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 .
Claim Status and Action Summary
This action is in response to the papers filed October 24, 2025.
Currently, claims 39-41 and 45-59 are pending. Claims 46-59 were newly added in the amendment filed October 24, 2025. Claims 56-57 are withdrawn as directed to non-elected species (see elections/restrictions section below).
Claims 39-41, 45-55, and 58-59 are under examination.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission filed on October 24, 2025 has been entered.
Any objections and rejections not reiterated below are hereby withdrawn.
The new matter rejections of record in the preceding final office action have been withdrawn in view of the amendments to the claims and the showing in the response that “a polynucleotide fragmentation reagent for use in preparing polynucleotides for next-generation sequencing” (i.e. fragmentation reagents found in NGS kits) were well-known in the art prior to and at the time of filing of the claimed invention. In particular, the table bridging page 7-8 of the remarks (reproduced below for convenience) demonstrates a number of well-known and widely used NGS kits comprising polynucleotide fragmentation reagents that were available prior to the filing date of the claimed invention.
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The 112(b) indefiniteness rejections of record have been withdrawn in view of the amendments to the claims requiring that the nucleotides in the artificial portion of [the control] polynucleotide have a same relative order as in a 5’ to 3’ portion of the target polynucleotide AND are connected in the 3’ to 5’ direction, wherein the 5’ to 3’ sequence of [the control] polynucleotide is distinguishable from the 5’ to 3’ portion of the target polynucleotide (i.e. the target polynucleotide is not a palindrome), AND wherein the 3’ to 5’ sequence of [the control] polynucleotide is the same sequence as the 5’ to 3’ sequence of the target polynucleotide (i.e. the only difference between the target and control polynucleotides is that the directionality of the control polynucleotide has been reversed relative to the target polynucleotide).
The provisional double patenting rejection over copending application number 18/412,450 has been withdrawn in view of the approved terminal disclaimer filed in the application 18/412,450 over the present application.
Election/Restrictions
Applicant’s election without traverse of human gene locus EGFR and the corresponding variation COSM6224 (claims 20-32, 35-37, and 39-43) in the reply filed on October 2, 2024 is acknowledged.
Claims 33-34, and 37-38 were withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on October 2, 2024.
Claims 56 and 57 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse to EGFR and COSM6224 (i.e. a single nucleotide polymorphism) in the reply filed on October 2, 2024.
Priority/Effective Filing Date
This application is a continuation filing of U.S. Patent Application No. 15/535,768 filed on June 14, 2017, which is a 371 of PCT/AU2015/050797, filed on December 15, 2015, and claims priority to Australian applications 2015903892 (filed September 24, 2015) and 2014905092 (filed on December 16, 2014).
AU2014905092 and AU2015903892 do not provide support for the claimed “reversed sequences”. Therefore, claims 39-41, 45-55, and 58-59 receive the benefit of priority to the December 15, 2015 PCT filing date.
Drawings
The drawings filed March 10, 2025 are acceptable.
Specification
The substitute specification filed March 10, 2025 is acceptable.
Claim Rejections - 35 USC § 112- Indefiniteness
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.
Claims 46 and 47-48 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, regards as the invention.
Claims 46 and 47-48 recite the limitation "the polynucleotide". There is insufficient antecedent basis for this limitation in the claim. Claim 39, upon which these claims depend, recites “A composition comprising… an amount of a target polynucleotide… and a predetermined amount of a polynucleotide comprising an artificial portion…”. It is unclear whether “the polynucleotide”, recited by claims 46 and 47-48 is intended to refer to the target polynucleotide, the polynucleotide comprising an artificial portion, both of these polynucleotides, or something else.
