DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I (claims 33-40, 42, and 47), drawn to products: an isolated polynucleotide sequence, a composition comprising two or more polynucleotide sequences, and a kit comprising a polynucleotide sequence, in the reply filed on 09/10/2025 is acknowledged.
Group II (claim 41), drawn to a method of making the polynucleotide sequence, and Group III (claims 43-46), drawn to methods of using the polynucleotide sequences, are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group I and Group II, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/10/2025.
Applicant’s election without traverse of patentably distinct species of product (claim 40), drawn to product: an isolated polynucleotide sequence, in the reply filed on 09/10/2025 is acknowledged.
Upon further consideration, Specie election II in the requirement for restriction/election filed on 06/10/2025 for claim 40, drawn to a vector comprising a DNA sequence encoding the isolated polynucleotide sequence of claim 33, claim 42, drawn a composition comprising two or more polynucleotide sequences of claim 33, and claim 47, drawn to a kit comprising a polynucleotide sequence of claim 33, has been withdrawn.
Claims Status
Claims 33-45 and 47are pending.
Claims 41 and 43-45 are withdrawn.
Claims 33-40, 42 and 47 are currently under examination
Priority
This application is a continuation of International Application No. PCT/AU2021/050123, filed February 12, 2021, which claims the benefit of Australian Application No. 2020900400, filed February 13, 2020, and Australian Application No. 2020900401, filed February 13, 2020.
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in AU 2020900400 and AU 2020900401 on February 13, 2020. It is noted, however, that the applicant has not filed a certified copy of the AU 2020900400 or AU 2020900401 application as required by 37 CFR 1.55. Accordingly, the priority date of instant claims is determined to be, February 12, 2021 the filing date of PCT/AU2021/050123.
Specification
The listing of references in the specification is not a proper information disclosure statement. The specification filed on 08/10/2022 includes a list of references on pages 79- 80. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Objections
Claim 39 is objected to because of the following informalities: the limitation Claim 39 recites “which is a DNA or an RNA polynucleotide sequence” (ln 1-2). The claim should read as to further limit the independent claim. Therefore, if the polynucleotide sequence is the subject being further limited, it should read “wherein the polynucleotide sequence is DNA or RNA.” Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 33-40, 42 and 47 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 33 and 37 are indefinite over the limitations “wherein the calibration sequences each independently represent a naturally occurring polynucleotide sequence” (Claim 33 ln 3-4), “wherein the calibration sequences are arranged consecutively within the polynucleotide sequence in an arrangement not found in any naturally occurring genome” (Claim 33 ln 4-6), and “wherein: i) one calibration sequence represents a maternally derived polynucleotide and another calibration sequence represents a paternally derived polynucleotide; and/or ii) the naturally occurring polynucleotide sequence is derived from a human, prokaryote, bacteria, virus, phage or organelle genome” (Claim 37 ln 2-5). Furthermore, the specification states “The polynucleotide sequences disclosed herein contain two or more calibration sequences that are artificially arranged to form a linear sequence that is not otherwise present in natural genomes or transcriptomes” (Pg. 25) and “the calibration sequences may be identical to naturally occurring genomic sequences, they may be provided in an unnatural form through their artificial arrangement in the adaptors disclosed herein. This unnatural form may simply be the presentation of the calibration sequences within the adaptor sequence disclosed herein. It will be appreciated that the preparation of the adaptor sequences disclosed herein requires the generation of a polynucleotide sequence that is not found in nature.” (Pg. 31). Therefore the claims are towards a product (an isolated polynucleotide sequence) that is limited by the phrase “not found in any naturally occurring genome”, that comprises two calibrations sequences which in themselves are considered naturally occurring (see claim 34-35). It is unclear as to what structures would not be found in nature, as every genome has not been identified and/or characterized for fusion arrangement. As such the limitation of “not found in any naturally occurring genome” does not clearly provide the metes and bounds of the isolated polynucleotide sequence. Therefore, the claim language of claims 33 and 37 are indefinite as to the unclear metes and bounds of a polynucleotide sequence in arrangement not found in any naturally occurring genome. Claims 34-40, 42 and 47 depend on claim 33.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 33-40, 42 and 47 are rejected under 35 U.S.C. 101 because the claimed invention is directed towards a naturally occurring nucleotide sequence which is a product of nature, without significantly more. The claim(s) recite(s) natural phenomena. This judicial exception is not integrated into a practical application because no additional elements integrate the judicial exceptions into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because no additional elements are considered significantly more than the judicial exceptions.
