DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim status
2. Claims 1-20 are currently pending and under exam herein.
Claims 1-20 are rejected.
Claims 10 and 12 are objected to.
Priority
3. The claimed benefit of U.S. Provisional Patent Application No. 63/322,506, filed 22 March 2022 is acknowledged. In this action, all claims are examined as though they had an effective filing date of 30 December 2021. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s).
Information Disclosure Statement
4. The information disclosure statement (IDS) submitted on 22 June 2023 is being considered by the examiner.
Drawings
5. The drawings submitted on 22 March 2023 are objected to for the reasons indicated below:
The headings of the table in Figure 4 is illegible.
The nucleic acid and amino acid sequences that appear in Figure 1b are not identified by sequence identifiers in accordance with 37 CFR 1.821(d)
Appropriate correction is required.
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:
6. Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings (Figure 1b).
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
7. Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Claim Objections
8. Claims 10 and 12 are objected to because of the following informalities:
Claim 10 recites “wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting what each of mutations is”, which is grammatically incorrect. A possible correction is to change the limitation to: “wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting what each of the mutations is”.
Claim 12 recites “a non-transitory processor-readable storage medium for computer programming instructions for execution by a processor to cause the processor”, which is grammatically incorrect. A possible correction is to change the limitation to: “a non-transitory processor-readable storage medium for storing computer programming instructions for execution by a processor to cause the processor”.
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.
9. Claims 1-20 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.
The term ‘well-suited’ in claims 1, 3, 12, 15 and 19 is a relative term which renders the claims indefinite. The term “well-suited” is not defined by the claims, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is therefore unclear which subsequence for a protein, gene sequence, or nucleic acid could be used for identifying mutations in gathered sequences of the protein or nucleic acid relative to a reference sequence. Dependent claims 2, 4-11, 13-14, 16-18 and 20 are similarly rejected as they do not resolve the indefiniteness issue.
The terms ‘ionize well’ and ‘exhibit good mass selectivity’ in claims 2 and 14 are relative terms which render the claims indefinite. The terms ‘ionize well’ and ‘exhibit good mass selectivity’ is not defined by the claims, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is therefore unclear which subsequence for a protein, gene sequence, or nucleic acid could be used for identifying mutations in gathered sequences of the protein or nucleic acid relative to a reference sequence.
Claim 12 recites: “for the at least one subsequence in the reference sequence”, but only a ‘a selected subsequence’ (singular) was introduced previously. Therefore, there is lack of antecedent basis for ‘the at least one subsequence’. For the purposes of examination ‘the at least one subsequence’ will be interpreted to mean ‘the selected subsequence”, which matches the claim language of claim 1. Dependent claims 13-18 are similarly rejected as they do not resolve the indefiniteness issue.
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.
10. Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 2A, Prong 1
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 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1 recites: programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein or nucleic acid relative to a reference sequence
Claim 1 recites: analyzing the gathered sequences with the processor to identify any variations in the selected subsequence where the selected subsequence in the gathered sequences is different from the selected subsequence in the reference sequence
Claim 1 recite: for ones of the gathered sequences where one or more variations in the selected subsequence have been identified, determining whether the variation constitutes a mutation or not
Claim 1 recites: by applying a statistical test based on the frequency of the variation across the gathered sequences
Claim 1 recites: determining frequencies of mutations in the gathered sequences;
Claim 2 recites: the method of claim 1, wherein the programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein, the gene sequence, or the nucleic acid relative to a reference sequence, comprises: designating subsequences that are specific to the protein, the gene sequence, or to the nucleic acid, subsequences in the protein, gene sequence, or nucleic acid that ionize well, and/or subsequences in the protein or nucleic acid that exhibit good mass selectivity as candidates for being the at least one selected subsequence in the protein, the gene sequence, or the nucleic acid that is well suited for identifying mutations in the gathered sequences relative to a reference sequence
Claim 2 recites: choosing one or more subsequences among the candidates to be the at least one selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence.
Claim 3 recites: the method of claim 1, wherein the programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein, gene sequence or nucleic acid relative to a reference sequence determines that multiple subsequences are well suited for identifying mutations in the gathered sequences relative to the reference sequence.