Claim 46 recites the limitation "the at least 10,000 contiguous nucleotides" in lines 7 and 10. There is insufficient antecedent basis for this limitation in the claim. Claim 46 begins “The composition of claim 39, wherein the polynucleotide consists of no more than 10,000 contiguous nucleotides…” Therefore, there is not sufficient antecedent basis for “the at least 10,000 contiguous nucleotides…” AND the limitations of the claim appear to be contradictory as presently amended. It is unclear whether applicant intends to claim that “the polynucleotide” has a maximum length of 10,000 nucleotides or that “the polynucleotide” has a minimum length of 10,000 nucleotides.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 39 and 45-48 are rejected under 35 U.S.C. 103 as being unpatentable over WO 9914376 A2 (Jian, 1999) in view of US 6395470 B2 (WalkerPeach, 2002), Tan et al., “Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities” Frontiers in Microbiology 6:1027 (published September 25, 2015), and Satinsky et al., “Microspatial gene expression patterns in the Amazon River Plume” PNAS vol. 111, no. 30, pp. 11085-11090 and supplemental methods (published July 29, 2014).
Regarding claim 39, Jian teaches 55-2,000 nucleotide long internal control DNA sequences comprising non-natural, synthetic DNA sequences corresponding to target human genomic DNA sequences. (Jian, claims 9, 10, and 14) Jian teaches that said synthetic control sequences are generated by scrambling the naturally occurring sequence. (Jian, page 11, lines 17-20) Jian does not teach that the non-natural, synthetic DNA sequences are in the same relative order as in a 5’ to 3’ gene locus and are connected in the 3’ to 5’ direction.
However, WalkerPeach teaches an internal control cassette (i.e. a polynucleotide) comprising a portion of a gene sequence wherein the 5’ to 3’ connectivity of the nucleic acid sequence is reversed (i.e. 3’ to 5’ direction) (WalkerPeach, figure 1 and column 4, lines 35-50) For example, Walker-Peach teaches an internal control cassette comprising a 148 base pair segment of the HSV gB gene, with the central 39 base pairs in the reverse orientation. (WalkerPeach, column 6, line 55-65 and SEQ ID NO 2; underline added to show inversion)
Furthermore, WalkerPeach teaches several advantages of inverted polynucleotide sequences as internal controls. Namely, WalkerPeach teaches that the control sequences generated by inverting a target sequence share many of the same biochemical characteristics of the target sequences (e.g. reaction kinetics, melting temperature, and melting composition). (WalkerPeach, Column 5, line 18-27) In addition, WalkerPeach teaches: “Another important feature of the present invention is the length and composition of the control sequence. The length and composition of the sequence amplified may affect the signal obtained from the assay. During polymerization, the action of the synthesizing enzyme traveling down the template strand is known as processivity. The processivity of the enzyme may decrease as the length of the target sequence increases. So, the longer the target sequences, the more likely that it is that the PCR enzyme will fall off the template before completing the synthesis of the replicated strand. Premature termination of polymerization results in a product that differs in length from the target sequence and that difference could be misread as a negative result. The positive control of the present invention eliminates this problem. Since the amplified region of the positive control plasmid is the same length as the target sequence, the rate of premature termination should be the same for both sequences. As a result, if there are apparent qualities of the target sequence which cause the PCR enzyme to fall off, those same characteristics should be present in the inverted control sequence and the PCR enzyme should fall off that sequence as well.” (WalkerPeach, Column 6, line 24-45)
Tan et al. teach several protocols have been developed to quantify absolute gene copy numbers or transcripts within a metagenome or metatranscriptome (i.e. using NGS) by benchmarking to standards wherein a known amount of standard was added to a sample prior to total RNA/DNA extraction, library construction, and high throughput sequencing (i.e. prior to fragmentation with a polynucleotide fragmentation reagent of a NGS polynucleotide sample preparation kit) (Tan et al., page 4, column 2, paragraph 3).
