitation “on the tabular, gene structure or sequence view” in line 4 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. This rejection can be overcome by amendment of claim 9 to recite “on a tabular, gene structure or sequence view”.
Claim 12 recites the limitation “based on the PWM constructed from a multiple sequence alignment” in lines 3-4 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 1, to which this claim depends. For the purpose of compact prosecution, this claim will be interpreted to be dependent on claim 8, which contains the alignment of a position weight matrix (PWM); however, correction is respectfully requested.
Claim 16 recites the limitation “differentially weighted scores of the promoter elements and enhancers” in line 5 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 13, to which this claim depends. This rejection can be overcome by amendment of claim 16 to recite “differentially weighted scores of promoter elements and enhancers”.
Claim 18 recites the limitations “at least one of the true poly-A site…” and “in the display for the user” in lines 3-4 and 12 of the claim, respectively. There is insufficient antecedent basis for these limitations in the claim, since there is no prior mention of these phrases in claim 17, to which this claim depends. This rejection can be overcome by amendment of claim 18 to recite “at least one of a true poly-A site…” and “in a display for a user”.
Claim 19 recites the limitation “in the display for the user,” in line 9 of the claim. There is insufficient antecedent basis for this limitation in the claim, since there is no prior mention of this phrase in claim 17, to which this claim depends. This rejection can be overcome by amendment of claim 19 to recite “in a display for a user”.
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 1-21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite both (1) mathematical concepts (mathematical relationships, formulas or equations, or mathematical calculations) and (2) mental processes, i.e., concepts performed in the human mind (including observations, evaluations, judgements or opinions) (see MPEP § 2106.04(a)).
Step 1:
In the instant application, claims 1-21 are directed towards a method, which falls into one of the categories of statutory subject matter (Step 1: YES).
Step 2A, Prong One:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) 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 One). The following instant claims recite limitations that equate to one or more categories of judicial exceptions:
Claim 1 recites a mental process (i.e., an evaluation of a nucleotide string) in “identifying, in a nucleotide string, at least two exons, at least one acceptor, at least one donor, and at least one intron between the at least two exons”, a mental process (i.e., an evaluation of a nucleotide sequence and a comparison of similarity scores) in “identifying, in the nucleotide string, a cryptic splice site comprising a sequence of nucleotides based on a similarity score with the at least one of the acceptor or donor”; and a mental process (i.e., an observation of a location on a display and a comparison of the similarity score with a threshold) in “graphically marking, the nucleotide string at a location indicative of the at least two exons, the at least one intron, a true splice site, or a cryptic splice site when the similarity score is higher or lower than, or equal to, a pre-selected threshold”.
Claim 2 recites a mental process (i.e., an evaluation of a nucleotide string to determine exons, open reading frames, branch points, or mutations) in “identifying, in the nucleotide string, a first exon that lacks the at least one acceptor and contains the at least one donor”, “identifying, in the first exon, an open reading frame between an initiator codon for a gene and a first splice junction within the at least one donor”, “identifying an open reading frame between a subsequent splice junction within the at least one acceptor and at least one donor, as a middle exon for a gene”, “identifying, in the nucleotide string, a last exon that contains the at least one acceptor and lacks the at least one donor, with an open reading frame between the splice junction within the at least one acceptor and the terminator codon for the gene”, “identifying, in the nucleotide string, a branch point within the at least one intron, wherein the branch point is associated with a splicing site of the nucleotide string to combine the at least two exons”, and “identifying, in the nucleotide string, a mutation, wherein the mutation comprises a modification in the at least two exons, the at least one intron, the at least one acceptor or the at least one donor, or a branch point, enhancer or silencer”; and a mental process (i.e., an observation of data on the display) in “graphically marking, the mutation in the nucleotide string, gene structure or sequence view of the display”.
Claim 3 recites a mental process (i.e., an evaluation the splicing site of a nucleotide string) in “identifying, in the nucleotide string, a cryptic branch point, enhancer, or a silencer within the at least two exons or at least one intron, wherein the cryptic branch point, enhancer, or silencer is associated with the splicing site of the nucleotide string to combine the at least two exons”.
Claim 4 recites a mathematical calculation (i.e., calculating a similarity sore using an algorithm) in “wherein the similarity scores are computed from one of: a) determining the similarity score of an element by executing instructions from an algorithm selected from a group consisting of algorithms such as Shapiro-Senapathy algorithm, a MaxEntScan algorithm, and NNSplice algorithm; b) determining the similarity score of an element by executing instructions from a modified algorithm selected from a group consisting of algorithms such as Shapiro-Senapathy algorithm, a MaxEntScan algorithm, and NNSplice algorithm, stored in a memory, based on characteristics of splicing element sequence signals such as length or variability; c) determining a combined score of the group of algorithms based on corresponding average or differentially weighted scores”.
Claim 5 recites a mental process (i.e., evaluation of the nucleotide string to determine a cryptic exon, cryptic branch point, cryptic splice enhancer site or cryptic splice silencer site or a comparison of scores to thresholds) in “identifying, in the nucleotide string, a cryptic exon that comprises at least one cryptic acceptor and one cryptic donor or an open reading frame, between the cryptic acceptor and the cryptic donor, when a cryptic splice site score is higher or lower than, or equal to, a pre-selected threshold, and a length of the cryptic exon conforms to a preselected threshold”, “identifying a cryptic branch point upstream of the cryptic exon”, “identifying a cryptic splice enhancer site within, upstream, or downstream of the cryptic exon”, and “identifying a cryptic splice silencer site within, upstream, or downstream of the cryptic exon”.
Claim 6 recites a mental process (i.e., an evaluation of binding sites to determine splice enhancer or silencer sites) in “identifying, within the at least two exons or the at least one intron, a splice enhancer site comprising a binding site for a spliceosome enhancer factor that promotes a splicing of the at least two exons of a gene, wherein the gene comprises at least a portion of the at least two exons and the at least one intron” and “identifying, within the at least two exons or the at least one intron, the splice silencer site comprising a binding site for an inhibitor factor that suppresses a splicing of at least two exons of the gene”.
Claim 7 recites a mathematical calculation in “determining a deleteriousness score of a mutation of the true or the cryptic splice site, a branch point site, enhancers, or silencers, based on variability in the similarity score, relative to a reference sequence”.
Claim 8 recites a mental process (i.e., an evaluation of a sequence alignment to determine a distinct PWM or variable sequence signature) in “determining a distinct PWM or variable sequence signature for a distinct splicing element, or regulatory element within the gene, based on a multiple sequence alignment within the gene or genome sequences of numerous individuals from a species or a group of organisms consisting of similar species”.