Claim 5 recites: the method of claim 1, further comprising sequence aligning the gathered sequences with the processor
Claim 6 recites: the method of claim 1, wherein the statistical test determines a likelihood for each variation and based on the likelihood, determines whether the variation is a mutation
Claim 11 recites: the method of claim 1, wherein the protein is one of a protein found in a virus, disease or disorder
Claim 12 recites: programmatically determine that a selected subsequence is well suited for identifying mutations in gathered sequences of a protein, gene sequence, or a nucleic acid relative to a reference sequence of the protein, gene sequence or nucleic acid
Claim 12 recites: analyze the gathered sequences to identify variations, wherein the selected subsequence in the gathered sequences is different from the at least one subsequence in the reference sequence
Claim 12 recites: for ones of the gathered sequences where the selected subsequence is identified as different from the one subsequence in the reference sequence, determine whether there is a mutation or a non-mutation variation by applying a statistical test
Claim 12 recites: determine frequencies of mutations in the gathered sequences
Claim 13 recites: the non-transitory processor-readable storage medium of claim 12, wherein the gathered sequences are one of protein sequences, gene sequences, DNA sequences or RNA sequences
Claim 14 recites: designate subsequences that are specific to the reference sequence, subsequences in the gathered sequences that ionize well, and/or subsequences that exhibit good mass selectivity as candidates for being the selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence
Claim 14 recites: choosing a subsequence among the candidates to be the selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence
Claim 15 recites: The non-transitory processor-readable storage medium of claim 12, wherein the programmatically determining that the selected subsequence in the gathered sequences is well suited for identifying mutations in the gathered sequences relative to a reference sequence determines that multiple subsequences are well suited for identifying mutations in the gathered sequences relative to the reference sequence
Claim 16 recites: the non-transitory processor-readable storage medium of claim 12, further storing computer programming instructions that when executed by the processor cause the processor to sequence align the gathered sequences
Claim 17 recites: the non-transitory processor-readable storage medium of claim 12, wherein the statistical test determines for each variation a likelihood of the variation is and based on the likelihood, determines whether the variation is a mutation
Claim 19 recites: programmatically determine that a selected subsequence is well suited for identifying mutations in the gathered sequences of a protein, gene sequence or nucleic acid relative to a reference sequence
Claim 19 recites: analyze the gathered sequences to identify variations where the selected subsequence in the gathered sequences is different from the selected subsequence in the reference sequence
Claim 19 recites: for ones of the gathered sequences where the selected subsequence is identified as different from the subsequence in the reference sequence, determine whether there is a mutation or a non-mutation variation by applying a statistical test
Claim 19 recites: determine frequencies of mutations in the gathered sequences
The limitations regarding ‘applying a statistical test’ and ‘determine whether there is a mutation or a non-mutation variation by applying a statistical test’, are verbal equivalents that describe a mathematical calculation that is performed as the limitation and are so simple that they could be performed in the human mind or with pen and paper. Therefore, these limitations fall under the "Mathematical concepts" and "Mental processes" groupings of abstract ideas.
The limitations directed to ‘determining that a selected subsequence is well suited for identifying mutations’, ‘analyzing the gathered sequences to identify variations’, ‘determining whether the variation constitutes a mutation or not’, ‘determining frequencies of mutations’, ‘designating subsequences that ionize well and/or exhibit good mass selectivity’, ‘choosing one or more sequences that is well suited for identifying mutations’, ‘aligning the gathered sequences’ are generically recited data analysis steps that can be practically performed in the human mind because the human mind is capable of identifying relevant information, comparing values, and determining information from other values. Therefore, these limitations fall under the "Mental processes" groupings of abstract ideas.
The limitations of claims 3 and 15 that further limit the ‘determining that a selected subsequence is well suited for identifying mutations’ to apply to multiple subsequences, the limitations of claims 6 and 17 that limit the statistical test, and the limitation of claims 11 and 13 that limits the type of sequences in which mutations are determined, further limit the abstract ideas, but do not change their position as data gathering activities.
While claims 1-20 recite performing some aspects of the analysis with a processor, there are no additional limitations that indicate that this processor requires anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the "Mental processes" grouping of abstract ideas.
As such, claims 1-20 recite an abstract idea (Step 2A, Prong 1: YES).