Furthermore, Satinsky et al. (cited by Tan et al.) explicitly teach adding DNA or RNA internal standards immediately prior to cell lysis (i.e. prior to fragmentation) (Satinsky et al., supplemental methods, page 2, paragraph 3 “Internal Standards”).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to modify the scrambled internal control DNA segments taught by Jian to comprise an inverted control sequence of equal length to the corresponding target nucleic acid as taught by WalkerPeach. The ordinary artisan would have been motivated to modify the controls of Jian to comprise inverted sequences as taught by WalkerPeach because of the suggestion of WalkerPeach that differences in length and base composition between a control and target sequence can contribute to false negative results in nucleic acid assays. (WalkerPeach, Column 6, line 24-45) Therefore, the ordinary artisan would have had a reasonable expectation that inversion of target sequences present in the internal control polynucleotides taught by Jian would have successfully lowered the rate of false negative results in the nucleic acid detection assays taught by Jian.
Even more, the ordinary artisan would have been motivated to introduce the internal control polynucleotides comprising inverted sequences prior to lysing cells for NGS library construction by the express teachings of Tan et al. and/or Satinsky et al. that internal standards are to be added prior to fragmentation and NGS library construction (Tan et al., page 4, column 2, paragraph 3; Satinsky et al., supplemental methods, page 2, paragraph 3 “Internal Standards”).
Regarding claim 45, Jian teaches 55-2,000 nucleotide long internal control DNA sequences comprising non-natural, synthetic DNA sequences corresponding to target human genomic DNA sequences. (Jian, claims 9, 10, and 14) Jian teaches that said synthetic control sequences are generated by scrambling the naturally occurring sequence. (Jian, page 11, lines 17-20) Jian further teaches a method of constructing a plasmid comprising the control DNA sequence. (Jian, page 11, line 21- page 12, line 34).
Jian does not teach that the control DNA sequences are in the same relative order as in a 5’ to 3’ gene locus and are connected in the 3’ to 5’ direction. However, WalkerPeach teaches a method of constructing an internal control cassette (i.e. synthesizing a polynucleotide) involving creating a DNA fragment containing a 148 bp portion of the HSV gB gene wherein a portion of said gene is reversed. (i.e. obtaining a sequence, reversing the sequence, and synthesizing the polynucleotide). (WalkerPeach, column 6, line 55- column 7, line 13).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to modify the method of designing and synthesizing internal control polynucleotides of length 55-2,000 (i.e. at least 1,000 nucleotides) taught by Jian by reversing, rather than scrambling, a given sequence as taught by WalkerPeach. The ordinary artisan would have been motivated to modify the control polynucleotides of Jian by reversing, rather than scrambling a given sequence because of the teaching of Jian and WalkerPeach that the target and control polynucleotides must be as similar in length and base composition as possible to reduce signal amplification bias in nucleic acid detection assays. Therefore, the ordinary artisan would have reasonably expected synthetic, sequence-inverted 55-2,000 nucleotide long polynucleotides to function as successful internal controls in nucleic acid detection assays.
Regarding claim 46, this claim differs from claims 39 and 45 only in that “the polynucleotide” (presumably the polynucleotide having the artificial portion; i.e. the internal standard) “consists of no more than 10,000 contiguous nucleotides” OR “at least 10,000 contiguous nucleotides”. WalkerPeach teaches the properties (length, sequence composition, etc.) of a control polynucleotide advantageously resemble those of a corresponding target polynucleotide as closely as possible to reduce biases in amplification (WalkerPeach, Column 6, line 24-45).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have prepared a control polynucleotide of any length (i.e. consisting/comprising of up to and/or including 10,000 contiguous nucleotides) corresponding to any particular sequence of interest, motivated by the teachings of WalkerPeach that target and control polynucleotides share as many physical properties (including length) as is possible. Therefore, the ordinary artisan would have had a reasonable expectation that reversing any particular nucleic acid sequence of interest (i.e. a target) would have predictably functioned as a control in PCR, NABSA, and/or NGS-based quantitative assays as taught by Jian in view of WalkerPeach, Tan et al., and Satinsky et al.
Regarding claims 47-48, Tan et al. and Satinsky et al. teach the internal standards can be RNA or DNA (Satinsky et al., supplemental methods, page 2, paragraph 3 “Internal Standards”).