Claim 9 recites a mental process (i.e., an observation of data on a display and a comparison of the similarity score with a threshold) in “graphically marking, a true or a cryptic exon, splicing elements or motifs, when the similarity score is higher or lower than, or equal to, a preselected threshold, on the tabular, gene structure or sequence view”.
Claim 10 recites a mathematical calculation in “determining an exon score as an average of scores or differentially weighted scores of the at least one acceptor and the at least one donor, branch point site, or splicing enhancers, and subtracting the average of the scores or the differentially weighted scores of splicing silencers”.
Claim 11 recites a mathematical concept in “modifying a Shapiro Senapathy algorithm based on a position weight matrix (PWM) or variable sequence signature for a genetic element constructed from mono, di, tri, or longer oligo-nucleotides”.
Claim 12 recites a mental process (i.e., an evaluation of a PWM from a sequence alignment to determine genetic elements) in “predicting novel genetic elements such as promoters, recognition sequences, binding sites or regulatory and splicing elements, based on the PWM constructed from a multiple sequence alignment of a nucleotide sequence at a specific chromosomal position in genomes from multiple individuals of a same organism”; and mental process (i.e., an evaluation of the PWM or statistical characteristics of a region compared to random) in “wherein the novel elements show variable nucleotide frequencies that exhibit non-random characteristics indicative of the PWM of genuine functional genetic elements, or statistically distinct characteristics indicative of functional regions, compared to random nucleotide positions”.
Claim 13 recites a mental process (i.e., an evaluation of a nucleotide string) in “identifying, in a nucleotide string, a true gene transcriptional regulatory element such as a promoter sequence comprising at least one of a TATA box, a CAAT box, a GC box or a transcription initiator box, or a transcription termination site”; a mathematical calculation in “by calculating a similarity score using a position weight matrix (PWM) based on a sequence length or variability of a gene transcriptional regulatory element”; a mental process (i.e., an evaluation of the similarity score to determine a score) in “associating a score to the gene transcriptional regulatory element based on the corresponding similarity score”; and a mental process (i.e., an observation of data on a display and a comparison of the similarity score with a threshold) in “graphically marking using graphical notations, the nucleotide string at a location indicative of the gene transcriptional regulatory element when the score is higher or lower than, or equal to, a preselected threshold”.
Claim 14 recites a mental process (i.e., an evaluation of the promoter elements) in “identifying a promoter motif that comprises a combination of a promoter elements such as the TATA box, the CAAT box, the GC box, or the transcription initiator box”; a mental process (i.e., an evaluation of the promoter box) in “identifying a cryptic version of a promoter box, motif or other elements such as enhancer or a silencer”; and mathematical calculations (i.e., determining a score) in “determining and assigning a score to the promoter motif based on combined or variably weighted scores of individual elements of the promoter motif” and “determining and assigning scores for various genetic element motifs such as splicing motifs (donor, acceptor, exon motifs), initiator motifs, enhancer or silencer motifs, and termination motifs”.
Claim 15 recites a mental process (i.e., an evaluation of promoter elements/motifs) in “identifying mutations within promoter elements or promoter motifs”; a mental process (i.e., an evaluation of score differences in mutated elements/motifs) in “determining a deleteriousness of the mutations, or alterations in binding strengths of the mutated promoter elements or motifs, based on score differences between normal elements or motifs, and the mutated elements or motifs”; a mental process (i.e., evaluating the output of an algorithm to identify elements/motifs) in “identifying the promoter elements or promoter motifs in a nucleotide string by modifying a Shapiro Senapathy algorithm, MaxEntScan algorithm, or NNSplice algorithm based on di, tri, or longer oligo-nucleotides”; and a mental process (i.e., an evaluation of genetic motifs) in “determining the deleteriousness of mutations in various genetic motifs such as splicing motifs, initiator motifs, enhancer or silencer motifs, and termination motifs”.
Claim 16 recites a mental process (i.e., an evaluation of genetic elements to determine a score) in “assigning a score to a functional genetic element such as a TATA box, CAAT box, GC box, Initiator box, donor, acceptor or poly A site or signal”; a mathematical calculation in “determining a score for a promoter complex, as an average of scores or differentially weighted scores of the promoter elements and enhancers, and subtracting the average of the scores or the differentially weighted scores of silencer elements”; and a mental process (i.e., an evaluation of motifs to determine scores) in “determining and assigning scores for various genetic regulatory or splicing regulatory or splicing motifs such as splicing motifs comprising donor, acceptor, exon motifs, initiator motifs, enhancer or silencer motifs, or termination motifs”.
Claim 17 recites a mental process (i.e., an evaluation of a nucleotide string) in “identifying, in a nucleotide string, a poly-A addition site, a signal, enhancer, silencer, or a Kozak sequence”; a mathematical calculation in “by calculating a similarity score using a position weight matrix (PWM) based on a sequence length and variability of the poly-A addition site, signal, enhancer, silencer, or the Kozak sequence”; and a mental process (i.e., an evaluation of the similarity scores) in “associating a score to the respective element based on the similarity score”.
Claim 18 recites a mental process (i.e., an evaluation of sequences or motifs in a nucleotide string) in “identifying, within the nucleotide string, a cryptic poly-A site, signal, enhancer, silencer, a Kozak sequence, a sequence of nucleotides resembling at least one of the true poly-A site, signal, enhancer, silencer, or the Kozak sequence”, “identifying, in the nucleotide string, a poly A motif comprising a combination of a poly A site, the signal, the enhancer, and the silencer”, and “identifying, in the nucleotide string, a Kozak motif comprising a combination of surrounding elements such as the enhancer, and the silencer”; a mathematical concept in “determining and assigning a score to the poly A motif comprising a combination of the poly A site, signal, enhancer, silencer, or Kozak sequence based on combined or variably weighted scores of individual elements of the poly A motif”; and a mental process (i.e., an observation of data on a display) in “graphically marking, the poly A elements or motifs, and Kozak elements or motifs”.
Claim 19 recites a mental process (i.e., an evaluation of the similarity score to determine a mutation) in “identifying a mutation of a true or a cryptic translational regulatory element such as the poly A site, a signal, enhancer, silencer, or Kozak sequence, based on a difference between the similarity score of an original element and a mutated element”; and a mental process (i.e., an evaluation of score differences to determine deleteriousness of a mutation) in “determining a deleteriousness of the mutation, or alteration in binding strength of a mutated translational regulatory element comprising an element or motif, based on a range of score difference between a normal element or motif and the mutated element or motif”; and a mental process (i.e., an observation of data on a display) in “graphically marking, the mutation in the nucleotide string, in gene structure or sequence view”.