Step 2A, Prong 2
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or insignificant extra-solution activity. Specifically, the claims recite the following additional elements:
Claim 1 recites: a processor of an electronic device
Claim 1 recites: outputting information regarding the frequencies of the mutations in the gathered sequences
Claim 4 recites: the method of claim 1, further comprising programmatically with the processor retrieving the gathered sequences from a database.
Claim 7 recites: the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences
Claim 8 recites: the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting graphics depicting the frequencies of the mutations in the gathered sequences
Claim 9 recites: the method of claim 8, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences outputs the frequencies sorted by location where the gathered sequences were gathered and/or the dates when the gathered sequences were gathered.
Claim 10 recites: the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting what each of mutations is and a frequency of each of the mutations
Claim 12 recites: a non-transitory processor-readable storage medium for computer programming instructions for execution by a processor to cause the processor
Claim 12 recites: output information regarding the frequencies of the mutations in the gathered sequences
Claim 14 recites: the non-transitory processor-readable storage medium of claim 12, wherein the computer programming instructions for execution by a processor to cause the processor to programmatically determine that selected subsequence is well suited for identifying mutations in gathered sequences of a protein, gene sequence, or a nucleic acid relative to a reference sequence of a protein or nucleic acid, comprises computer programming instructions that cause the processor to [perform the method]
Claim 18 recites: the non-transitory processor-readable storage medium of claim 12, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences outputs the frequencies sorted by location where the gathered sequences were gathered and/or the dates when the gathered sequences were gathered
Claim 19 recites: a storage for storing computer programming instructions
Claim 19 recites: a processor configured to execute the computer programming instructions
Claim 19 recites: output information regarding the frequencies of the mutations in the gathered sequences
Claim 20 recites: the electronic device of claim 19, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences
The limitations for ‘retrieving the gathered sequences from a database’ merely serve to gather data that is used an input for the judicial exception. Therefore, these limitations are mere data gathering activities. As set forth in MPEP 2106.05(g), mere data gathering activity has been identified by the courts as insignificant extra-solution activity that does not provide a practical application.
The limitations for ‘outputting information’ are post-solution activity steps that merely serve to output data from the judicial exception. In addition the limitations directed to storing data in memory are also tangential to the claimed method and system. As set forth in MPEP 2106.05(g), output activity that is incidental to the primary process are insignificant extra-solution activity that do not have a practical application. The limitations that limit the type of data output fail to integrate the judicial exception into a practical application because they merely further limit the tangential output activities but do not change their position as output activities.
The limitations in claims 7-10, 18 and 20 further limit the outputting of the additional element limitations, but do not integrate the judicial exception into a practical application because they just further limit how the data are output (i.e. as a webpage, graphic depiction or sorted data) or what data are output (i.e. frequency of mutation and what mutation is) but don’t change their position as output activities. Specifically, the limitations in claims 9, 10 and 18 that limit the data types output, amount to field-of-use (MPEP 2106.05(h)) or mere instructions to apply (MPEP 2106.05(f)).
There are no limitations that indicate that the electronic device or processor requires anything other than a generic computing system. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 1-20 are directed to an abstract idea (Step 2A, Prong 2: 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 mere instructions to apply the recited exception in a generic computing environment or well-understood, and conventional activity.
The limitations of claim 4, directed to retrieving data from a database and the limitations of claims 12, 14 and 18-19, directed to storing data and programs and limitations of claims 1, 12 and 19 directed to outputting data do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As set forth in MPEP section 2106.05(g), the courts have decided that limitations that merely add an insignificant extra-solution activity, do not amount to an inventive concept, particularly when the activities are well-understood and conventional. As set forth in MPEP section 2106.05(d), the courts have recognized that limitations directed to data gathering that are claimed as insignificant extra-solution activity are routine, well understood and conventional (Mayo Collaborative servs. V. Prometheus Labs., Inc., 566 U.S. at 79, 101 USPQ2d at 1968). Additionally, storing and retrieving information from memory has also been deemed well-understood, routine and conventional activity (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
The limitations of claims 7, 9-10 that merely further limit the type of data or the format of the data that is output, do not change the fact that generically outputting data is well-understood, routine and conventional.
The limitations of claims 8 and 20, directed outputting information to a web page, user interface, equate to receiving or transmitting data over a network, which has been decided by the courts as well-understood, routine and conventional activity (Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 and buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014).
