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 .
Election/Restrictions
Applicant’s election without traverse of Group II in the reply filed on 04/15/2026 is acknowledged.
Claims 1-10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 04/15/2026.
Claims Status
Claims 1-21 are pending.
Claims 1-10 are withdrawn.
Claims 11-21 are examined on the merits.
Priority
The instant application is a continuation of Application PCT/US2021/047027, filed 08/20/2021, which claims priority to provisional Application No. 63/166803, filed 03/26/2021, and provisional Application No. 63/166829, filed 03/26/2021. Therefore, the Effective Filing Date (EFD) assigned to each of the claims 11-21 is the provisional filing dates of Applications No. 63/166803 and No. 63/166829, filed 03/26/2021.
Information Disclosure Statement
The Information Disclosure Statements filed 06/17/2022 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Drawings
The drawings filed 03/18/2022 and 05/19/2022 are accepted.
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because the abstract contains legal phraseology such as “said nucleotide string”. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Sequence Listing
The Sequence Listing filed 05/19/2022 is accepted.
Claim Objections
Claims 11, 12, and 20 are objected to because of the following informalities:
In claim 11, “a portion of one or more individual patients genome” should read “a portion of one or more individual patient’s genome”
In claim 12, “a enhancer” should read “an enhancer”
In claim 20, “or in animation;” should read “or in animation.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
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 11-21 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.
With respect to claim 11, the claim recites the limitation of “identifying a variant from the plurality of nucleotides; determining a pathogenic or strength altering mutation in a gene corresponding to the nucleotide string”. The claim is indefinite because it is unclear if there is a nexus between the step of “identifying a variant” and the rest of the claims. The claim also recite determining a mutation, and thus it is unclear if the identified variant is used at all.
With further respect to claim 11, the claim recites the limitation of “determining a pathogenic or strength altering mutation in a gene”. The claim is indefinite because it is unclear what a strength altering mutation is and whether this is referring to alterations in expression of a gene.
With respect to claims 12-16, 18, and 19, the claims recite the limitation of “determining an effect of a mutation”. The claims are indefinite because it is unclear if the “a mutation” is the same “pathogenic or strength altering mutation” determined in claim 11, or a different mutation.
With respect to claim 14, the claim recites the limitation of “wherein the cryptic exon score is equal or greater than the score of a true exon”. The claim is indefinite because there is no antecedent basis for “the cryptic exon score” and there is no antecedent basis for “the score of a true exon”.
With respect to claim 15, the claim recites the limitation of “wherein the mutated exon score is lower than the score of the original exon”. The claim is indefinite because there is no antecedent basis for “the mutated exon score” and there is no antecedent basis for “the score of the original exon”.
With respect to claim 16, the claim recites the limitation of “determining an effect of a mutation in a true promoter element such as TATA box…”. The claim is indefinite because 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).
With respect to claim 20, the claim recites the limitation of “displaying the mutated gene”. The claim is indefinite because there is no antecedent basis for “the mutated gene”.
With respect to claim 21, the claim recites the limitation of “determining that a mutation within an exon”. The claims are indefinite because it is unclear if the “a mutation” is the same “pathogenic or strength altering mutation” determined in claim 11, or a different mutation.
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 11-21 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims are directed to a method.
