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 9-13 are cancelled.
Claims 1-8 and 14-23 are currently pending and under examination herein.
Claims 1-8 and 14-23 are rejected.
Priority
3. This is a national phase entry under 35 USC 371. Claimed benefit of International Patent Application No. PCT/CN2021/127600, filed on 29 October 2021 is recognized. In this action, all claims are examined as though they had an effective filing date of 29 October, 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 submitted 30 June 2023 has been considered by the examiner.
Drawings
5. The drawing submitted on 6 January 2023 are accepted by the examiner.
Specification
The disclosure is objected to because nucleotide sequences appearing in the specification 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 specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, 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.
Claim Objections
7. Claim 3 is objected to because of the following informalities:
Claims 3 recites: “if at least one of the upstream sequence and the downstream sequence has an acquired SNV, a sub-interval where the at least one of the upstream sequence and the downstream sequence is located being a mutation region, and determining the mutation region as an avoidance region in the target interval”, which is grammatically incorrect. One possible correction is to change “a sub-interval” to “determining a sub-interval” to match the language of claim 18.
Appropriate correction is required.
Claim Interpretation
8. Claims 3, 4, 5, 18, 19 and 20 have contingent limitations. As indicated in the MPEP (section 2111.04(II)), the broadest reasonable interpretation of a method claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the conditions precedent are not met. Therefore, for the method claims 3, 4 and 5, the indicated steps below will not be considered to be part of the method; however, for the system claims 18, 19, and 20, the system will be considered to require components that can perform the indicated steps. The contingent limitations begin with ‘if’ that are not required to be performed in the method are indicated below:
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has a GC content greater than 75% or less than 35%, determining a sub-interval where the at least one of the upstream sequence is located and the downstream sequence is located as an avoidance region in the target interval
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has an acquired SNV, a sub-interval where the at least one of the upstream sequence and the downstream sequence is located being a mutation region, and determining the mutation region as an avoidance region in the target interval
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has a complexity lower than a preset complexity threshold, determining a sub-interval
Claims 4 and 19 recite: if the length of the target interval is greater than the preset amplification length, acquiring a number of sub-intervals to be split from the target interval, and acquiring a range of a number of primers of a target fragment in the target interval
Claims 5 and 20 recite: if the length of the target interval is less than or equal to the preset amplification length, determining that the target interval is amplified by using a pair of primers
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 7 and 22 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 7 and 22 recite: aligning the generated primers to a genome to sort binding sites of the primers and the genome in reverse order and screen out a primer pair with least non-specific binding in each sub-interval, so as to obtain remaining primers after screening. It is unclear if the limitation ‘to sort binding sites of the primers and the genome in reverse order and screen out a primer pair with least non-specific binding in each sub-interval, so as to obtain remaining primers after screening’ is a necessary step of the invention or intended use. Under broadest reasonable interpretation, the ‘sort’, ‘screen’ and ‘obtain’ steps will not be considered steps of the invention.
Claims 7 and 22 use relative terms which renders the claims indefinite. The terms are 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. The relative terms “to sort binding sites of the primers and the genome in reverse order”. It is unclear of what the reverse order is relative to because the metric is being used to sort the binding sites is undefined.
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 1-8 and 14-23 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:
Claims 1 and 14 recite: performing iterative design of PCR primers, avoiding the at least one avoidance region, for the plurality of sub-intervals to generate primers
Claims 1 and 14 recite: filtering and screening the (generated) primers according to a preset filtering condition to obtain target primers
Claims 1 and 14 recite: combining the obtained target primers to generate a primer pool
Claims 2 and 17 recite: determining a part of the plurality of sub-intervals as the at least one avoidance region in the target interval according to the flanking information
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has a GC content greater than 75% or less than 35%, determining a sub-interval where the at least one of the upstream sequence is located and the downstream sequence is located as an avoidance region in the target interval
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has an acquired SNV, (a sub-interval where the at least one of the upstream sequence and the downstream sequence is located being a mutation region), and determining the mutation region as an avoidance region in the target interval
Claims 3 and 18 recite: if at least one of the upstream sequence and the downstream sequence has a complexity lower than a preset complexity threshold, determining a sub-interval where the at least one of the upstream sequence and the downstream sequence is located as an avoidance region in the target interval.