The limitations of claims 1 and 19, pertaining to the computer system used to execute the method, are directed to performing judicial exceptions with a generic computing system on a generic computer. These limitations are not sufficient to amount to significantly more than the judicial exception because, as set forth in the MPEP section 2106.05(d)(II)), using a generic computing environment or generic computer to perform the judicial exception, has been deemed well-understood, routine and conventional activity including receiving or transmitting data over a network (Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362), performing repetitive calculations (Bancorp Services v. Sun Life, 687 F.3d 1266, 1278, 103 USPQ2d 1425, 1433 (Fed. Cir. 2012)), and storing and retrieving information in memory (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)). Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception are insufficient to provide significantly more.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-20 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.
(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.
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.
11. Claims 1-3, 8-10, 12-15 and 18-19 are rejected under 35 U.S.C. 102 (a)(1) as being unpatentable over Spaans et al. (PLOS ONE, 2014, Vol. 9, p. 1-11; IDS 22 June 2023). The italicized text corresponds to the instant claim limitations.
Pertaining to claims 1, 12 and 19, Spaans et al. discloses designing a high-throughput somatic mutation profiling panel and using it to identify mutations detectable in tumors by MALDI-TOF. Spaans et al. further discloses Data were analysed with MassARRAY Typer Analyser softwar (TYPER 4.0.22, Sequenom, Hamburg, Germany) and that statistical analyses were performed with IBM SPSS statistics Data Editor version 20.0. Running software inherently performs the method on a processor with computer-readable storage (p. 2, col. 1, para. 2; a method performed by a processor of an electronic device (claim 1); a non-transitory processor-readable storage medium for [storing] computer programming instructions for execution by a processor to cause the processor [to perform the method] (claim 12); an electronic device, comprising: a storage for storing computer programming instructions; and a processor configured to execute the computer programming instructions to [perform the method] (claim 19).
Pertaining to claims 1, 12 and 19, Spaans et al. discloses that they created a MALDI-TOF-based gene mutation panel and used it to detect a wide range of mutations in various types of gynecological tumors (i.e. they determined which mutations could be identified by MALDI-TOF). Spaans et al. teaches doing this in two steps: 1) Developing GynCarta 1.0, a gynecological specific ‘hotspot’ gene panel comprised of 89 assays to detect 154 mutations in 12 genes (i.e. selected subsequences), and GynCarta 2.0 with a few more subsequences added. These mutation-detection assays were designed computationally using mySequenom.com online assay design tools to select subsequences with detectable differences between wild-type versus mutant conditions in the assay. 2) Analyzing this panel by using MALDI-TOF assay across 546 cervical, endometrial, ovarian and vulvar carcinoma samples to identify which of the subsequences had mutations detectable by the MALDI-TOF assay. Spaans et al. further disclose that the samples used for the MALDI-TOF test were wild type and mutant DNA amplified by PCR (i.e. gathered sequences and a reference sequence) (p. 2, col. 1, para. 2; p. 2, col. 1, para. 5 – col. 2, para. 1; p. 8, col. 1, para. 2; Table 2; programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein or nucleic acid relative to a reference sequence)(claim 1); programmatically determine that a selected subsequence is well suited for identifying mutations in gathered sequences of a protein, gene sequence, or a nucleic acid relative to a reference sequence of the protein, gene sequence or nucleic acid (claim 12); programmatically determine that a selected subsequence is well suited for identifying mutations in the gathered sequence of a protein, gene sequence, or a nucleic acid relative to a reference sequence (claim 19).
Regarding claims 1, 12 and 19, Spaans et al. discloses identifying specific mutations in the GynCarta 2.0 panel across the 546 tumor samples using the MALDI-TOF mass spectrometry assay. Spaans et al. further shows the mutation frequencies for each locus that were detected by the assay (Table 3) and a complete overview of the mutations included in the GynCarta 2.0 mutation panel (Table 2). Spaans et al. further discloses that the reference sequence was a wild-type DNA sample derived from leukocytes and that to identify mutations using the MALDI-TOF assay, was done by discriminating mutant and wild type alleles (p. 6, col. 1, para. 4; p. 6, col. 1, para. 1; p. 4, col. 1, para. 2; p. 2, col. 2, para. 1-2; analyzing the gathered sequences with the processor to identify any variations in the selected subsequence where the selected subsequence in the gathered sequences is different from the selected subsequence in the reference sequence) (claim 1); analyze the gathered sequences to identify variations, wherein the selected subsequence in the gathered sequences is different from the at least one subsequence in the reference sequence (claim 12); analyze the gathered sequences to identify variations where the selected subsequence in the gathered sequences is different from the selected subsequence in the reference sequence (claim 19).
