DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims / Response to Amendment
This office action is in response to an amendment filed on May 23, 2025.
Claims 1-12 and 14-19 were previously pending. Applicant amended claim 1 and cancelled claim 3.
Claims 1-2, 4-12 and 14-19 are currently pending, with claims 9-11, 15-19 withdrawn.
Claims 1-2, 4-8, 12 and 14 are under consideration.
Applicant's claim amendment overcame the following rejections:
Rejections of claims 1-4 and 6-8 35 U.S.C. 103 as being unpatentable over Mir, as evidenced by Joseph and Wikipedia;
Rejections of claims 5, 12 and 14 under 35 U.S.C. 103 as being unpatentable over Mir and further in view of Kamberov.
The previously set forth 103 rejections have been withdrawn in view of the recent claim amendment filed on May 23, 2025, which added new limitation to the independent claim 1, thereby modifying the scope of the claims.
This office action contains new grounds of 103 rejections necessitated by Applicant's amendments. Although the claims were previously rejected as being unpatentable over the same reference(s), Applicant's amendments have necessitated the inclusion of new grounds of rejections in this Office action.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority
The priority date of the instant claims 1-2, 4-8, 12 and 14 is 02/15/2019, filling date of the US provisional application NO. 62/806,698.
Claim Rejections - 35 USC § 103 -- New Grounds
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.
Claims 1-2, 4-8, 12 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Mir (US20160304935A1- Systems and methods for whole genome amplification; Published on 2016-10-20), in view of Kamberov (US20180030522A1- Amplification and analysis of whole genome and whole transcriptome libraries generated by a dna polymerization process ; Published on 2018-02-01);
as evidenced by
Joseph (US7833709B2- Thermo-controllable chips for multiplex analyses; published on 2010-11-16),
NCBI (Polymerase Chain Reaction (PCR),web.archive.org/web/20180816224757/https://www.ncbi.nlm.nih.gov/probe/docs/techpcr/; Archived August 16, 2018 on WaybackMachine), and
Wikipedia (Genome size - Wikipedia; Archived July 15, 2017 on WaybackMachine).
A) Mir teaches methods for whole genome amplification and sequencing for detection of nucleic acid variants in samples (entire document).
Regarding claim 1, Mir teaches a method of detecting single nucleotide polymorphism (SNP) and copy number variation (CNV) in a sample (entire document, [0008] for example), the method comprising:
using a sample comprising nucleic acid molecules ([0007-0008]; [0019-0020] and [0022] single cells for example), wherein the nucleic acid molecules comprise genomic DNA or RNA ([0007], samples of genomic DNA and/or RNA) ;
simultaneously ([0008] teaches a subset of primers for whole genome amplification are specific for nucleic acid target of interest, see lines 21-23)contacting the nucleic acid molecules with a population of primers for whole genome amplification ([0008]line7; [0023]; [0020]; [0021]) and to at least two target- specific primers for targeted amplification ([0008]line7, 20-22 “at least subsets of said primers are specific for a nucleic acid target of interest” subsets are at least two; 28-31 “the amplification comprises both WGA (e.g., with a single primer) and PCR (e.g., with a plurality of target specific primers)”; [0021]) to generate a mixture of amplicons ([0008]line 12) produced by the whole genome amplification and the targeted amplification;
subjecting the mixture of amplicons produced in step b) to an additional targeted amplification ([0032]lines 1-3) using at least one nested primer pair ([0032] line 9, nested PCR, which inherently requires at least one primer pair for the reaction to be carried out) to further amplify amplicons generated by the targeted amplification;
sequencing the mixture of amplicons using a sequencing assay on a sequencer to generate sequencing reads ([0008] lines 16-19; [0084] illumina MiSeq sequencer); and
assessing the sequencing reads ([0020]; [0084]) to determine the SNP and CNV in the sample([0020]).
Mir teaches and suggests all of the claim limitations of claim 1. While Mir does not explicitly teach a step of obtaining a sample, this is inherently taught/suggested by Mir because its methods rely on the presence of a sample containing nucleic acids to perform the amplification and sequencing. A method for analyzing nucleic acids in a sample cannot be practiced without first having the sample. Thus, obtaining the sample is an inherently necessary step for the methods taught by Mir. A skilled artisan would have recognized that in any method requiring nucleic acid analysis, a sample must be obtained as an initial step to analyze the nucleic acids. Additionally, Mir inherently teaches obtaining a sample by citing Joseph in para. [0048], incorporated by reference in its entirety. Joseph teaches obtaining a sample comprising nucleic acids for nucleic acid amplification (col 21, lines 50-67 to col 22, lines 1-11).
The method in claim 1 has been amended by Applicant to recite: "subjecting the mixture of amplicons produced in step b) 1to an additional targeted amplification using at least one nested primer pair to further amplify amplicons generated by the targeted amplification."
Mir teaches and suggests this newly added limitation.