Claims 4 and 19 recite: comparing the length of the target interval with the preset amplification length
Claims 5 and 20 recite: after comparing the length of the target interval with the present amplification length, if the length of the target interval is less than or equal to the preset amplification length, determining that the target interval is amplified by using a pair of primers
Claims 6 and 21 recite: according to a position of an avoidance region and flanking information of the target interval, determining whether a sub-interval is adjacent to the avoidance region
Claims 6 and 21 recite: if the sub-interval is adjacent to the avoidance region, shifting the sub-interval to skip the avoidance region
Claims 6 and 21 recite: if the sub-interval is not adjacent to the avoidance region, maintaining a position of the sub-interval
Claims 7 and 22 recite: filtering dimers in the remaining primers in the same amplification interval directly
Claims 7 and 22 recite: labeling dimers in the remaining primers in different amplification intervals
Claim 8 recites: selecting primers within a preset temperature range according to the obtained target primers
Claim 8 recites: splitting a combination of primers with dimer mutual exclusion into different primer pools
Claim 8 recites: selecting primers without mutual exclusion for combination to generate the final primer pool
Claim 16 recites: the method for designing multiplex PCR primers based on iteration according to claim 8, wherein the preset temperature range includes an optimal temperature range and a sub-optimal temperature range
Claim 23 recites: screening a temperature range adapted to the obtained target primers
Claim 23 recites: distinguishing a combination of primers with dimer mutual exclusion
Claim 23 recites: splitting the combination of primers with dimer mutual exclusion into different primer pools
The limitations regarding performing iterative design of PCR primers, comparing the length of the target interval with the preset amplification length, distinguishing a combination of primers with dimer mutual exclusion, screening a temperature range, filtering and screening the primers, combining the primers, determining a part of sub-intervals as an avoidance region, determining a sub-interval as an avoidance region, determining the mutation region as an avoidance region, determining that the target interval is amplified by using a pair of primers, determining whether a sub-interval is adjacent to the avoidance region, shifting the sub-interval to skip the avoidance region, maintaining a position of the sub-interval, filtering dimers in the remaining primers in the same amplification interval directly, labeling dimers in different amplification intervals, selecting primers within a preset temperature range, splitting a combination of primers with dimer mutual exclusion into different primer pools, selecting primers without mutual exclusion for combination, splitting the combination of primers into different primer pools 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.
The limitation of claim 16 further limits the temperature range used for ‘selecting primers within a preset temperature’ but does not change the position of the selecting as a mental process.
While claims 14-15 and 17-23 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 1-8 and 14-23 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 14 recites: a computer device, comprising a memory and a processor, wherein the memory has stored therein a computer program capable of being run on the processor; when executing the computer program, the processor performs the method
Claims 1 and 14 recite: acquiring at least one target interval of one of DNA to be tested and RNA to be tested, a plurality of sub-intervals in a target interval, and at least one avoidance region in the target interval
Claim 14 recites receiving the at least one avoidance region in the target interval
Claim 14 recites: receiving the generated primers
Claim 14 recites: receiving the obtained target primers
Claims 2 and 17 recite: acquiring flanking information of each sub-interval in the target interval; the flanking information including at least one of guanine-cytosine (GC) contents, single nucleotide variants (SNVs) and complexities of upstream and downstream sequences of the sub- interval
Claim 17 recites receiving the flanking information
Claims 4 and 19 recite: acquiring a length of each target interval according to a preset amplification length of the primers
Claims 4 and 19 recite: if the length of the target interval is greater than the preset amplification length, acquiring a number of sub-intervals to be split from the target interval, and acquiring a range of a number of primers of a target fragment in the target interval
Claims 7 and 22 recite: aligning the generated primers to a genome to sort binding sites of the primers and the genome in reverse order and screen out a primer pair with least non-specific binding in each sub-interval, so as to obtain remaining primers after screening
Claim 15 recites: a non-transitory computer-readable storage medium having stored therein a computer program that, when executed by a processor, causes the processor to perform the method according to claim 1.