With respect to claims 1, 12 and 19, Spaans et al. discloses that mutation frequencies were detected across the 546 cervical, endometrial, ovarian and vulvar carcinoma samples based on the MALDI-TOF assay data and were compared with the predicted numbers of mutations based on the frequencies reported in the COSMIC database and corrected for the panel coverage. Spaans et al. discloses two types of statistical analyses that were performed based on the frequencies of variation across the gathered sequences: 1) mutations in the gathered tumor samples were detected by a minimum 5% threshold of the mutant allele peak. Using this threshold, PIK3CA mutations were detected twice as frequently in cervical cancer samples than predicted from the database data; and 2) mutation frequencies determined by the assay were compared between tumor types to identify statistically-significant tumor-type enrichment. Using this method, it was found that in endometrial cancer, PIK3CA mutations were found most frequently on hotspots located on exon 0 and exon 20 with an even distribution between the exons, but in cervical cancer, however, mutations ere almost exclusively on exon 9. This difference was significant with p<0.0001 using a Fisher’s exact test with 95% confidence intervals. Statistical analyses were performed with IBM SPSS statistics Data Editor version 20.0 (p. 6, col. 2, para. 3; p. 6, col. 1, para. 5; Table 4; p. 2, col. 2, para. 3; for ones of the gathered sequences where one or more variations in the selected subsequence have been identified, determining with the processor whether the variation constitutes a mutation or not by applying a statistical test based on the frequency of the variation across the gathered sequences) (claim 1); for ones of the gathered sequences where the selected subsequence is identified as different from the one subsequence in the reference sequence, determine whether there is a mutation or a non-mutation variation by applying a statistical test (claim 12); for ones of the gathered sequences where the selected subsequence is identified as different from the subsequence in the reference sequence, determine whether there is a mutation or a non-mutation variation by applying a statistical test (claim 19).
Pertaining to claims 1, 12 and 19, Spaans et al. discloses determining and outputting the frequencies of each mutation detected by the MALDI-TOF assay in the GynCarta 2.0 panel across the 546 tumor samples (Table 3) as well as the mutation spectrum (Fig. 2) (Table 3; Fig. 2; p. 6, col. 1, para. 4; determining frequencies of mutations in the gathered sequences; and outputting information regarding the frequencies of the mutations in the gathered sequences (claim 1); determine frequencies of mutations in the gathered sequences; and output information regarding the frequencies of the mutations in the gathered sequences (claim 12); and determine frequencies of mutations in the gathered sequences; and output information regarding the frequencies of the mutations in the gathered sequences (claim 19).
Pertaining to claims 2 and 14, Spaans et al. discloses using a MALDI-TOF assay to identify mutations in the gathered sequences of the genes. Spaans et al. discloses using a subsequence design method to ensure good mass selectivity for the mutant-wild-type comparisons: mysequenom.com online assay design tools were used to design the somatic mutation detection assays with 12 assays per well multiplexing. Where possible, mutant allele extension peaks were designed as first detected allele peaks and the wild type extension peaks as the last detected allele peaks. All assay were validated on wild type DNA and known positive mutation samples. In addition to this design-level selection, Spaans et al. further discloses an experiment-level selection in that they first ran the assay with a first panel of subsequences (GynCarta 1.0), and then later improved the panel to GynCarta 2.0 by removing subsequences that either were not detected by MALDI-TOF, or proved to be difficult to interpret because of small artefact peaks. Finally, Spaans et al. discloses validating specificity of the subsequences to the reference sequence by performing allele-specific qPCR (p. 2, col. 1, para. 7 – col. 2, para. 1; p. 4, col. 1, para. 2- p. 6, col. 1, para. 1; the method of claim 1, wherein the programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein, the gene sequence, or the nucleic acid relative to a reference sequence, comprises: designating subsequences that are specific to the protein, the gene sequence, or to the nucleic acid, subsequences in the protein, gene sequence, or nucleic acid that ionize well, and/or subsequences in the protein or nucleic acid that exhibit good mass selectivity as candidates for being the at least one selected subsequence in the protein, the gene sequence, or the nucleic acid that is well suited for identifying mutations in the gathered sequences relative to a reference sequence; and choosing one or more subsequences among the candidates to be the at least one selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence) (claim 2); the non-transitory processor-readable storage medium of claim 12, wherein the computer programming instructions for execution by a processor to cause the processor to programmatically determine that selected subsequence is well suited for identifying mutations in gathered sequences of a protein, gene sequence, or a nucleic acid relative to a reference sequence of a protein or nucleic acid, comprises computer programming instructions that cause the processor to: designate subsequences that are specific to the reference sequence, subsequences in the gathered sequences that ionize well, and/or subsequences that exhibit good mass selectivity as candidates for being the selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence; and choosing a subsequence among the candidates to be the selected subsequence that is well suited for identifying mutations in the gathered sequences relative to the reference sequence (claim 14).