Claim 20 recites a mental process (i.e., evaluating the output of an algorithm to identify elements/motifs) in “identifying a poly A or Kozak element or motif in a nucleotide string by modifying a Shapiro Senapathy, MaxEntScan, NNSplice or other algorithms based on di, tri, or longer oligo-nucleotides”.
Claim 21 recites a mental process (i.e., an evaluation of an element to assign a score) in “assigning a score to a functional genetic element”; and mathematical calculations in “determining a score for a poly A motif, as an average of scores, or differentially weighted scores of a plurality of poly A elements such as poly-A signals, sites, enhancers, and subtracting the average of the scores or the differentially weighted scores of silencer elements” and “determining a score for a Kozak motif, as an average of scores, or differentially weighted scores of a plurality of Kozak elements including enhancers, and subtracting the average of the scores or the differentially weighted scores of the silencer elements”.
These recitations are similar to the concepts of collecting information, and displaying certain results of the collection and analysis is Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)), and organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships.
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification, and are determined to be directed to mental processes that in the simplest embodiments are not too complex to practically perform in the human mind. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. The instant claims must therefore be examined further to determine whether they integrate the abstract idea into a practical application (Step 2A, Prong One: YES).
Step 2A, Prong Two:
In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a 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)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP § 2106.04(d)(III)). The following claims recite limitations that equate to additional elements:
Claims 1, 2, 9, 13, and 18-19 recite “in a display for a user”.
Claim 4 further recites “stored in memory”
Claim 8 further recites “aligning a plurality of nucleotides from regular, uncommon or unusual regulatory or splicing elements, or cryptic versions thereof in the gene from a plurality of individuals from a same organism to create a recognizable pattern of a position weight matrix (PWM) including invariable or a variable nucleotides of the plurality of nucleotides at a given sequence position of a particular element in a particular gene” and “creating a database of the distinct PWMs or variable sequence signatures for one or more elements from a genome of an organism”.
Regarding the above cited limitations in claims 1, 2, 4, 9, 13, and 18-19 of (i) in a display for a user; and (ii) stored in memory. These limitations require only a generic computer component, which does not improve computer technology. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitations in claim 8 of (iii) aligning a plurality of nucleotides from regular, uncommon or unusual regulatory or splicing elements, or cryptic versions thereof in the gene from a plurality of individuals from a same organism to create a recognizable pattern of a position weight matrix (PWM) including invariable or a variable nucleotides of the plurality of nucleotides at a given sequence position of a particular element in a particular gene; and (iv) creating a database of the distinct PWMs or variable sequence signatures for one or more elements from a genome of an organism. These limitations equate to insignificant, extra-solution activity of mere data gathering because these limitations gather data before or after the recited judicial exceptions of graphically marking the nucleotide string at a location indicative of the at least two exons, the at least one intron, a true splice site, or a cryptic splice site (claim 1) (see MPEP § 2106.04(d)). As such, claims 1-21 are directed to an abstract idea (Step 2A, Prong Two: NO).
Step 2B:
Claims found to be directed to 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 well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite same additional elements described in Step 2A, Prong Two above.
Regarding the above cited limitations in claims 1, 2, 4, 9, 13, and 18-19 of (i) in a display for a user; and (ii) stored in memory. These limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept (see MPEP § 2106.05(d) and MPEP § 2106.05(f)).
Regarding the above cited limitations in claim 8 of (iii) aligning a plurality of nucleotides from regular, uncommon or unusual regulatory or splicing elements, or cryptic versions thereof in the gene from a plurality of individuals from a same organism to create a recognizable pattern of a position weight matrix (PWM) including invariable or a variable nucleotides of the plurality of nucleotides at a given sequence position of a particular element in a particular gene; and (iv) creating a database of the distinct PWMs or variable sequence signatures for one or more elements from a genome of an organism. These limitations when viewed individually and in combination, are WURC limitations as taught by Rogan et al. (U.S. Patent Application Publication US 2018/0051326 A1). Rogan et al. discloses the sequence logo and weight matrices of splicing regulatory sequence binding sites within a reference genome, wherein the sequences are aligned prior to the calculation of the PWMs (limitation (iii)) (Fig. 11, and Para. [0061]). Rogan et al. also discloses the creation of a database containing distributions of annotated exons, wherein the PWMs were incorporated into the computation of a cumulative information value for a binding site contributing to exon recognition (limitation (iv)) (Para. [0005], [0034], and [0059-0061]).
These 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 instant claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-21 are not patent eligible.
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 1-4, 6, and 9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by de Boer et al. (Activation of cryptic splice sites in three patients with chronic granulomatous disease. Mol. Genet Genomic Med. 7(9): e854 (2019); published 7/30/2019).
Regarding claim 1, de Boer et al. teaches the schematic representation of the CYBB wild type (WT) sequence in Fig. 1A. The figure shows two exons (exons 6 and 7) with an intron between them (intron 6). The locations of the acceptor, donor, and cryptic donor splice sites are shown in green (i.e., identifying, in a nucleotide string, at least two exons, at least one acceptor, at least one donor, and at least one intron between the at least two exons and identifying, in the nucleotide string, a cryptic splice site comprising a sequence of nucleotides) (Pg. 5, Fig. 1A). de Boer et al. further teaches an example case where the Analyser Splice Tool indicated a score (i.e., the similarity score) for the WT CYBA exon 1 donor splice site of 70.4, but this was decreased by the mutation to below threshold. For this reason, the cryptic donor splice site in intron 1, with a score of 71.3, was preferred (i.e., identifying, in the nucleotide string, a cryptic splice site based on a similarity score with the at least one of the donor) (Pg. 5, Col. 1, Para. 2 and Pg. 4, Table 1). de Boer et al. further teaches a graphical rendering of the nucleotide string, which highlights the two exons, one intron, true splice site (the donor site in the WT), and the cryptic splice site (i.e., graphically marking, the nucleotide string at a location indicative of the at least two exons, the at least one intron, a true splice site, or a cryptic splice site) (Pg. 5, Fig. 1A). de Boer et al. further teaches the use of in silico prediction tools (i.e., on a computer which contains a display for a user) (Pg. 3, Col. 1, Para. 4 – Col. 2, Para. 1). de Boer et al. further teaches that the Analyser Splice tool compared the scores (i.e., the similarity score) to a threshold, and identified the cryptic donor site (i.e., marking a cryptic splice site when the similarity score is higher or lower than, or equal to, a pre-selected threshold) (Pg. 5, Col. 1, Para. 2).