The limitations for acquiring at least one target interval, receiving the at least one avoidance region, receiving the generated primers, receiving the obtained target primers, acquiring flanking information, receiving the flanking information, acquiring a length of each target interval, acquiring a number of sub-intervals, acquiring a range of a number of primers 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 limitation in claim 7 for aligning the generated primers to a genome does not integrate the judicial exception into practical application because it is insignificant pre-solution activity to the designing of the PCR primers as it is done to gather data about non-specific binding of candidate primers in the process of screening primers against non-specific binding. Aligning sequences to a genome does not impose meaningful limits on the claim such that it is not nominally related to the invention and thus, as set forth in the MPEP section 2106.05(g), it is insignificant extrasolution activity that does not integrate the judicial exception into a practical application.
There are no limitations that indicate that the processor or computer readable storage medium 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 1-8 and 14-23 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.
As discussed above, there are no additional limitations to indicate that the claimed processor requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. 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. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
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. Parker v. Flook, 437 U.S. 584, 588-89, 198 USPQ 193, 196 (1978). Furthermore, aligning sequences to a genome was well-understood, routine and conventional activity at the time of the effective filing date as evidenced by Yong et al. (Biobanking Methods and Protocols, 2019, Springer protocols, Methods in Molecular Biology, Humana Press, p. 1-434). Yong et al. discloses that there are many software offerings which can perform transcript alignment and DNA alignment to a genome (p. 351, para. 5).
Storing data and retrieve information in memory are well-understood, routine, conventional computer functions as recognized by Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93.
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 1-8 and 14-23 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.
11. Claims 1-6, 14-15 and 17-21 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being unpatentable over Bruand et al. (US 2020017994A1; 30 June 2023 IDS document). The italicized text corresponds to the instant claim limitations.
Regarding claim 14, Bruand et al. discloses a non-transitory memory configured to store executable instructions and a hardware processor programmed by the executable instructions to perform a method of PCR primer design (para. 0003-0004; A computer device, comprising a memory and a processor, wherein the memory has stored therein a computer program capable of being run on the processor; when executing the computer program, the processor the method).
Regarding claims 1 and 14, Bruand et al. teaches receiving a plurality of target gene sequences (from a transcriptome or genome), determining a designability score of each target gene sequence and splitting each target gene sequence into a plurality of ‘sub-target regions’ (i.e. sub-intervals) based on the score. Bruand et al. further teaches that in order to tile a large region of one or more target sequences, each target gene sequence can be split into multiple subpools based on estimated designability across the region. Bruand et al. further discloses performing specificity checks against a reference genome, when designing primers for target gene sequences, and against a transcriptome for RNA design. Braund et al. further teaches ‘bad regions’ (i.e. avoidance regions), which are regions of low designability that are considered bad for various reasons including presence of a poly-N or GC stretch that can be in the target gene sequence (para. 0004, 0020-0022, 0044, Fig. 1A and 1B; Fig. 5; acquiring at least one target interval of one of DNA to be tested and RNA to be tested, a plurality of sub-intervals in a target interval, and at least one avoidance region in the target interval).
Pertaining to claims 1 and 14, Bruand et al. teaches an amplicon scoring function to generate penalty scores as a method of avoiding bad regions, which is based on GC content, primer melting temperatures and amplicon length. Bruand et al. teaches that the primer design process is iterative; for example, to determine a set of optimized primers for a target sequence, the computing system may iteratively replace a first set of primers with an updated set of primers to obtain an updated set of primers with a lower penalty score. Bruand et al. further discloses that scoring is applied to primer design in sub-target regions (para. 0004; 0051; 0063; performing iterative design of PCR primers, avoiding the at least one avoidance region, for the plurality of sub-intervals to generate primers).
Pertaining to claims 1 and 14, Bruand et al. discloses that primers may be first designed across the entire large region, and then bad primers may be filtered out based on designability or other design criteria. (para. 0021-0022; filtering and screening the generated primers according to a preset filtering condition to obtain target primers).