Claim analysis
The instant claim 33 is directed towards: An isolated polynucleotide sequence comprising: a primer sequence; and two or more calibration sequences, wherein the calibration sequences each independently represent a naturally occurring polynucleotide sequence, and wherein the calibration sequences are arranged consecutively within the polynucleotide sequence in an arrangement not found in any naturally occurring genome.
The “the calibration sequences each independently represent a naturally occurring polynucleotide sequence” is a natural phenomenon. See MPEP 2106.04(b).
Dependent claims set forth further limitations about calibration sequence and polynucleotide sequence.
Claim 34-35 are directed to a structures of calibration sequence that comprise naturally occurring sequence to any one or more of cancer, inherited disease, a pathogen, drug-resistance, circulating tumor DNA, circulating fetal DNA, circulating maternal DNA which is considered a product of nature.
Claim 36-39, 42 do not add any structural element apart from the structures that are considered products of nature.
Claim 40 is drawn to the structures in vectors. The vectors are not limited to any particular vectors and therefore can encompass naturally occurring bacterial plasmid vectors. Therefore the claim does not add any structures that are not considered products of nature.
Claim 47 is a kit comprising the isolated polynucleotide and one or more enzymes. The term “kit” is not defined and therefore does not provide any structural limitations. Furthermore, the enzymes can include enzymes found in nature such as nuclease.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case, the Step 1 requirement is satisfied as the claims are directed towards a composition of matter.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, natural phenomena.
With regard to claim 33, the claim recites “An isolated polynucleotide sequence comprising: a primer sequence; and two or more calibration sequences, wherein the calibration sequences each independently represent a naturally occurring polynucleotide sequence, and wherein the calibration sequences are arranged consecutively within the polynucleotide sequence in an arrangement not found in any naturally occurring genome.” The “the calibration sequences each independently represent a naturally occurring polynucleotide sequence” is a natural phenomenon.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? No, there are no additional steps that integrate the claims into a practical application.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, there are no additional elements that are significantly more than the judicial exceptions.
As stated in the 35 U.S.C. 112 (b) rejection above, claim 33 is indefinite as to the metes and bound of a polynucleotide not found in nature.
Regarding claim 33, the claim requires the natural phenomenon of an isolated polynucleotide sequence comprising: a primer sequence; and two or more calibration sequences, wherein the calibration sequences each independently represent a naturally occurring polynucleotide sequence, and wherein the calibration sequences are arranged consecutively within the polynucleotide sequence in an arrangement not found in any naturally occurring genome similar to that of Timothy Mercer (“Mercer”; Patent App. Pub. US 20180148778 A1, May 31, 2018). Additionally, even though these sequence appear to attempt to limit the structure, the components of the structure are all nucleic acid sequences which do not have a structural difference between those in the prior art.
Dependent claims require further limitations about the calibration sequence(s) and polynucleotide sequence That do not add any structural component that is different from products of nature.
Claim Rejections - 35 USC § 102
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.
Claims 33-40, 42 and 47 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Timothy Mercer (“Mercer”; Patent App. Pub. US 20180148778 A1, May 31, 2018).