Pertaining to claims 3 and 15, Spaans et al. taught that multiple genes in the GynCarta 2.0 panel had mutations that were positively identified by the MALDI-TOF assay in a subset of the tumors analyzed. For example, Spaans et al. taught that mutations in PIK3CA and PTEN were detected more frequently in tumor subgroups than predicted based on their prevalence in the database. Spaans et al. also taught that the MALDI-TOF assay was also capable of detecting and differentiating multiple different mutations per gene (Table 4; p. 6, col. 1, para. 5; Fig. 2; Table 3; the method of claim 1, wherein the programmatically determining with the processor that a selected subsequence for a protein, gene sequence, or nucleic acid is well suited for identifying mutations in gathered sequences of the protein, gene sequence or nucleic acid relative to a reference sequence determines that multiple subsequences are well suited for identifying mutations in the gathered sequences relative to the reference sequence) (claim 3); the non-transitory processor-readable storage medium of claim 12, wherein the programmatically determining that the selected subsequence in the gathered sequences is well suited for identifying mutations in the gathered sequences relative to a reference sequence determines that multiple subsequences are well suited for identifying mutations in the gathered sequences relative to the reference sequence (claim 15).
Pertaining to claim 8, Spaans et al. teaches outputting a graphic representation showing frequencies of the mutations in the 546 gynaecological carcinoma samples tested in the assay (Fig. 2; p. 6, col. 1, para. 4, p. 8, col. 2, para. 5; the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting graphics depicting the frequencies of the mutations in the gathered sequences).
Pertaining to claims 9 and 18, in the output graphic disclosed by Spaans et al. the mutations are sorted by location of the tumors (i.e. mutations are shown separately for each of cervical cancers, endometrial cancers, ovarian cancers and vulvar cancers) (Fig. 2; the method of claim 8, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences outputs the frequencies sorted by location where the gathered sequences were gathered and/or the dates when the gathered sequences were gathered) (claim 9); the non-transitory processor-readable storage medium of claim 12, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences outputs the frequencies sorted by location where the gathered sequences were gathered and/or the dates when the gathered sequences were gathered. (claim 18).
Pertaining to claim 10, Spaans et al. teaches outputting frequencies of mutations from the MALDI-TOF assay including: 1) what each mutation is (see column 2 labelled ‘gene’ in Figure 2, column 1 of Table 4 and column 1 labelled ‘gene’ of Table 3, and 2) a frequency of each mutation (see columns labelled ‘N’ and ‘%’, columns labelled’ percentage’ in Table 4, and columns labelled ‘CC’, ‘EC’, ‘OC’ and ‘VC’ for frequencies of each gene mutation in Table 3) (Fig. 2; Table 3; Table 4; the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises outputting what each of mutations is and a frequency of each of the mutations).