Pertaining to claims 1 and 14, Bruand et al. discloses assigning each sub-target region to one or more pools of sub-target regions and for each pool, computing a ‘primer pool score’ between sets of candidate primers across sub-target regions within the pool and selecting a set of primers from the sets of candidate primers for each sub-target region in the pool based on the computed penalty scores (para. 0005; combining the obtained target primers to generate a primer pool).
Regarding claim 14, Bruand et al. discloses a processor with a network interface that provides connectivity to one or more networks or computing systems to receive information and instructions from other computing systems and to communicate to and from memory. Burand et al. further discloses that the memory may include or communicate with the data store and other data stores that store data for and results of multiplex primer selection method referenced above. Therefore, the system and methods taught by Burand et al. include receiving the primers and target intervals used and/or generated by the method referenced above (para. 0072-0074; receiving the at least one avoidance region in the target interval, receiving the generated primers, receiving the obtained target primers).
Regarding claims 2 and 17, no limiting definition of the term ‘sub-interval’ was found in the specification, so under broadest reasonable interpretation, ‘sub-interval’ will be considered to be any interval within the target interval (including avoidance regions) and the flanking region of a sub-interval could be another sub-interval. Additionally, according to the specification of the instant application, regions with low complexity include regions with polyN sequences (instant specification para. 0062). Bruand et al. discloses that the designability score of the target gene sequence may include a designability score of each sub-target region of the target gene sequence (i.e. sub-interval) and that the score of each sub-target region may be determined based on GC content, presence of poly-N stretches or the presence of a single nucleotide polymorphism (SNP). Bruand et al. further discloses ‘bad regions’ (i.e. avoidance regions in the target interval) have low designability based on GC content (i.e if the GC content for the 20-bps window around it is either less than 0.35 or more than 0.65), the number or the lack of single nucleotide polymorphisms (SNPs) and/or the number or lack of poly-N stretches of six or more base pairs. (para.0056; 0020-0022; acquiring flanking information of each sub-interval in the target interval; the flanking information including at least one of guanine-cytosine (GC) contents, single nucleotide variants (SNVs) and complexities of upstream and downstream sequences of the sub-interval; and determining a part of the plurality of sub-intervals as the at least one avoidance region in the target interval according to the flanking information.)
Pertaining to claim 17, Braund et al. discloses that SNP information may be obtained from a NP database (dbSNP) and Catalogue of Somatic Mutations in Cancer (cosmic). Bruand et al. discloses a processor with a network interface that provides connectivity to one or more networks or computing systems to receive information and instructions from other computing systems and to communicate to and from memory. Burand et al. further discloses that the memory may include or communicate with the data store and other data stores that store data for and results of multiplex primer selection method referenced above. (para. 0021 0072-0074; receiving the flanking information).
Note that claims 3 and 18 are contingent claims. As set forth in MPEP section 2111.04(II)), the broadest reasonable interpretation of a method claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met. Therefore, the method does not necessarily include the steps of claim 3.
Pertaining to claims 3 and 18, Burand et al. discloses splitting target gene sequences into multiple subpools based on designability of primers. Burand et al. further discloses that designability includes GC content of the target gene sequence. Burand et al. further discloses that criteria for estimating designability can be based on preferred GC content range of 0.35-0.65. Therefore, the disclosure is inclusive of having a subpool with a high designability score (i.e. subinterval) based on having a GC content between 0.35-0.65 that is adjacent to a subpool with a low designability score with GC content outside of this range (i.e. an avoidance region). The ranges for the GC content of an avoidance region of the instant application (i.e. >75% or <35%) overlap with and lie inside of the ranges of >65% or <35% disclosed by Burand et al. (i.e. the ranges of Burand et al. include the ranges claimed in the instant limitation). As set forth in the MPEP 2144.05(I), the GC content ranges claimed are unpatentable over Burand et al. as they are prima facie obvious (para. 0020-0021; if at least one of the upstream sequence and the downstream sequence has a GC content greater than 75% or less than 35%, determining a sub-interval where the at least one of the upstream sequence is located and the downstream sequence is located as an avoidance region in the target interval).