First, Mir teaches step b) by teaching performing whole genome amplification (WGA) by contacting the sample comprising genomic DNA with primers for whole amplification ([0008], lines 1-7), and that "at least subsets of said primers are specific for a nucleic acid target of interest." ([0008] lines 21-23). Thus, a skilled artisan would understand, in view of the disclosure above, that Mir teaches simultaneously contacting the nucleic acid molecules in a sample with a population of primers for whole genome amplification and at least two target-specific primers for targeted amplification.
Mir further states that "[t]he methods disclosed herein for WGA and optionally target-specific amplification may comprise conducting one or more amplification reactions," and teach that nested PCR is one of the amplification techniques suitable for such use ([0032]). Thus, Mir suggests that nested PCR may be used to further amplify the amplicons generated in the initial amplification step. While Mir does not expressly recite "at least one nested primer pair," this limitation is inherently taught, as PCR by definition requires at least one primer pair to function, as evidenced by NCBI (page 1 "How it works").
Second, the specific approach of performing targeted nest PCR amplification following initial whole genome and targeted amplification is further supported by Kamberov.
Similar to Mir, Kamberov teaches methods for whole genome amplification (WGA) using a primer mixture, followed by sequencing, for detection of nucleic acid variants in samples (entire document).
Kamberov further provides detailed teaching of performing nested PCR with primer pairs ([0348-0353]) as a secondary targeted amplification step following whole genome amplification and targeted amplification ([0349] lines 10-13; [0353]). Kamberov suggests that for complex genomes, the additional nested PCR may be necessary to achieve the desired level of purity for the amplicons of interest ([0348]; [0290]"Those skilled in the art will recognize that genomic complexity may dictate the requirement for sequential or nested amplifications to amplify a single species of DNA to purity from a complex WGA library").
Kamberov provides further motivation for this approach, such as improved enrichment by additional two orders of magnitude ([0349] lines 10-13) and improved assay performance in sensitivity and specificity by compensating for non-specific priming in initial amplification reactions ([0352] lines 11-18).
Accordingly, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply an additional amplification step using nested PCR, to the method of Mir comprising simultaneous amplification with both whole genome and target-specific primers. Mir already teaches nested PCR as a suitable amplification approach within its teachings, and Kamberov provides further support and motivation for applying this specific approach to improve target amplicon enrichment and assay performance in complex genome samples.
The person of ordinary skill would have had a reasonable expectation of success in applying nested PCR to further amplify the amplicon mixture generated in Mir because Mir explicitly identifies nested PCR as one of the amplification techniques suitable for use in its method. Thus, a skilled artisan would have appreciated that nested PCR is technically compatible with the whole genome amplification and sequencing methods disclosed in Mir. It is well within the skill level of a person of ordinary skill to perform further targeted amplification of an existing amplicon library using nested PCR. Doing so would have yielded the predictable result of a method for detection of nucleic acid variants with improved enrichment of detection targets.
The skilled artisan would have been motivated to do so, to leverage the potential benefits of performing an additional nested PCR step in the detection of rare nucleic acid variants within complex genomes, such as significantly enhanced target enrichment and improved amplification specificity, as suggested by Kamberov.
B) Regarding claim 2, Mir teaches nucleic acid molecules are amplified by using a polymerase chain reaction ([0008] lines 28-31).
Regarding claim 4, Mir teaches using the sequencing reads to genotype single nucleotide variation (SNV), detect insertion and/or deletion , gene fusions ([0008], lines 12-19).
Regarding claim 5, Kamberov teaches degenerate primers that are non-self- complementary and non-complementary to other primers in the population, and comprise in a 5' to 3' orientation a constant region and a variable region ([0059-60];[0061]lines 6-9), wherein the constant region sequence has a known sequence that is constant among a plurality of primers of the population and the variable region sequence is degenerate among the plurality of primers of the population ([0063]), and further wherein the sequence of the constant and variable regions consists will not cross-hybridize or self-hybridize under nucleic acid processing conditions (Abstract, lines 8-10).
Regarding claim 6, Mir teaches plurality of nucleic acid molecules is at least 50 base pairs by teaching genomic DNA ([0007] for example). Genomic DNAs are nucleic acid molecules that are more than 50 base pairs, as evidenced by Wikipedia (page 1).
Regarding claim 7, Mir teaches primers comprise at least 10 nucleotides (SEQ ID Nos: 1-7).
Regarding claim 8, Mir teaches at least two target-specific primer is specific to two or more target sequences ([0008]lines 21-23; [0028]lines19-23).
Regarding claim 12, Kamberov teaches melting temperature of the primers is at least 30 degrees Celsius ([0351] line 6).
Regarding claim 14, Kamberov teaches using biopsied embryo ([0111]) as a sample type.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 Step b) in claim 1 recites:
“b) simultaneously contacting the nucleic acid molecules with:
(i) a population of primers for whole genome amplification or whole transcriptome amplification; and
(ii) at least two target-specific primers for targeted amplification;
to generate a mixture of amplicons produced by the whole genome amplification or whole transcriptome amplification and the targeted amplification."
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