Regarding claim 13, Spaans et al. discloses developing a MALDI-TOF-based high-throughput mutation panel that covers somatic mutations in 13 genes that re most frequently reported to be involved in gynaecological malignancies and tested and validated the panel on a set of 546 cervical, endometrial, ovarian and vulvar carcinoma samples (p. 2, col.1, para. 2; that the gathered sequences the non-transitory processor-readable storage medium of claim 12, wherein the gathered sequences are one of proteins sequences, DNA sequences or RNA sequences).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102
and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory
basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of
rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same
under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections
set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is
not identically disclosed as set forth in section 102, if the differences between the claimed invention
and the prior art are such that the claimed invention as a whole would have been obvious before the
effective filing date of the claimed invention to a person having ordinary skill in the art to which the
claimed invention pertains. Patentability 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.
12. Claims 4-5, 7, 11, 16 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Spaans et al. (PLOS ONE, 2014, Vol. 9, p. 1-11; IDS 22 June 2023), as applied to claims 1-3, 8-10, 12-15 and 18-19 above, in view of Miller et al. (Cell Systems, 2015, Vol. 1, p. 197-209; IDS 22 June 2023). The italicized text corresponds to the instant claim limitations.
The limitations of claims 1-3, 8-10, 12-15 and 18-19 have been taught by Spaans et al. above.
Pertaining to claim 4, Spaans et al. taught that mutation frequencies detected by the assay were compared with the predicted numbers of mutations based on the frequencies reported in the COSMIC database, which included data from tumors (other than the gathered sequences); therefore, they demonstrate retrieving sequence data from a database. Regarding the gathered sequences (i.e. sequences from the 546 tumor samples), Spaans et al. discloses validating the results of the assay by using allele-specific qPCR, which is experimentally determining the sequences rather than obtaining them from a database (p. 8, col. 2, para. 2; p. 4, col. 1, para. 2; p. 6, col. 1, para. 5; the method of claim 1, further comprising programmatically with the processor retrieving the gathered sequences from a database).
Regarding claims 4-5, 7, 11, 16 and 20, Spaans et al. is silent to specifically retrieving the gathered sequences from a database (claim 4); the method of claim 1, further comprising sequence aligning the gathered sequences with the processor) (claim 5); the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences) (claim 7); wherein the protein is one of a protein found in a virus, disease or disorder (claim 11); the non-transitory processor-readable storage medium of claim 12, further storing computer programming instructions that when executed by the process or cause the processor to sequence align the gathered sequences (claim 16); and the electronic device of claim 19, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences (claim 20). However, these limitations were known in the art at the time of the effective filing date of the invention as taught by Miller et al.
Pertaining to claim 4, Miller et al. teaches a method of analysis of mutations in protein domains across various cancers. Miller et al. discloses analyzing 5496 tumor normal pairs of 22 different tumor types profiled by the TCGA consortium and domains from the protein family database Pfam-A, and by using multiple sequence analysis, determining whether conserved residues in protein domains were affected by mutation across related genes and identified many putative ‘domain hotspots’. In this study, the gathered sequences are the tumor profiles from the TCGA consortium database (Fig. 1; p. 199, col. 1, para. 3 – col. 2. Para. 1; the method of claim 1, further comprising programmatically with the processor retrieving the gathered sequences from a database).
Pertaining to claims 5 and 16, Miller et al. teaches that their method involves aligning the gathered protein sequences. For example, Miller et al. discloses that domains are aligned across related proteins by multiple sequence alignment and mutations are tallied at each residue of the alignment (Fig. 1C; p. 200, col. 2, para. 1; the method of claim 1, further comprising sequence aligning the gathered sequences with the processor) (claim 5); the non-transitory processor-readable storage medium of claim 12, further storing computer programming instructions that when executed by the process or cause the processor to sequence align the gathered sequences (claim 16).
Regarding claim 7 and 20, Miller et al. discloses generating outputs of their analysis showing frequencies of mutations in specific protein domains in the tumor samples. Miller et al. further discloses making the results of the analysis available to the community through an interactive web service (http://www. Mutationaligner.org) (Fig. 4; p. 207, col. 1, para. 3; the method of claim 1, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences) (claim 7); the electronic device of claim 19, wherein the outputting information regarding the frequencies of the mutations in the gathered sequences comprises generating a web page, a file or a user interface element for display that contains the information regarding the frequencies of the mutations in the gathered sequences (claim 20).