Pertaining to claims 3 and 18, Burand et al. discloses splitting target gene sequences into multiple subpools based on designability of primers. Burand et al. further discloses that designability includes the presence and number of known variants in the target gene sequence, with desired subpools having a fewer number or lack of single nucleotide polymorphisms (SNPs). This disclosure is inclusive of having a subpool with a high designability score (i.e. a subinterval) based on having fewer or no SNPs adjacent to a subpool with a low designability score (i.e an avoidance region) with SNPs (para. 0020-0021; if at least one of the upstream sequence and the downstream sequence has an acquired SNV, a sub-interval where the at least one of the upstream sequence and the downstream sequence is located being a mutation region, and determining the mutation region as an avoidance region in the target interval).
Pertaining to claims 3 and 18, according to the specification of the instant application, regions with low complexity include regions with polyN sequences (para. 0062). Burand et al. discloses splitting target gene sequences into multiple subpools based on designability of primers. Burand et al further discloses that designability includes the presence and number and length of poly-N stretches in the target sequence and that subpools with a fewer number or lack of poly-N stretches of six or more base pairs have high designability. This disclosure is inclusive of having a subpool with a high designability score (i.e. a subinterval) based on having fewer or no poly-N stretches of 6 or more that is adjacent to a subpool with a low designability score (i.e an avoidance region) with a higher number of poly-N stretches of 6 or more (para. 0020-0021; if at least one of the upstream sequence and the downstream sequence has a complexity lower than a preset complexity threshold, determining a sub-interval where the at least one of the upstream sequence and the downstream sequence is located as an avoidance region in the target interval).
Claims 4 and 19 contain the contingent limitation: “ if the length of the target interval is greater than the preset amplification length, acquiring a number of sub-intervals to be split from the target interval, and acquiring a range of a number of primers of a target fragment in the target interval”. As set forth in MPEP section 2111.04(II)), the broadest reasonable interpretation of a method claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met. Therefore, the method does not necessarily include this contingent limitation of claim 4.
Regarding Claims 4 and 19, Burand et al. discloses that the target gene sequence may be split into two sub-target regions based on a minimum allowed sub-target region length, a maximum allowed sub-target region length, a length of the target gene sequence, or a combination thereof (i.e. preset amplification length). Burand et al. further discloses that after splitting a target gene sequence into a plurality of sub-target regions, each sub-target region can be assigned to one of two or more pools of sub-target regions, which may be done by balancing by target gene sequences and by lengths such that each target gene sequence has similar numbers of amplicons in each pool, and the pools have similar distributions of lengths of sub-target regions. Burand et al. further discloses that after assigning the sub-target regions to the two pools, a set of primers for each sub-target region in each pool, and a penalty score associated with the set of primers, can be determined (para. 0027, 0043, 0057; [the method or computer device of claim 1 or 14, respectively] acquiring a length of each target interval according to a preset amplification length of the primers; and comparing the length of the target interval with the preset amplification length; if the length of the target interval is greater than the preset amplification length, acquiring a number of sub-intervals to be split from the target interval, and acquiring a range of a number of primers of a target fragment in the target interval).
With respect to claims 5 and 20, Burand et al. discloses that the target gene sequence may be split into two sub-target regions based on a minimum allowed sub-target region length, a maximum allowed sub-target region length, a length of the target gene sequence, or a combination thereof (i.e. preset amplification length). This disclosure is inclusive of not splitting a target sequence into sub-target regions if the length of the target sequence is less than or equal to a preset amplification length (para. 0057; [the method of claim 4 and computer device of claim 19, respectively] after comparing the length of the target interval with the preset amplification length, if the length of the target interval is less than or equal to the preset amplification length, determining that the target interval is amplified by using a pair of primers).