Mercer discloses “artificial controls for genetic sequencing and quantitation assays, which can be used to calibrate a wide variety of genetic sequencing and quantitation methods. For example, the controls disclosed herein can be used to calibrate a wide variety of high throughput sequencing methods (for example, those referred to as next generation sequencing methods). The present disclosure also generally relates to the use of the sequencing controls in a wide variety of applications including, for example, in the calibration of a wide variety of sequencing methods” (Abstract).
Regarding claim 33, Mercer teaches a polynucleotide sequence comprising “primer sequences” (Para. 193). Mercer teaches a polynucleotide sequence comprising “two or more fragments … conjoined to form a contiguous polynucleotide sequence.” (Para. 15). Mercer teaches a polynucleotide sequence comprising “nucleotides of the artificial polynucleotide sequence can have less than 100% sequence identity with any known naturally occurring genomic sequence of the same length” (Para. 10). ”artificial polynucleotide sequence” reads on not found naturally found. “nucleotides of the artificial polynucleotide sequence can have less than 100% sequence identity with any known naturally occurring genomic sequence of the same length” reads on comprising a fragment of naturally occurring polynucleotide sequence. Thus, Mercer teaches an isolated polynucleotide sequence comprising: a primer sequence; and two or more calibration sequences, wherein the calibration sequences each independently represent a naturally occurring polynucleotide sequence, and wherein the calibration sequences are arranged consecutively within the polynucleotide sequence in an arrangement not found in any naturally occurring genome.
The teachings of Mercer are documented above in the rejection of claim 33 under 35 U.S.C. 102 (a)(1). Claims 34-40, 42 and 47 depend on claim 33.
Regarding claim 34, Mercer teaches a polynucleotide sequence wherein one or more of the calibration sequences are present in two or more copy numbers within the polynucleotide sequence; and/or wherein a first calibration sequence represents an exon, intron, gene, allele, chromosome or genome sequence, and wherein a second calibration sequence differs from the first calibration sequence and independently represents a different exon, intron, gene, allele, chromosome or genome sequence. (Para. 12; Para. 142)
Regarding claim 35, Mercer teaches a polynucleotide sequence wherein the first calibration sequence and/or the second calibration sequence is indicative of any one or more of cancer, inherited disease, a pathogen, drug-resistance, circulating tumor DNA, circulating fetal DNA, circulating maternal DNA, or other attribute of interest. (Para. 40; Para 63; Para. 88).
Regarding claim 36, Mercer teaches a polynucleotide sequence wherein “the two or more copy numbers are selected to replicate naturally occurring frequencies of the naturally occurring sequences represented by the calibration sequences. (Para. 191)
Regarding claim 37, Mercer teaches a polynucleotide sequence wherein: i) one calibration sequence represents a maternally derived polynucleotide and another calibration sequence represents a paternally derived polynucleotide; and/or ii) the naturally occurring polynucleotide sequence is derived from a human, prokaryote, bacteria, virus, phage or organelle genome. (Para. 121)
Regarding claim 38, Mercer teaches a polynucleotide sequence wherein the calibration sequences are independently between 18 nucleotides and 20,000 nucleotides in length. (Para. 115; Para. 172)
Regarding claim 39, Mercer teaches a polynucleotide sequence which is a DNA or an RNA polynucleotide sequence. (Para. 15)
Regarding claim 40, Mercer teaches a vector comprising a DNA sequence encoding the isolated polynucleotide sequence of claim 33, operably linked to any one or more of the following: a 5' promoter; flanking (3' and 5') endonuclease sites; and a 3' poly-adenine repeat tract. (Para. 16; Para. 173)
Regarding claim 42, Mercer teaches A composition comprising two or more isolated polynucleotide sequences of claim 33. (Para. 105)
Regarding claim 47, Mercer teaches A kit comprising an isolated polynucleotide sequence of claim 33 and one or more nuclease enzymes capable of fragmenting the polynucleotide sequence. (Para. 41; Para. 226)
Conclusion
No claims are in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/KATHERINE D SALMON/Primary Examiner, Art Unit 1682