Pertaining to claim 11, Miller et al. discloses performing a systematic and comprehensive analysis of mutations in protein domains using data from more than 5,000 tumor-normal pairs from 22 cancer types profiled by the TCGA consortium and domains from the protein family database Pfam-A. Miller et al. further disclose that mutations in the study correspond to oncogenic ‘hotspot’ mutations in cancer (p. 198, col., 1, para. 2-3; the method of claim 1, wherein the protein is one of a protein found in a virus, disease or disorder).
An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Miller et al. taught that their method of analyzing somatic mutations of protein domains in tumor samples from a database associated rare mutations in potential cancer genes with therapeutically actionable hotspots in known oncogenes, underlining the potential clinical implications of their findings (p. 199, col 1, para. 3). Therefore, one of ordinary skill in the art would have been motivated to utilize the protein domain-based mutation detection method taught by Miller et al. in the tumor mutation detection method taught by Spaans et al. in order to improve detection of rare mutations in actionable hotspots in known oncogenes. Furthermore, one of ordinary skill in the art would predict that the mutation detection method taught by Miller et al. could be readily added to the method of Spaans et al. with a reasonable expectation of success because they both pertain to analyzing variants to identify functional mutations in specific tumors types. The invention is therefore prima facie obvious.
13. Claims 6 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Spaans et al. (PLOS ONE, 2014, Vol. 9, p. 1-11; IDS 22 June 2023), as applied to claims 1-3, 8-10, 12-15 and 18-19 above, in view of Halperin et al. (Frontiers in Oncology, 2019, Vol. 9, p. 1-19). The italicized text corresponds to the instant claim limitations.
The limitations of claims 1-3, 8-10, 12-15 and 18-19 have been taught by Spaans et al. above.
Regarding claim s 6 and 17 Spaans et al is silent to: the method of claim 1, wherein the statistical test determines a likelihood for each variation and based on the likelihood, determines whether the variation is a mutation (claim 6); the method of claim 1, wherein the statistical test determines a likelihood for each variation and based on the likelihood, determines whether the variation is a mutation (claim 17). However, these limitations were known in the art at the time of the effective filing date of the invention as taught by Halperin et al.
Regarding claims 6 and 17, Halperin et al. teaches a method of improved somatic variant calling for archival tumor samples that do not have a matching wild-type or normal control sample. Halperin et al. teaches software called lumosVar 2.0 to jointly analyze multiple samples from the same patient using a Bayesian algorithm to calculate the probability of a variant being a somatic mutation. The algorithm is based on the assumption that allelic fraction of somatic variants and germline variants follow different patterns as tumor content and copy number state change. Halperin et al. further teaches applying the method to find mutations in glioblastoma samples (using multiple tumor samples from the same patient with different purities) by applying two statistical approaches to identify mutations including: 1) jointly calling variants using two samples of different purities and 2) pooling the two samples resulting in one sample with average purities. Both approaches calculate likelihoods/probability that variants are somatic or germline. (p. 3, col. 2, para. 1 – p. 4, col. 1, para. 1; Fig. 7; p. 5, col. 2, para. 1- p. 6, col. 1, para. 1; p. 17, col. 1, para. 2; wherein the statistical test determines a likelihood for each variation and based on the likelihood, determines whether the variation is a mutation (claim 6); the method of claim 1, wherein the statistical test determines a likelihood for each variation and based on the likelihood, determines whether the variation is a mutation (claim 17).
An invention would have been prima facie obvious to one of ordinary skill in the art at the effective filing date of the invention if some motivation in the prior art would have led that person to combine the prior art teachings to arrive at the claimed invention. Halperin et al. taught that their method of calling a variant as somatic or germline (based on using a less pure tumor sample as a reference) is useful when analyzing archived tumor samples that do not have a matching normal sample (p. 2, col. 1, para. 1 – col. 2, para. 1). Therefore, one of ordinary skill in the art would have been motivated to utilize the likelihood-based variant calling method taught by Halperin et al. in the tumor mutation detection method taught by Spaans et al. in order to apply the method to samples without good matching normal samples to use as a reference. Furthermore, one of ordinary skill in the art would predict that the mutation detection method taught by Halperin et al. could be readily added to the method of Spaans et al. with a reasonable expectation of success because they both pertain to analyzing variants to identify mutations in tumors. The invention is therefore prima facie obvious.
Conclusion
14. No claims are allowed.
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/J.J.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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