Regarding claims 6, Burand et al. discloses target splitting (or tiling), wherein based on the designability score, each target gene sequence can be split into a plurality of sub-target regions. Burand et al. further discloses that a split point can allow 30 base pairs on each side to allow enough room for probe design. This demonstrates capacity to detect regions adjacent to sub-intervals. Burand et al. further discloses that a split window may be selected using a moving average of the badness score and a badness score vector (which equates to shifting a sub-interval). Burand et al. further discloses that a preferred split point is one having ‘goodness’ on either side of the split (thus a sub-interval is preferred to be adjacent to another good sub-interval instead of a bad region (i.e. an avoidance region). Additionally, Burand et al. discloses that bad regions (i.e. avoidance regions) include adjacent regions (e.g. a bad region is bad if the adjacent 20 bp window around it has GC content less than 0.35 or more than 0.65 or if there are more than two SNPs in the 20 bp window around it. Because bad regions include adjacent regions, these adjacent regions would naturally be excluded from good sub-target regions (para. 0022-0024, 0026 [the method of claim 2], wherein performing the iterative design of PCR primers, for the plurality of sub-intervals to generate the primers, includes: according to a position of an avoidance region and flanking information of the target interval, determining whether a sub-interval is adjacent to the avoidance region; if the sub-interval is adjacent to the avoidance region, shifting the sub-interval to skip the avoidance region; and if the sub-interval is not adjacent to the avoidance region, maintaining a position of the sub-interval).
Pertaining to claim 21, Burand et al. discloses an iterative design of PCR primers, wherein to determine the first sets of optimized primers for the first target gene sequence, the computing system may iteratively replace a first set of primers with an updated first set of primers of the first sets of candidate primers to obtain an updated first sets of primers with a lower first penalty score (para. 0063; [the computer device of claim 17] performing the iterative design of PCR primers for the plurality of sub-intervals)
Regarding claim 21, Burand et al. discloses target splitting (or tiling), wherein based on the designability score, each target gene sequence can be split into a plurality of sub-target regions. Burand et al. further discloses that a split point can allow 30 base pairs on each side to allow enough room for probe design. This demonstrates capacity to detect regions adjacent to sub-intervals. Burand et al. further discloses that a split window may be selected using a moving average of the badness score and a badness score vector (which equates to shifting a sub-interval). Burand et al. further discloses that a preferred split point is one having ‘goodness’ on either side of the split (thus a sub-interval is preferred to be adjacent to another good sub-interval instead of a bad region (i.e. an avoidance region). Additionally, Burand et al. discloses that bad regions (i.e. avoidance regions) include adjacent regions (e.g. a bad region is bad if the adjacent 20 bp window around it has GC content less than 0.35 or more than 0.65 or if there are more than two SNPs in the 20 bp window around it. Because bad regions include adjacent regions, these adjacent regions would naturally be excluded from good sub-target regions (para. 0022-0024, 0026; determining whether a sub-interval is adjacent to an avoidance region according to a position of the avoidance region and flanking information of the target interval; shifting the sub-interval to skip the avoidance region if the sub-interval is adjacent to the avoidance region; and maintaining a position of the sub-interval if the sub-interval is not adjacent to the avoidance region.
Regarding claim 15, Bruand et al. discloses a system and a method for amplifying sub-target regions of target gene sequences including non-transitory memory configured to store executable instructions and a hardware processor programmed by the executable instructions to perform the method (para. 0004, Fig. 9; a non-transitory computer-readable storage medium having stored therein a computer program that, when executed by a processor, causes the processor to perform the method according to claim 1).
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.
12. Claims 7, 8, 16 and 22-23 are rejected under 35 U.S.C. 103 as being unpatentable over Bruand et al. (US 2020017994A1; 30 June 2023 IDS document), as applied to claims 1-6, 14-15 and 17-21 above, in view of Brown et al. (Biology Methods and Protocols, 2017, p. 1-10). The italicized text corresponds to the instant claim limitations.
The limitations of claims 1-6, 14-15 and 17-21 have been taught by Bruand et al. above.
Pertaining to claims 7 and 22, a limiting definition of the term ‘amplification interval’ has not been identified in the specification. For the purposes of examination and under broadest reasonable interpretation, an amplification interval will be considered to be any region desired to be amplified by primer pairs.