Response to Arguments
The response argues that said including a polynucleotide fragmentation reagent renders the internal control polynucleotide taught by Jian in view of WalkerPeach inoperable. This argument has been thoroughly reviewed but is not persuasive. Claim 39 is a composition claim (i.e. products) and is not directed to methods or method steps as argued. Furthermore, Tan et al. and Satinsky et al. expressly teach adding known quantities of internal standards to samples comprising target nucleic acids prior to cell lysis and NGS library construction (i.e. prior to nucleic acid fragmentation) which necessarily results in a composition comprising the internal standards, target nucleic acids, and a polynucleotide fragmentation reagent of a NGS kit.
Claims 49-52 are rejected under 35 U.S.C. 103 as being unpatentable over WO 9914376 A2 (Jian, 1999) in view of US 6395470 B2 (WalkerPeach, 2002), Tan et al., and Satinsky et al., as applied to claims 39 and 45-48, and further in view of Zook et al. “Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.” Nat Biotechnol 32, 246–251 (2014).
Regarding claims 49-52, Jian in view of WalkerPeach, Tan et al., and Satinsky et al. does not teach sequence-reversed control polynucleotides are derived from a specific human reference genome, namely NA12878. However, Zook teaches NA12878 as a “genome in a bottle”, “a whole-genome reference material… for sequencing and assessing variant-call accuracy and understanding biases.” (Zook, page 246, line 3-7) Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to modify the internal control sequence of Jian in view of WalkerPeach, Tan et al., and Satinsky et al. to select an extremely well characterized benchmark genome (i.e. a reference genome; from a specific human) as a source material for derived control polynucleotides as taught by Zook. The ordinary artisan would have been motivated to use the NA12878 as taught by Zook as a source material for spike-in control polynucleotides for modification of the polynucleotides that are sequence-reversed taught by Jian in view of WalkerPeach, Tan et al., and Satinsky et al. because Zook teaches that “high-confidence genotype calls from a well-characterized whole genome are useful for assessing biases and rates of accurate and inaccurate genotype calls in any combination of sequencing and bioinformatics methods. High-confidence genotype calls for publicly available genomes will be particularly useful for performance assessment of rapidly evolving sequencing and bioinformatics methods.” (Zook, page 251, column 1, paragraph 3) Therefore, the ordinary artisan would have had a reasonable expectation that sequence-reversed polynucleotides derived from NA12878 would have been successful as spike-in controls for quantitation of the corresponding 5’ to 3’ sequences in an experimental sample.
Claims 52-55 and 58-59 are rejected under 35 U.S.C. 103 as being unpatentable over WO 9914376 A2 (Jian, 1999) in view of US 6395470 B2 (WalkerPeach, 2002), Tan et al., and Satinsky et al., as applied to claims 39 and 45-48, and further in view of US 2015/0133314 A1 (Shahbazian, Published May 14, 2015).
Regarding claims 52-55, Jian in view of WalkerPeach, Tan et al., and Satinsky et al. teaches sequence-reversed control polynucleotides can be derived from human gene loci. (Jian, page 12, line 35- page 13, line 10) Jian in view of WalkerPeach does not teach sequence-reversed control polynucleotides are derived from a specific human reference genome, namely hg19. However, Shahbazian teaches control reagents for Next-Generation Sequencing (NGS) assays. Shahbazian teaches “designing a control sequence comprising a representative sequence of a particular gene of interest and/or variants thereof (e.g., those targeted by commercially-available NGS tests such as the AMPLISEQ Cancer Hotspot Panel v2… (i.e. a single nucleotide polymorphism (SNP)) …[comprising] identifying sequence from a genome reference source (e.g., Genome Reference Consortium Human Reference 37 (GRCh37)).” (i.e. hg19) (Shahbazian, 0045-0047)
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to modify the hg19-derived control sequences taught by Shahbazian by inverting the corresponding sequence of interest as taught by Jian in view of WalkerPeach, Tan et al., and Satinsky et al. The ordinary artisan would have been motivated to modify the control sequences taught by Shahbazian by inverting the sequence of interest as taught by Jian in view of WalkerPeach, Tan et al., and Satinsky et al. because of the teaching of WalkerPeach that “Premature termination of polymerization results in a product that differs in length from the target sequences and that difference could be misread as a negative result. The positive control of the present invention eliminates this problem. Since the amplified region of [the inverted control] is the same length as the target sequence, the rate of premature termination should be the same for both sequences. (WalkerPeach, column 6, line 33-41) Therefore, the ordinary artisan would have had a reasonable expectation that modifying the human NGS-control polynucleotides taught by Shahbazian by inverting a sequence of interest, as taught by Jian in view of WalkerPeach, Tan et al., and Satinsky et al. would have successfully produced ideal internal control polynucleotides for wild-type and variant human gene loci.