Regarding claim 2, de Boer et al. teaches an example wherein the mutant sequence, the donor is located in exon 6, and the acceptor is located at the junction between intron 6 and exon 7 (i.e., identifying, in the nucleotide string, a first exon that lacks the at least one acceptor and contains the at least one donor) (Pg. 5, Fig. 1A). de Boer et al. further teaches an example wherein a one-nucleotide deletion in exon 4 induces a shift in the reading frame that predicts termination of protein synthesis 108 codons downstream (Pg. 5, Col. 2, Para. 5 and Pg. 7, Fig. 1C). Fig. 1A shows an example that highlights the splice junction between the exons and introns (Pg. 5, Fig. 1A), while Fig. 1C shows the cDNA on the protein level, indicating the codons corresponding to initiation and termination (i.e., identifying, in the first exon, an open reading frame between an initiator codon for a gene and a first splice junction with the at least one donor) (Pg. 7, Fig. 1C). In this example, exon 5 is included as a middle exon between the donor and the acceptor (i.e., identifying an open reading frame between a subsequent splice junction within the at least one acceptor and at least one donor, as a middle exon for a gene) (Pg. 7, Fig. 1C). de Boer et al. further teaches an example of a mutant sequence where exon 7 is the last exon, containing the acceptor, but not the donor. On the cDNA and protein level, the terminator codon corresponds with the acceptor located in the splicing junction between intron 6 and exon 7 (i.e., identifying, in the nucleotide string, a last exon that contains the at least one acceptor and lacks the at least one donor, with an open reading frame between the splice junction within the at least one acceptor and the terminator codon for the gene) (Pg. 5, Fig. 1A). de Boer et al. further teaches an example where in the mutant allele of a patient, the mutation/splice site in intron 4 causes the insertion of 14 intronic nucleotides into exon 5 (i.e., identifying, in the nucleotide string, a branch point within the at least one intron, wherein the branch point is associated with a splicing site of the nucleotide string to combine the at least two exons) (Pg. 7, Fig. 1D). de Boer et al. further teaches an example with a mutation shown in red in Exon 6, changing the donor site compared to the WT sequence (i.e., identifying, in the nucleotide string, a mutation, wherein the mutation comprises a modification in the at least two exons, the at least one intron, the at least one acceptor or the at least one donor, or a branch point, enhancer or silencer) (Pg. 5, Fig. 1A). de Boer et al. further teaches a graphical rendering of the mutated nucleotide string, highlighting the mutation in red (i.e., graphically marking, the mutation in the nucleotide string, sequence view of the display) (Pg. 5, Fig. 1A). de Boer et al. further teaches the limitation of in the display for the user as described for claim 1 above.
Regarding claim 3, de Boer et al. teaches that for the new acceptor splice site in patient 3, Hexplorer predicted about 60% enhanced exonic splicing enhancer (ESE) binding in the most 5' region of the new exon (Pg. 5, Col. 2, Para. 2). The nucleotide string for patient 3 is shown in Fig. 1D, and contains 2 exons and 1 intron (i.e., identifying, in the nucleotide string, an enhancer within the at least two exons or at least one intron, wherein the enhancer is associated with the splicing site of the nucleotide string to combine the at least two exons) (Pg. 7, Fig. 1D).
Regarding claim 4, de Boer et al. teaches the use of several software packages to analyze possible splice sites, including MaxEntScan and NNSPLICE (i.e., determining the similarity score of an element by executing instructions from an algorithm selected from a group consisting of algorithms such as a MaxEntScan algorithm and NNSplice algorithm) (Pg. 3, Col. 2, Para. 1 and Pg. 4, Table 1). de Boer et al. further teaches that the method was performed on a computer, as described for claim 1 above (i.e., stored in memory).
Regarding claim 6, de Boer et al. teaches that the scores for splicing enhancer and silence binding sites were evaluated for the WT and mutant sequences (Pg. 7, Col. 1, Para. 1 and Pg. 4, Table 1). The sequences contain at least two exons and one intron (i.e., identifying, within the at least two exons or the at least one intron, a splice enhancer site comprising a binding site for a spliceosome enhancer factor that promotes a splicing of the at least two exons of a gene, wherein the gene comprises at least a portion of the at least two exons and the at least one intron and, and identifying, within the at least two exons or the at least one intron, the splice silencer site comprising a binding site for an inhibitor factor that suppresses a splicing of at least two exons of the gene) (Pg. 5, Fig. 1A).
Regarding claim 9, de Boer et al. teaches a graphical representation of DNA in a patient, containing exons, introns, mutations, and cryptic donor splice sites. Both the genomic level sequences and the protein level sequences are shown (i.e., graphically marking, a true exon, splicing elements or motifs on the gene structure or sequence view). de Boer et al. further teaches the limitations of in the display for the user and when the similarity score is higher or lower than, or equal to, a preselected threshold, as described for claim 1 above.
Therefore, de Boer et al. teaches all the limitations in claims 1-4, 6, and 9.
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.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over de Boer et al. as applied to claims 1-4, 6, and 9 above, and further in view of Desmet et al. (Bioinformatics identification of splice site signals and prediction of mutation effects. In Research Advances in Nucleic Acids Research, RM Mohan, Global Research Network Publishers, pp.1-14 (2010); published online 12/21/2017).
Regarding claim 5, de Boer et al. teaches that the scores for splicing enhancer and silence binding sites were evaluated for the WT and mutant sequences (Pg. 7, Col. 1, Para. 1 and Pg. 4, Table 1). The Sroogle algorithm was used to determine the number and position of putative exonic splicing enhancer (PESE) and silencer (PESS) motifs in the complete exon 6, the 5' part (c.484_617) and the 3' part (c.618_684) of this exon. This showed that the 5' part (upstream of the cryptic donor splice site) had a much higher putative exonic splicing enhancer (PESE) and silencer (PESS) motifs (PESE:PESS) ratio than the 3' part, which thus favored skipping of the 3' part from the mature mRNA (i.e., identifying a cryptic splice enhancer site within, upstream, or downstream of the cryptic exon and identifying a cryptic splice silencer site within, upstream, or downstream of the cryptic exon) (Pg. 3, Col. 2, Para. 5).
De Boer et al., as applied to claims 1-4, 6, and 9 above, does not teach identifying, in the nucleotide string, a cryptic exon that comprises at least one cryptic acceptor and one cryptic donor or an open reading frame, between the cryptic acceptor and the cryptic donor, when a cryptic splice site score is higher or lower than, or equal to, a pre-selected threshold, and a length of the cryptic exon conforms to a preselected threshold; and identifying a cryptic branch point upstream of a the cryptic exon.