Pertaining to claims 7 and 22, Bruand et al. discloses that a set of primers (e.g. a primer pair or primer pairs) can be designed and selected using a penalty score based on a non-linear combination of a primer-level penalty score and a set-level penalty score. Bruand et al. further discloses a set of primers can be designed and selected in silico using intended target specificity, which is used to determine a set-level penalty score. Bruand et al. further discloses that ‘specificity checking’ can be done against the whole human genome when designing multiplex primers for a human panel of target gene sequences. Bruand et al. further discloses sorting primers based on penalty score and selecting primers based on the ranking (e.g. picking the first candidate primer that gives a minimum desirable improvement in penalty against the rest of the pool, such as 5%). Bruand et al. further discloses a method of scoring binding specificity of sequences based on the number of mismatches in an alignment of the sequences (para. 0019, 0044, 0047, 0049-0050, 0052, Fig. 3A-B; [the method of claim 6], wherein filtering and screening the generated primers according to the preset filtering condition to obtain the target primers, includes; aligning the generated primers to a genome to sort binding sites of the primers and the genome in reverse order and screen out a primer pair with least non-specific binding in each sub-interval, so as to obtain remaining primers after screening (claim 7); [the computer device according to claim 21] aligning the generated primers to a genome to sort binding sites of the primers and the genome in reverse order and screen out a primer pair with least non-specific binding in each sub-interval, so as to obtain remaining primers after screening (claim 22).
Pertaining to claims 7 and 22, Bruand et al. further teaches that a set of primers can be designed and selected in silico using thermodynamic properties of primers and/or dimer formation properties. Bruand et al. further teaches that along with intended target specificity, thermodynamic properties and dimer formation properties of primers may be used to determine a primer-level penalty score and that the score may be used to determine a set-level penalty score. Bruand et al. further discloses a dimer scorer that may assign a penalty to two sequences indicating how bad of a dimer they could form (e.g. that they are likely to form a forward-reverse dimer) (para. 0019, 0047-0048; filtering dimers in the remaining primers in the same amplification interval directly).
Pertaining to claim 8, Bruand et al. discloses that primer melting temperature (primer Tm) has an allowable range. (Fig. 4; para. 0011, 0046; [the method of claim 7] wherein combining the obtained target primers to generate the primer pool, includes: selecting primers within a preset temperature range according to the obtained target primers).
Pertaining to claim 23, Bruand et al. discloses that primer melting temperature (primer Tm) has an allowable range (para. 0046; the computer device according to claim 22, wherein when executing the computer program, the processor further performs: screening a temperature range adapted to the obtained target primers).
Regarding claims 7, 8, 22 and 23 Bruand et al. is silent to: labeling dimers in the remaining primers in different amplification intervals (claims 7 and 22) and splitting a combination of primers with dimer mutual exclusion into different primer pools, selecting primers without mutual exclusion for combination to generate the final primer pool (claim 8); and distinguishing a combination of primers with dimer mutual exclusion and splitting the combination of primers with dimer mutual exclusion into different primer pools (claim 23). However, these limitations were known in the art at the time of the effective filing date of the invention as taught by Brown et al.
Regarding claims 7 and 22, Brown et al. teaches software for automated primer pooling to prepare a library for targeted sequencing, wherein 1) primers are first analyzed for predicted inter-primer hybridizations (i.e. primer dimers) and intra-primer hybridizations during genome alignment which identifies overlapping primer pairs and 2) automatic primer swapping to swap primer pairs between a given number of subpools until low-potential interactions are attained. Brown et al. further discloses labeling each primer with the assigned pool (by putting the primers in different results files, each labelled with the pool number (Fig. 1, Fig. 5, p. 2, col. 2, para. 2 (steps 1-3); labeling dimers in the remaining primers in different amplification intervals).