With respect to step (2A)(1): The claims are directed to abstract ideas of mental processes and laws of nature.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claim 11:
identifying a variant from the plurality of nucleotides
determining a pathogenic or strength altering mutation in a gene corresponding to the nucleotide string
determining, based on the mutation in the gene, various aberrations that occur in gene transcription, splicing, or translation, wherein the various aberrations comprise abolition, increase or decrease of rate or quantity of transcription, exon skipping, partial exon deletion, intron retention, intron skipping, premature termination of translation, polyadenylation, or translation
determining, for the various aberrations, a mechanism of a causation of an aberration due to the mutation in the gene, gene transcript, or the resulting defective protein, in one or more patients
graphically illustrating the various aberrations in a structure or sequence view
Dependent claims 12-21 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 11, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 12: “determining an effect of a mutation in a true acceptor, a true donor, a true branch point site, a true enhancer, or a true silencer in the gene, abased on a position and a similarity score of a cryptic acceptor, donor, a branch point site, an enhancer, or a silencer within the exon or intron, as a partial exon deletion, exon skipping, intron retention, or intron skipping”
Claim 13: “determining an effect of a mutation in a cryptic acceptor, donor, branch site, enhancer or silencer in the gene or within the exon or intron, based on a position and a similarity score relative to a true or cryptic acceptor, donor, branch point, enhancer or silencer within the exon or intron, as a partial exon deletion, exon skipping, intron retention, or intron skipping”
Claim 14: “determining an effect of a mutation in a cryptic acceptor, donor, branch site, enhancer or silencer in the gene, as a cryptic exon creation causing intron retention, wherein the cryptic exon score is equal or greater than the score of a true exon bordering it”
Claim 15: “determining an effect of a mutation in a true acceptor, donor, branch point site, enhancer or silencer in a gene, wherein the mutated exon score is lower than the score of the original exon or an adjacent true exon, as an exon skipping”
Claim 16: “determining an effect of a mutation in a true promoter element such as TATA box, CAAT box, GC box or initiator box, a promoter motif, enhancer or silencer within, upstream, or downstream of the gene, leading to pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic promoter box, motifs, enhancer or silencer, as enhanced or reduced transcription, abolition of transcription, or use of a cryptic element leading to erroneous transcription”
Claim 17: “determining an effect of the mutation in a cryptic promoter element, a cryptic promoter motif, cryptic enhancer or silencer within, upstream, or downstream of the gene, leading to a pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic promoter box, cryptic motifs, cryptic enhancer or silencer, as enhancement, reduction, or abolition of transcription, or use of a cryptic element leading to erroneous transcription”
Claim 18: “determining an effect of a mutation in a true polyA site or signal, a polyA motif, enhancer or silencer within, upstream, or downstream of the gene, leading to pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic polyA element, motif, enhancer or silencer, as enhancement, reduction, or abolition of polyadenylation, or use of a cryptic element leading to erroneous polyadenylation”
Claim 19: “determining an effect of a mutation in a cryptic polyA site or signal, a cryptic polyA motif, cryptic enhancer or silencer within, upstream, or downstream of the gene, leading to pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic polyA element, motif, enhancer or silencer, as enhancement, reduction, or abolition of polyadenylation, or use of a cryptic element lead to erroneous polyadenylation”
Claim 20: “graphically displaying the mutated gene and showing an effect of splicing aberrations such as exon skipping, partial exon deletion, intron retention, intron skipping, frameshift, premature termination, or amino acid deletion or insertion, in gene or protein structure, sequence views, or in animation”
Claim 21: “determining that a mutation within an exon, indicative of a coding sequence mutation leading to an amino acid change, is a splicing mutation based on a presence of splicing signals such as donor, acceptor, branch point, enhancers, silencers, or their cryptic versions containing that mutation, their position relative to real or cryptic splicing signals, or a difference between an original similarity score and a mutated similarity score, and, leading to the splicing aberrations; and graphically displaying a comparison of an effect of a same mutation when considered as an exonic coding region mutation or a splicing mutation”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and laws of nature because the claims recite no more than identifying variants and determining the effect of these variants, which comprise mental processes. Furthermore, graphically illustrating the effects is a mental processes because it can be performed mentally with the aid of a pencil and paper (see MPEP 2106.04(a)(2).III.B). Thus, the claims are directed to using mental processes to identify laws of nature of the correlation between mutations and the genetic effect of the mutations.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claim 11 recites the following additional elements that are not abstract ideas:
computer-implemented
receiving a nucleotide string comprising a plurality of nucleotides from at least a portion of one or more individual patient’s genome, wherein the portion of the genome includes at least one of: a 5’-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a splice acceptor, a splice donor, a branch point site, a 3’-UTR, a Kozak sequence, a poly-A addition site or signal, or a cryptic version thereof, from a known protein coding gene or a non-protein coding RNA gene, and within genes not yet identified in a Dark Matter genome
The step of receiving a nucleotide string generates the data on which the judicial exceptions are performed and is thus directed to data gathering. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)). The element of a computer-implemented method is directed to a generic computer performing the method. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)).