Regarding claim 5, Desmet et al. teaches the prediction of the activation of cryptic exons from deep intronic mutations (Abstract). The intronic mutations are located in the intron, between the donor splice site and the acceptor splice site (i.e., identifying, in the nucleotide string, a cryptic exon that comprises at least one cryptic acceptor and one cryptic donor or an open reading frame, between the cryptic acceptor and the cryptic donor) (Pg. 4, Fig. 1). Desmet et al. further teaches the scoring of splicing sites using several algorithms. The Senapathy and Shapiro algorithm defines position weight matrices (PMW), which are based upon sequence alignments. Application software based on PWM processes a given sequence into short sequences (whose length is equal to that of the 5’ or the 3’ splice site). A weight is then attributed to each nucleotide according to its position within the PWM. If the sum of the consecutive nucleotides weights is superior or equal to a specific threshold, a motif is consequently detected (i.e., when a cryptic splice site score is higher or lower than, or equal to a preselected threshold) (Pg. 2, Col. 2, Para. 2). Desmet et al. further teaches that the algorithm analyzes mutations in the splice sites, branch points and exons based on specific positions (i.e., a length of the cryptic exon conforms to a preselected threshold) (Pg. 3, Col. 2, Para. 4 and Pg. 4, Fig. 1). Desmet et al. further teaches the identification of branch points upstream of the cryptic exon (i.e., identifying a cryptic branch point upstream of the cryptic exon) (Pg. 4, Fig. 1).
Therefore, regarding claim 5, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of analyzing cryptic splice sites of de Boer et al. with the teachings of Desmet et al. because accurately and efficiently predicting the effects of sequence variation on splice site recognition is crucial in the diagnosis of human genetic diseases (Desmet et al., Pg. 3, Col.2, Para. 3). One of ordinary skill in the art would be able to combine the teachings of de Boer et al. with Desmet et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for analyzing the effect of mutations on splice sites. Therefore, regarding claim 5, the instant invention is prima facie obvious (MPEP § 2142).
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over de Boer et al. as applied to claims 1-4, 6, and 9 above, and further in view of Jaganathan et al. (Predicting Splicing from Primary Sequence with Deep Learning. Cell. 176(3): 535-548.e24 (2019); published 1/24/2019).
De Boer et al., as applied to claims 1-4, 6, and 9 above, does not teach determining a deleteriousness score of a mutation of the true or the cryptic splice site, a branch point site, enhancers, or silencers, based on variability in the similarity score, relative to a reference sequence.
Regarding claim 7, Jaganathan et al. teaches the calculation of a Δ score for the splicing change due a single nucleotide variant. The calculation compares acceptor and donor scores of the mutant to a reference nucleotide (Pg. e5, Δ Score of a single nucleotide variant). Jaganathan et al. further teaches that predicted cryptic splice variants are strongly deleterious in human populations based on Δ scores greater than 0.8 (i.e., determining a deleteriousness score of a mutation of the true or the cryptic splice site based on variability in the similarity score relative to a reference sequence) (Pg. 542, Fig. 4).
Therefore, regarding claim 7, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of analyzing cryptic splice sites of de Boer et al. with the calculation of a deleteriousness score of Jaganathan et al. because the deep learning method of Jaganathan et al. accurately predicts cryptic splice mutations, which are strongly deleterious in the human population and a major cause of rare genetic diseases (Jaganathan et al., Pg. 545, Col. 2, Para. 1). One of ordinary skill in the art would be able to combine the teachings of de Boer et al. with Jaganathan et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for analyzing the effect of mutations on splice sites. Therefore, regarding claim 7, the instant invention is prima facie obvious (MPEP § 2142).
Claims 8, 10 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over de Boer et al. as applied to claims 1-4, 6, and 9 above, and further in view of Rogan et al. (U.S. Patent Application Publication US 2018/0051326 A1; published 2/22/2018; provided in the IDS dated 6/17/2022).
De Boer et al., as applied to claims 1-4, 6, and 9 above, does not teach aligning a plurality of nucleotides from regular, uncommon or unusual regulatory or splicing elements, or cryptic versions thereof in the gene from a plurality of individuals from a same organism to create a recognizable pattern of a position weight matrix (PWM) including invariable or a variable nucleotides of the plurality of nucleotides at a given sequence position of a particular element in a particular gene; determining a distinct PWM or variable sequence signature for a distinct splicing element, or regulatory element within the gene, based on a multiple sequence alignment within the gene or genome sequences of numerous individuals from a species or a group of organisms consisting of similar species; creating a database of the distinct PWMs or variable sequence signatures for one or more elements from a genome of an organism; determining an exon score as an average of scores or differentially weighted scores of the at least one acceptor and the at least one donor, branch point site, or splicing enhancers, and subtracting the average of the scores or the differentially weighted scores of splicing silencers; and predicting novel genetic elements such as promoters, recognition sequences, binding sites or regulatory and splicing elements, based on the PWM constructed from a multiple sequence alignment of a nucleotide sequence at a specific chromosomal position in genomes from multiple individuals of a same organism, wherein the novel elements show variable nucleotide frequencies that exhibit non-random characteristics indicative of the PWM of genuine functional genetic elements, or statistically distinct characteristics indicative of functional regions, compared to random nucleotide positions.
Regarding claim 8, Rogan et al. teaches the sequence logo and weight matrices of splicing regulatory sequence binding sites within a reference genome. The sequences are aligned prior to the calculation of sequence logo plots or position weight matrices (PWM) (i.e., aligning a plurality of nucleotides from regular, uncommon or unusual regulatory or splicing elements, or cryptic versions thereof in the gene from a plurality of individuals from a same organism to create a recognizable pattern of a position weight matrix (PWM) including invariable or a variable nucleotides of the plurality of nucleotides at a given sequence position of a particular element in a particular gene) (Fig. 11 and Para. [0061]). Rogan et al. further teaches the sequence logo plots and position weight matrices for several types of regulatory enhancers in the reference genome, including ASF/SF2 (SRSF1), SC35 (SRSF2), SRp40 (SRSF5), SRp55 (SRSF6) and hRNP-H (HRNPH). Each enhancer type has its own unique sequence pattern and PWM (Fig. 11 and Para. [0061]). Rogan et al. further teaches that after scanning the reference genome and locating all predicted binding sites with the SF2/ASF and SC35 matrices, their distributions were determined separately for intronic and exonic binding sites in closest proximity to adjacent constitutive splice sites (i.e., determining a distinct PWM or variable sequence signature for a distinct splicing element, or regulatory element within the gene, based on a multiple sequence alignment within the gene or genome sequences of numerous individuals from a species or a group of organisms consisting of similar species) (Para. [0061]). Rogan et al. further teaches the creation of the annotation database containing distributions of annotated exons. The PWMs were incorporated into the computation of Ri,total (the cumulative information content values of each of these distinct binding sites contributing to exon recognition) for the various regulatory sequences, and the Ri,total is part of the annotation database (i.e., creating a database of the distinct PWMs or variable sequence signatures for one or more elements from a genome of an organism) (Para. [0005], [0034], and [0059-0061]).