Pertaining to claim 8, Brown et al. teaches that before PCR, careful primer design includes ensuring that all of the primers have similar melting temperatures (i.e. within a narrow range). Brown et al. teaches software for automated primer pooling to prepare a library for targeted sequencing, wherein 1) primers are first analyzed for predicted inter-primer hybridizations (i.e. primer dimers) and intra-primer hybridizations during genome alignment which identifies overlapping primer pairs and 2) then, automatic primer swapping is performed to swap primer pairs between a given number of subpools until low-potential interactions are attained. Brown et al. further discloses that the resulting pools contain primers with low dimerization potential. Brown et al. further discloses using PrimerPooler software to assign multiple primers to multiple subpools, each containing multiple primer pairs with DG values (for inter-primer pair interaction) weaker than -1.5 at 60 degrees (the user can define the temperature) and using each pool for PCR reactions (p. 2, col. , para. 2; Fig. 1; Fig. 5; p. 2, col. 2, para. 2 (steps 1-3); Table 3; p. 8, col. 1, para. 4 – p. 9, col. 1, para. 1; p. 9, col. 1, para. 4. – col. 2, para. 1; [the method of claim 7] splitting a combination of primers with dimer mutual exclusion into different primer pools, selecting primers without mutual exclusion for combination to generate the final primer pool).
Pertaining to claim 23, Bruand et al. discloses that primer melting temperature (primer Tm) has an allowable range. (para. 0046; the computer device according to claim 22, wherein when executing the computer program, the processor further performs: screening a temperature range adapted to the obtained target primers; and distinguishing a combination of primers with dimer mutual exclusion and splitting the combination of primers with dimer mutual exclusion into different primer pools).
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. Brown et al. taught that PrimerPooler provides an innovative solution to the problem of primer interactions in large multiplex reactions and offers a reliable and efficient way to choose and combine a large number of primers for PCR-based target enrichment (p. 9, col 2, para. 2). Therefore, one of ordinary skill in the art would have been motivated to utilize the method of choosing and combining a large number of primers for PCR-based target enrichment taught by Brown et al. in the method and system for multiplex PCR primer selection taught by Bruand et al. in order to minimize primer interactions in large multiplex reactions. Furthermore, one of ordinary skill in the art would predict that the primer-dimer reduction methods taught by Brown et al. could be readily added to the method system of Bruand et al. with a reasonable expectation of success because they both pertain to multiplex PCR primer selection. The invention is therefore prima facie obvious.
Pertaining to claims 16 and 23, Bruand et al. discloses that primer melting temperature (primer Tm) has an allowable range and that primers with suboptimal melting temperatures get higher penalty scores (para. 0011; Fig. 4, 0046, 0065; the method for designing multiplex PCR primers based on iteration according to claim 8, wherein the preset temperature range includes an optimal temperature range and a sub-optimal temperature range) (claim 16) and screening a temperature range adapted to the obtained target primers (claim 23)
Bruand et al. does not specifically disclose using suboptimal melting temperatures (claim 16) and screening a temperature range (claim 23), but this would be obvious to try because Bruand et al. disclose that primer melting temperature (Tm) tends to be correlated to amplicon GC content. Bruand et al. further discloses that increasing primer Tm can help amplify low GC amplicons. Bruand et al. further discloses using a scoring function based on linear regression that takes in as features amplicon GC, amplicon length and primer Tm together. Therefore, in the case of an amplicon with low GC content, the best scoring function would have a sub-optimal primer melting temperature (para. 0051; Fig. 4; the method for designing multiplex PCR primers based on iteration according to claim 8, wherein the preset temperature range includes an optimal temperature range and a sub-optimal temperature range).
It would be obvious to try using a suboptimal temperature range (or screening temperature ranges) because Bruand et al. taught that a suboptimal range is necessary for PCR amplification of amplicons that have low GC content (para. 0051; Fig. 4). Additionally, there is a finite range of melting temperatures for PCR primers, which can be classified into two categories as optimal or suboptimal. A person having ordinary skill in the art could have tried using a suboptimal melting temperature with reasonable expectation of success because Bruand et al. discloses a relationship between melting temperature and GC content in optimizing conditions for PCR amplification (para. 0051). Therefore, using a suboptimal temperature and screening temperature ranges are prima facia obvious.
Conclusion
13. 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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