None of the dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d).I, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 11: The additional elements of a computer-implemented method and receiving a nucleotide string do not rise to the level of significantly more than the judicial exception. With respect to the computer-implemented method, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). With respect to receiving a nucleotide string, as recited in the MPEP at 2106.05(d).II with respect to Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546, analyzing DNA to provide sequence information or detect allelic variants is a well-understood, routine, and conventional activity. As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 11-21 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Rogan et al. (US 2018/0051326 A1, IDS reference).
Regarding claim 11, Rogan et al. teaches a computer-implemented method comprising:
receiving a nucleotide string comprising a plurality of nucleotides from at least a portion of one or more individual patient’s genome, wherein the portion of the genome includes at least one of: a 5’-UTR, a promoter, an enhancer, a silencer, an exon, an intron, a coding sequence, a splice acceptor, a splice donor, a branch point site, a 3’ UTR, a Kozak sequence, a poly-A addition site or signal, or a cryptic version thereof, from a known protein coding gene or a non-protein coding RNA gene, and within genes not yet identified in a Dark matter genome: Rogan et al. teaches extracting mRNA and determining the sequence of one or more mRNA molecules derived from the gene, or extracting proteins from a cell expressing the gene and determining the sequence of one or more protein molecules derived from the gene of interest (paragraph [0012]); Rogan et al. also teaches receiving nucleotide string comprising splice acceptors and donors, thus non-coding nucleotides, and thus nucleotide strings of the dark matter genome because they are non-coding (paragraph [0011], a);
identifying a variant from the plurality of nucleotides (paragraphs [0023]; [0024], etc.);
determining a pathogenic or strength altering mutation in a gene corresponding to the nucleotide string (paragraphs [0023]; [0024]);
determining, based on the mutation in the gene, various aberrations that occur in gene transcription, splicing, or translation, wherein the various aberrations comprise abolition, increase or decrease of rate or quantity of transcription, exon skipping, partial exon deletion, intron retention, intron skipping, premature termination of translation, polyadenylation, or translation (paragraph [0020]);
determining, for the various aberrations, a mechanism of a causation of an aberration due to the mutation in the gene, gene transcript, or the resulting defective protein, in one or more patients (paragraph [0020]); and
graphically illustrating the various aberrations in a structure or sequence view (Figure 3A).
Furthermore, Rogan et al. teaches the method being performed by a computer processor executing instructions in tangible memory (claims 1, 31, and 34).
Regarding claim 12, the claim is directed to determining an effect of a mutation in a true acceptor, a true donor, a true branch point site, a true enhancer, or a true silencer in the gene, based on a position and a similarity score of a cryptic acceptor, donor, a branch point site, an enhancer, or a silencer within the exon or intron, as a partial exon deletion, exon skipping, intron retention, or intron skipping. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining an effect of a mutation in a true acceptor and true donor based on a position and computed similarity scores by determining scores for each possible set of acceptor and donor within the sequence, calculated based on distances of the acceptor and donor pairs, and thus determining the effect of the mutation, such as causing cryptic acceptor and donor sites, as a part of partial exon deletion or exon skipping (paragraphs [0026]; [0032]).
Regarding claim 13, the claim is directed to determining an effect of a mutation in a cryptic acceptor, donor, branch site, enhancer or silence in the gene or within the exon or intron, based on a position and a similarity score relative to a true or cryptic acceptor, donor, branch point, enhancer or silencer within the exon or intron, as a partial exon deletion, exon skipping, intron retention, or intron skipping. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining an effect of a mutation in a true acceptor and true donor based on a position and computed similarity scores by determining scores for each possible set of acceptor and donor within the sequence, calculated based on distances of the acceptor and donor pairs, and thus determining the effect of the mutation, such as causing cryptic acceptor and donor sites, as a part of partial exon deletion or exon skipping (paragraphs [0026]; [0032]).
Regarding claim 14, the claim is directed to determining an effect of a mutation in a cryptic acceptor, donor, branch site, enhancer or silencer in the gene, as a cryptic exon creation causing intron retention, wherein the cryptic exon score is equal or greater than the score of a true exon bordering it. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining an effect of a mutation in cryptic acceptors and donors causing intron retention and calculating scores for the sites (paragraph [0020]).