Regarding claim 10, Rogan et al. teaches the total information content of an exon, Ri,total, is the sum of the information contents of its corresponding acceptor and donor splice sites, adjusted for the self-information of the exon length (Abstract). The total exon information content (Ri,total) can be adjusted by the gap surprisal value if either the predicted exon length is suboptimal or splice site pairs are derived from different exons (Para. [0010]). The gap surprisal penalty was then normalized so that the most common internal exon length was zero bits, by subtracting a value of 6.59 bits (i.e., determining an exon score as an average of scores or differentially weighted scores of the at least one acceptor and the at least one donor, and subtracting the average of the scores) (Para. [0083]).
Regarding claim 12, Rogan et al. teaches a methodology that predicts cryptic and exon skipping isoforms in mRNA produced by splicing mutations from the combined information contents and the distribution of the splice sites and other regulatory binding sites defining these exons (i.e., predicting novel genetic elements such as promoters, recognition sequences, binding sites or regulatory and splicing elements) (Abstract). Rogan et al. further teaches the effects of mutations are taken into account by correcting the total information content (Ri,total) by changes in strengths of the binding sites and by applying a gap surprisal term to the computation, wherein the gap surprisal may be determined by scanning the genome for binding sites of said binding protein with a position weight matrices (PWM) to determine the frequency of each interval length between known natural sites and the nearest binding site for said RNA binding protein, separately for exons and introns (i.e., based on the PWM constructed from a multiple sequence alignment of a nucleotide sequence at a specific chromosomal position in genomes from multiple individuals of a same organism) (Para. [0033]). Rogan et al. further teaches distinct sequences and PWM for different regulatory sequence binding sites (i.e., wherein the novel elements show variable nucleotide frequencies that exhibit non-random characteristics indicative of the PWM of genuine functional genetic elements, or statistically distinct characteristics indicative of functional regions, compared to random nucleotide positions) (Fig. 11).
Therefore, regarding claims 8, 10, and 12, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of analyzing cryptic splice sites of de Boer et al. with the teachings of Rogan et al. because the method of Rogan et al. streamlines the assessment of abnormal and normal splice isoforms resulting from splicing mutations (Rogan et al., Para. [0002]). One of ordinary skill in the art would be able to combine the teachings of de Boer et al. with Rogan et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method of analyzing cryptic splice sites. Therefore, regarding claims 8, 10 and 12, the instant invention is prima facie obvious (MPEP § 2142).
Claims 11, 17, and 20 are rejected under 35 U.S.C. 103 as being unpatentable over de Boer et al. as applied to claims 1-4, 6, and 9 above, and further in view of Beroud et al. (Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Research. 37(9): e67 (2009); published 4/1/2009).
Regarding claim 17, de Boer et al. teaches that the translation termination codon in the mutated CYBA mRNA of patient 2 lies within the poly‐adenylation signal in the 3' UTR (Pg. 7, Col. 2, Para. 2 – Pg. 8, Col. 1, Para. 1). de Boer et al. further teaches the scoring of splicing enhancers and silencers in the nucleotide sequence (i.e., identifying, in a nucleotide string, a poly-A addition site, enhancer, or silencer) (Pg. 11, Fig. 4). de Boer et al. further teaches that the scores associated with mutations, branch point calculations, enhancers, and silencers are found in Table 1 for the three patients (i.e., associating a score to the respective element based on the similarity score) (Pg. 4, Table 1).
Regarding claim 20, de Boer et al. teaches the limitation of identifying a poly A motif in a nucleotide string as described for claim 17 above.
de Boer et al., as applied to claims 1-4, 6, and 9 above, does not teach modifying a Shapiro Senapathy algorithm based on a position weight matrix (PWM) or variable sequence signature for a genetic element constructed from mono, di, tri, or longer oligo-nucleotides; calculating a similarity score using a position weight matrix (PWM) based on a sequence length and variability of the poly-A addition site, signal, enhancer, silencer, or the Kozak sequence; and modifying a Shapiro Senapathy, MaxEntScan, NNSplice or other algorithms based on di, tri, or longer oligo-nucleotides.
Regarding claim 11, Beroud et al. teaches the development of the Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence (Abstract). Beroud et al. further teaches the weight matrices of Shapiro and Senapathy were used to predict the 5' and 3' splice points. A potential splice site is defined as an n-mer sequence. The strength of a site is thus defined as the sum of each nucleotide’s weight plus a constant that is used for normalization. Only n-mer sequences with consensus values (CV) higher or equal to a given threshold are considered as potential 5' or 3' splice sites (i.e., modifying a Shapiro Senapathy algorithm based a position weight matrix (PWM) or variable sequence signature for a genetic element constructed from mono, di, tri, or longer oligo-nucleotides) (Pg. 2, Col. 2, Para. 3).
Regarding claim 17, Beroud et al. teaches the calculation of the strength of the site, wherein only sequences with consensus values (i.e., similarity score) higher than a threshold are considered for potential sites. The calculation is based on a weight of each nucleotide based on its frequency and the relative importance of its position in the sequence motif using position weight matrices (PWM). Calculation of the strength for a splice site uses a 9-mer or 14-mer matrix (i.e., calculating a similarity score using a position weight matrix (PWM) based on a sequence length) (Pg. 2, Col. 2, Para. 3-4). Beroud et al. further teaches the weight matrices are variable for different proteins, enhancers, or silencers involved in splicing (i.e., based on variability of the enhancer, or silencer) (Pg. 3, Col. 1, Para. 4-5 and Fig. 1, Pg. 3, Fig. 2).
Regarding claim 20, Beroud et al. teaches the limitation of modifying a Shapiro Senapathy algorithm based on di, tri, or longer oligo-nucleotides as described for claim 11 above.