Regarding claim 58-59, Shahbazian teaches synthesizing control sequences for “particular gene(s) of interest and/or variants thereof (e.g., those targeted by commercially-available NGS tests such as the AMPLISEQ Cancer Hotspot Panel v2)…” (Shahbazian, 0046) Shahbazian further teaches control polynucleotides comprising a portion of the EGFR gene locus (Shahbazian 0034) and multiple variants thereof including COSM6224 (Shahbazian, Tables 1 and 5).
Claims 40-41 are rejected under 35 U.S.C. 103 as being unpatentable over WO 9914376 A2 (Jian, 1999) in view of US 6395470 B2 (WalkerPeach, 2002), Tan et al., and Satinsky et al., as applied to claims 39 and 45-48, and further in view of WO-2015095689-A1 (Tyler, 2015).
Regarding claims 40 and 41, Jian in view of WalkerPeach, Tan et al., and Satinsky et al. teaches a composition comprising a known amount of 55-2,000 nucleotide long internal control cassettes (ICC) (the reversed polynucleotide) and target templates are present in the same experimental tube. (WalkerPeach, column 12, line 60- column 13, line 2).
Satinsky et al. teach approximately 1% (i.e. 0.1-10%) of polynucleotides in the composition are internal standard polynucleotides (Satinsky et al., supplemental methods, page 2, paragraph 3 “Internal standards”)
Jian in view of WalkerPeach, Tan et al., and Satinsky et al. do not teach that less than 0.5% of polynucleotides in the composition comprise the “artificial” portion of claim 20. However, Tyler teaches a “run control” composition comprising control polynucleotides and a target nucleic acid (Tyler, claim 10). Tyler teaches said control polynucleotides are “synthetic DNA strands configured to mimic stool sample target DNAs with respect to their characteristics and/or behavior during sample processing and results produced in DNA detection assays, e.g. to detect… a mutation).” (Tyler, page 17, line 1-5) Finally, Tyler teaches that the ratio between the target and control polynucleotides is associated with the presence of disease in a subject (Tyler, claim 10) and that said ratio is between 0.01 to 0.06 (Tyler, claim 14) or 0.03 to 0.15 (Tyler, claim 12) (i.e. said composition contains less than 0.5% control polynucleotide) (i.e. said composition contains between 0.1 and 10% control polynucleotide)
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to prepare a composition of control and target polynucleotides wherein less than 0.5% of polynucleotides in the composition are 55-2,000 nucleotide long control polynucleotides prepared by the sequence reversing method taught by Jian in view of WalkerPeach because Tyler teaches compositions within said range and suggests that “a useful set of controls comprises amounts of the diagnostic biomarkers that reflect typical high, low, and negative DNA values found in [patient samples].” (Tyler, page 28, line 28-30) Therefore, the ordinary artisan would have been reasonably confident that inclusion of a low amount (less than 0.5%) of control polynucleotide would have successfully enabled detection of low frequency mutations in a sample.
Conclusion
No claim is allowed.
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682