Regarding claim 15, the claim is directed to determining an effect of a mutation in a true acceptor, donor, branch point sire, enhancer or silencer in a gene, wherein the mutated exon score is lower than the score of the original exon or an adjacent true exon, as an exon skipping. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining an effect of a mutation in a true acceptor and donor site pair wherein the mutated exon score has a lower abundance score than the original and it is an exon skipping (paragraph [0020]).
Regarding claim 16, the claim is directed to determining an effect of a mutation in a true promoter element such as TATA box CAAT box, GC box or initiator box, a promoter motif, enhancer or silencer within, upstream, or downstream of the gene, leading to a pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic promoter box, motifs, enhancer or silencer, as enhanced or reduced transcription, abolition of transcription, or use of a cryptic element leading to erroneous transcription. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining the effect of enhancers upstream or downstream of the gene, leading to strength altering effects, based on position and similarity to the true enhancer as enhancement or reduction of transcription (paragraphs [0076]; [0089]; Figure 9).
Regarding claim 17, the claim is directed to determining an effect of the mutation in a cryptic promoter element, a cryptic promoter motif, cryptic enhancer or silencer within, upstream, or downstream of the gene, leading to a pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic promoter box, cryptic motifs, cryptic enhancer or silencer, as enhancement, reduction, or abolition of transcription, or use of a cryptic element leading to erroneous transcription. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining the effect of cryptic enhancers upstream or downstream of the gene, leading to strength altering effects, based on position and similarity to the true enhancer as enhancement or reduction of transcription (paragraphs [0076]; [0089]; Figure 9).
Regarding claim 18, the claim is directed to determining an effect of a mutation in a true polyA site or signal, a polyA motif, enhancer or silencer within, upstream or downstream of the gene, leading to pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic polyA element, motif, enhancer or silencer, as enhancement, reduction, or abolition of polyadenylation, or use of a cryptic element leading to erroneous polyadenylation. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining the effect of enhancers upstream or downstream of the gene, leading to strength altering effects, based on position and similarity to the true enhancer (paragraphs [0076]; [0089]; Figure 9) and predicts enhancement of polyadenylation sites (paragraph [0111]).
Regarding claim 19, the claim is directed to determining an effect of a mutation in a cryptic polyA site or signal, a cryptic polyA motif, cryptic enhancer or silencer within, upstream, or downstream of the gene, leading to pathogenic or strength altering effect, based on a position and a similarity score of a true or cryptic polyA element, motif, enhancer or silencer, as enhancement, reduction, or abolition of polyadenylation, or use of a cryptic element leading to erroneous polyadenylation. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches determining the effect of cryptic enhancers upstream or downstream of the gene, leading to strength altering effects, based on position and similarity to the true enhancer (paragraphs [0076]; [0089]; Figure 9) and predicts enhancement of polyadenylation sites (paragraph [0111]).
Regarding claim 20, the claim is directed to graphically displaying the mutated gene and showing an effect of splicing aberrations such as exon skipping, partial exon deletion, intron retention, intron skipping, frameshift, premature termination, or amino acid deletion or insertion, in gene or protein structure, sequence views, or in animation. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches graphically displaying the mutated gene and showing the effect of splicing aberrations, such as exon skipping in a sequence view (paragraph [0036]; Figure 3A).
Regarding claim 21, the claim is directed to determining that a mutation within an exon, indicative of a coding sequence mutation leading to an amino acid change, is a splicing mutation based on a presence of splicing signals such as donor, acceptor, branch point, enhancers, silencers, or their cryptic versions containing that mutation, their position relative to real or cryptic splicing signals, or a difference between an original similarity score and a mutated similarity score, and, leading to the splicing aberrations; and graphically displaying a comparison of an effect of a same mutation when considered as an exonic coding region mutation or a splicing mutation. Rogan et al. teaches the method of claim 11. Rogan et al. also teaches a determined coding sequence mutation found in the prior art, which thus causes coding for a different amino acid, is a splicing mutation based on the presence of splicing signals of donor or acceptor sites based on the strength scores, leading to a splicing aberration (paragraph [0101]). Rogan et al. also teaches graphically displaying comparisons of the effect of the same gene mutations when considered as an exonic coding region mutation or intronic splice site mutations (paragraph [0040]; Figure 7; paragraph [0065]; paragraph [0086]).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.S./Examiner, Art Unit 1686
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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