Therefore, regarding claims 11, 17 and 20, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of analyzing cryptic splice sites of de Boer et al. with the teachings of Beroud et al. because the HSF algorithm of Beroud et al. efficiently predicts a variety of cryptic splice site predictions, including mutations at both the penultimate and the last nucleotide of an exon, as well as exonic mutations that activate a cryptic splice site leading to partial exonic deletion (Beroud et al., Pg. 10, Col. 1, Para. 2). One of ordinary skill in the art would be able to combine the teachings of de Boer et al. with Beroud et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method of analyzing cryptic splice sites. Therefore, regarding claims 11, 17, and 20, the instant invention is prima facie obvious (MPEP § 2142).
Claims 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over Oubounyt et al. (Robust Promoter Predictor Using Deep Learning. Front Genet. 10: 286 (2019); published 4/4/2019) in view of Beroud et al. (Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Research. 37(9): e67 (2009); published 4/1/2009) and Rogan et al. (U.S. Patent Application Publication US 2018/0051326 A1; published 2/22/2018; provided in the IDS dated 6/17/2022).
Regarding claim 13, Oubounyt et al. teaches the development of a deep learning model to analyze the characteristics of short eukaryotic promoter sequences, and accurately recognize the human and mouse promoter sequences (Abstract). The datasets used for training and testing include two distinctive classes of the promoters, namely TATA promoters (i.e., the sequences that contain TATA box) and non-TATA promoters (i.e., identifying, in a nucleotide string, a true gene transcriptional regulatory element such as a promoter sequence comprising at least one of a TATA box, a CAAT box, a GC box or a transcription initiator box, or a transcription termination site) (Pg. 3, Col. 1, Para. 2). Oubounyt et al. further teaches that the model outputs a real-valued score and differentiates between human TATA, human non-TATA, mouse TATA, and mouse non-TATA promoters (i.e., associating a score to the gene transcriptional regulatory element based on the corresponding similarity score) (Pg. 4, Col. 2, Para. 1 and Pg. 7, Col. 1, Para. 2).
Regarding claim 14, Oubounyt et al. teaches that the datasets used for training and testing include two distinctive classes of the promoters namely TATA promoters (i.e., the sequences that contain TATA box) and non-TATA promoters (i.e., identifying a promoter motif that comprises a combination of a promoter elements such as the TATA box) (Pg. 3, Col. 1, Para. 2). Oubounyt et al. further teaches the model accepts a raw genomic sequence S={N1,N2,...,Nl} where N
∈
{A,C, G, T} and l is the length of the input sequence, as input and outputs a real-valued score (i.e., determining and assigning a score to the promoter motif based on combined or variably weighted scores of individual elements of the promoter motif) (Pg. 4, Col. 1, Para. 2 - Col. 2, Para. 1).
Oubounyt et al. does not teach calculating a similarity score using a position weight matrix (PWM) based on a sequence length or variability of a gene transcriptional regulatory element; graphically marking using graphical notations, in a display for a user, the nucleotide string at a location indicative of the gene transcriptional regulatory element when the score is higher or lower than, or equal to, a preselected threshold; identifying a cryptic version of a promoter box, motif or other elements such as enhancer or a silencer; and determining and assigning scores for various genetic element motifs such as splicing motifs (donor, acceptor, exon motifs), initiator motifs, enhancer or silencer motifs, and termination motifs.
Regarding claim 13, Beroud et al. teaches the limitation of calculating a similarity score using a position weight matrix (PWM) based on a sequence length or variability of a gene transcriptional regulatory element) as described for claim 17 above.
Regarding claim 13, Rogan et al. teaches a server that outputs a displays containing exons, potential cryptic exons, or isoforms with an incorrect splice order. The minimum reportable total information content (Ri,total) value may also be selected using horizontal sliding scale bar which filters out potential exons below this threshold (i.e., graphically marking using graphical notations, in a display for a user, the nucleotide string at a location indicative of the gene transcriptional regulatory element when the score is higher or lower than, or equal to, a preselected threshold) (Para. [0062]-[0065]).
Regarding claim 14, Beroud et al. teaches that the algorithm can identify cryptic splice sites, exonic splicing enhancers (ESE) and exonic splicing silencers (ESS) (i.e., identifying a cryptic version of a motif or other elements such as enhancer or a silencer) (Pg. 10, Col. 1, Para. 2 and Pg. 11, Col. 1, Para. 2). Beroud et al. further teaches the calculation the strength for a potential splice site, including 5' splice sites and 3' splice sites using PWM matrices. The matrices are also used to evaluate enhancer and silencer motifs (i.e., determining and assigning scores for various genetic element motifs such as splicing motifs (donor, acceptor), and enhancer or silencer motifs) (Pg. 2, Col. 2, Para. 3-4 and Pg. 3, Col.1, Para. 3-4).
An invention would have been prima facie obvious to one or ordinary skill in the art before the effective filing date of the claimed invention if some teaching, suggestion or motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Oubounyt et al. discloses the development of a deep learning model to analyze the characteristics of short eukaryotic promoter sequences, and accurately recognize the human and mouse promoter sequences (Oubounyt et al., Abstract). Beroud et al. discloses the development of the Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence (Beroud et al., Abstract). Rogan et al. discloses a methodology that predicts cryptic and exon skipping isoforms in mRNA produced by splicing mutations from the combined information contents and the distribution of the splice sites and other regulatory binding sites defining the exons (Rogan et al., Abstract).
Therefore, one of ordinary skill in the art would have been motivated to combine the method for analyzing and characterizing promotor sites shown by Oubounyt et al. with the teachings of Beroud et al. and Rogan et al. because the HSF method of Beroud et al. could help to predict the theoretical impact on splicing of any sequence variation affecting a human gene (Beroud et al., Pg. 11, Col. 1, Para. 3). Additionally, the method of Rogan et al. streamlines the assessment of abnormal and normal splice isoforms resulting from splicing mutations (Rogan et al., Para. [0002]). One of ordinary skill in the art would be able to combine the teachings of Oubounyt et al., Beroud et al., and Rogan et al. with reasonable expectation of success due to the same nature of the problem to be solved, since all three are drawn toward a method for predicting characteristics of nucleotide sequences. Therefore, regarding claims 13-14, the instant invention is prima facie obvious (MPEP § 2142).
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over de Oubounyt et al. in view of Beroud et al. and Rogan et al. as applied to claims 13-14 above, and further in view of Jaganathan et al. (Predicting Splicing from Primary Sequence with Deep Learning. Cell. 176(3): 535-548.e24 (2019); published 1/24/2019).
Regarding claim 15, Oubounyt et al. teaches that for each promoter sequence in the test set, they perform computational mutation scanning to evaluate the effect of mutating every base of the input subsequence (150 substitutions on the interval -40~10 bp subsequence). Blue color represents a drop in the output score due to mutation while the red color represents the increment of the score due to mutation (i.e., identifying mutations within the promotor elements or promoter motifs) (Pg. 7, Col. 2, Para. 1 and Pg. 7, Fig. 6-7). Oubounyt et al. further teaches the limitation of identifying the promoter elements as described for claim 13 above.
Regarding claim 15, Beroud et al. teaches the limitation of modifying of a Shapiro Senapathy algorithm based on di, tri, or longer oligo-nucleotides as described for claim 11 above.
Oubounyt et al. in view of Beroud et al. and Rogan et al., as applied to claims 13-14 above, does not teach determining a deleteriousness of the mutations, or alterations in binding strengths of the mutated promoter elements or motifs, based on score differences between normal elements or motifs, and the mutated elements or motifs; and determining the deleteriousness of mutations in various genetic motifs such as splicing motifs, initiator motifs, enhancer or silencer motifs, and termination motifs.
Regarding claim 15, Jaganathan et al. teaches the calculation of a Δ score for the splicing change due a single nucleotide variant. The calculation compares acceptor and donor scores of the mutant to a reference nucleotide (Pg. e5, Δ Score of a single nucleotide variant). Jaganathan et al. further teaches that predicted cryptic splice variants are strongly deleterious in human populations based on Δ scores greater than 0.8 (i.e., determining a deleteriousness of the mutations, or alterations in binding strengths of the mutated promoter elements or motifs, based on score differences between normal elements or motifs, and the mutated elements or motifs and determining the deleteriousness of mutations in various genetic motifs such as splicing motif) (Pg. 542, Fig. 4).
Therefore, regarding claim 15, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of characterizing promotor sequences of Oubounyt et al. in view of Beroud et al. and Rogan et al. with the teachings of Jaganathan et al. because the deep learning method of Jaganathan et al. accurately predicts splice mutations, which are strongly deleterious in the human population and a major cause of rare genetic diseases (Jaganathan et al., Pg. 545, Col. 2, Para. 1). One of ordinary skill in the art would be able to combine the teachings of Oubounyt et al. in view of Beroud et al. and Rogan et al. with Jaganathan et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for predicting characteristics of nucleotide sequences. Therefore, regarding claim 15, the instant invention is prima facie obvious (MPEP § 2142).
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over de Boer et al. in view of Beroud et al. as applied to claims 11, 17, and 20 above, and further in view of Jaganathan et al. (Predicting Splicing from Primary Sequence with Deep Learning. Cell. 176(3): 535-548.e24 (2019); published 1/24/2019).
Regarding claim 19, de Boer et al. teaches the limitation of identifying the mutations as described for claim 2 above. de Boer et al. further teaches the scoring of splicing enhancers and silencers in the nucleotide sequence (i.e., identifying a mutation of a true or a cryptic translational regulatory element, such as an enhancer or silencer) (Pg. 11, Fig. 4). de Boer et al. further teaches the limitation of graphically marking, in the display for the user, the mutation in the nucleotide string, gene structure or sequence view as described for claim 2 above.
De Boer et al. in view of Beroud et al., as applied to claims 11, 17, and 20 above, does not teach based on a difference between the similarity score of an original element and a mutated element; and determining a deleteriousness of the mutation, or alteration in binding strength of a mutated translational regulatory element comprising an element or motif, based on a range of score difference between a normal element or motif and the mutated element or motif.
Regarding claim 19, Jaganathan et al. teaches the calculation of a Δ score for the splicing change due a single nucleotide variant. The calculation compares acceptor and donor scores of the mutant to a reference nucleotide (i.e., based on a difference between the similarity score of an original element and a mutated element) (Pg. e5, Δ Score of a single nucleotide variant). Jaganathan et al. further teaches that predicted cryptic splice variants are strongly deleterious in human populations based on Δ scores greater than 0.8 (i.e., determining a deleteriousness of the mutation, or alteration in binding strength of a mutated translational regulatory element comprising an element or motif, based on a range of score difference between a normal element or motif and the mutated element or motif) (Pg. 542, Fig. 4).
Therefore, regarding claim 19, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of analyzing cryptic splice sites of de Boer et al. in view of Beroud et al. with the calculation of a deleteriousness score of Jaganathan et al. because the deep learning method of Jaganathan et al. accurately predicts cryptic splice mutations, which are strongly deleterious in the human population and a major cause of rare genetic diseases (Jaganathan et al., Pg. 545, Col. 2, Para. 1). One of ordinary skill in the art would be able to combine the teachings of de Boer et al. in view of Beroud et al. with Jaganathan et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for analyzing the effect of mutations on splice sites. Therefore, regarding claim 19, the instant invention is prima facie obvious (MPEP § 2142).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 19/012,687 (‘687). Although the claims at issue are not identical, they are not patentably distinct from each other because the copending claim only has minor differences compared to the instant claim. Instant claim 1 encompasses all the limitations recited in claim 1 of Application ‘687. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims allowed.
Claim 16 is free from the prior art because the prior art does not fairly suggest or teach determining a score for a promoter complex, as an average of scores or differentially weighted scores of the promoter elements and enhancers, and subtracting the average of the scores or the differentially weighted scores of silencer elements. The closest prior art is Oubounyt et al. (Robust Promoter Predictor Using Deep Learning. Front Genet. 10: 286 (2019)). Oubounyt et al. discloses a deep learning model developed to analyze the characteristics of the short eukaryotic promoter sequences and accurately analyzes the output score to characterize them as human or mouse promoter sequences. However, Oubounyt et al. does not teach that the score is calculated as an average of scores or differentially weighted scores of the promoter elements and enhancers, and subtracting the average of the scores or the differentially weighted scores of silencer elements, as disclosed in instant claim 16.
Claims 18 and 20 are free from the prior art because the prior art does not fairly suggest or teach the determination of a score or subsequent graphical display of Kozak elements or motifs, or the determination of the score for the Kozak motif as an average of scores or differentially weighted scores of a plurality of Kozak elements. The closest prior art is Rogan et al. (U.S. Patent Application Publication US 2018/0051326 A1). Rogan et al. discloses a method for calculating the total information content of an exon (i.e., a score) as the sum of the information contents of its corresponding acceptor and donor sites, and the display of sequence motifs for splicing regulatory sequence binding sites. However, Rogan et al. does not teach the determination of the score for the Kozak motif as an average of the scores or differentially weighted scores, or the graphical marking of the Kozak elements, as disclosed in instant claims 18 and 20.
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/D.P.S./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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