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 .
DETAILED ACTION
1. Election of group I with traverse is acknowledged. The traversal is based on no burden to examine all the groups together and method of treatment is related to method of diagnosis. The arguments were found unpersuasive because as indicated in the previous office action both groups distinct as shown by their different classification and each group requires different searches. The issues are not same for each group in terms of 35 USC 112 and 101 statutes. Thus, restriction as indicated is proper.
Status of the Application
2. Claims 1, 3, 6, 8, 10-12, 14-16, 18-19, 22-23, 26-27, 29 and 34-35 are considered for examination. Claim 41 is withdrawn from further consideration as being drawn to nonelected group.
Priority
3. This application filed on February 23, 2023 is a CON of PCT/IL2021/051045 filed on August 25, 2021 which claims priority benefit of US 63/069,826 filed on August 25/2020.
Specification
4. The disclosure is objected to because of the following informalities:
(i) The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (para 0081). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the term (sybrGold, sybr green in para 0057, 0062, 0132), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks. Appropriate correction is required.
Informalities
5. The following informalities are noted:
(i) Claim 1. 8, 14, 19, 26, 29 and 35 recite method steps represented by a., b., c., d., e., f., g, which indicates a full stop at each method step. Amendment the claims to delete full stop of each step is suggested. Appropriate correction is required.
Claim Rejections - 35 USC § 103
6. 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.
Claims 1, 3, 6, 8, 10-12, 14-16, 18-19, 22-23, 26-27, 29 and 34-35 are rejected under 35 U.S.C. 103 as being unpatentable over Vigneault et al. (US 2016/0032282) in view of Davis (WO 2018/069484).
Vigneault et al. teach a method of claim 1, for quantifying a first species of RNA within a sample, the method comprising: a) receiving a sample comprising RNA and substantially devoid of DNA polymers (para 0874);
b) contacting said sample with a first primer that hybridizes to said first species of RNA under conditions sufficient for reverse transcription (RT) of said first species of RNA to cDNA, thereby producing a first cDNA strand complementary to at least a portion of said species of RNA and comprising said first primer (para 0881, 0874);
c) treating said sample with an RNAse enzyme thereby producing a sample comprising said first cDNA strand and substantially devoid of RNA polymers (para 0881, 0874);
d) contacting said sample with a second primer that hybridizes to said first cDNA strand and performing 1-5 cycles of amplification to produce amplification products with a first termini that is identical to a sequence of said first primer and a second termini that is a reverse complement to a sequence of said second primer or with a first termini that is a reverse complement of a sequence of said first primer and a second termini that is identical to a sequence of said second primer (para 0881, 0874, 0566);
e) treating said sample with a proteinase enzyme to produce a solution substantially devoid of polypeptides other than said proteinase (para 0882); and
f) quantifying a species of RNA within a sample (para 0883-0885).
With reference to claim 3, Vigneault et al. that said receiving comprises receiving a sample of isolated RNA or receiving a cell lysate contacted with a DNAse enzyme (para 0266, 0403, 0753).
With reference to claim 6, Vigneault et al. that (b) comprises contacting said sample with a reverse transcriptase and DNA nucleotides (para 0881, 0874, 0575).
With reference to claim 8, Vigneault et al. that said step (c) a. occurs before said step (d); and said RNAse treatment produces a sample comprising said first cDNA strand and said amplification products are substantially devoid of RNA (para 0881, 0874).
With reference to claim 11-12, Vigneault et al. that said proteinase is proteinase K, wherein said treating with a proteinase is under conditions sufficient for degradation of polypeptides to single amino acids, conditions sufficient for protection of said proteinase from autolysis or both (para 0882).
With reference to claim 14, 23-24, Vigneault et al. that wherein said amplification product is a) at least 20 nucleotides shorter than said first cDNA strand; b) not larger than 10,000 nucleotides (para 0454).
With reference to claim 15, Vigneault et al. that said first primer, said second primer or both are DNA primers, is are specific to said RNA species, are 100% complementary to said RNA species or both a combination thereof (para 0627, 0347, 0566).
With reference to claim 16, Vigneault et al. that the method comprising a single cycle of amplification thereby producing on average a single amplification product for each molecule of said species of RNA (para 0507, 0702).
With reference to claim 18, Vigneault et al. that said amplification does not comprises integrating a detectable moiety into said amplification products, said method is devoid of a washing or isolation step after step (a) or both (para 0874-0885).
With reference to claim 22, Vigneault et al. that further comprising in step (b) contacting said sample with a third primer that hybridizes to a second species of RNA, thereby producing a first cDNA strand complementary to at least a portion of said second species of RNA and comprising said second primer; and further comprising in step (d) contacting said sample with a fourth primer that hybridizes to said first cDNA strand complementary to at least a portion of said second species of RNA to produce amplification products with a first termini that is identical to a sequence of said third primer and a second termini that is a reverse complement to a sequence of said fourth primer or with a first termini that is a reverse complement of a sequence of said third primer and a second termini that is identical to a sequence of said fourth primer (para 0275, claim 302).
With reference to claims 29, 34-35, Vigneault et al. a method of diagnosing a disease in a subject in need thereof, performing the method of claim 1, wherein said sample is from said subject, said first RNA species is an mRNA of a gene associated with said disease, and detection of said first RNA species in said sample indicates said subject suffers from said disease (para 0581-0588, 0740-0744).
However, Vigneault et al. did not teach nanopore apparatus to quantify amplification product.
Davis teaches a method for quantifying a target polynucleotide using a nanopore apparatus, wherein the method comprising amplifying a target nucleic acid, passing the nucleic acid through a nanopore apparatus, applying a potential difference across the nanopore, measuring a change in current across the nanopore that produces one or more electrical signals by translocation of the polynucleotide through the pore and quantifying target polynucleotide (para 0048-0062, 0075, 0080-0092, 0115, 0008). Davis also teaches providing an oligonucleotide (probe) set, hybridizing to the target polynucleotide and ligating the oligonucleotides to form ligated products to quantitate the polynucleotide (para 0048-0062, 0075, 0080-0092, 0115, 0008).
It would have been prima facie obvious to an ordinary person skilled in the art before the effective filling date of the invention to combine the method of Vigneault et al. with nanopore method as taught by Davis to improve the method for quantifying target nucleic acid. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would improve the sensitivity of the method because Davis explicitly taught use of a nanopore device to accurately quantitate a polynucleotide, which allows precise and accurate measurement of the polynucleotides in a sample (para 0075) and such a modification of the method to derive at the claimed method is considered obvious over the cited prior art.
Claim Rejections - 35 USC § 101
7. 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 1, 29, 34-35 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims 29, 34-35 in combination with claim 1 recite a method of diagnosing a disease in a subject, a process, statutory category. Claims 29, 34-35 in combination with claim 1 recite a judicial exception (law of nature, natural phenomenon) because claims recite a correlation of RNA species with a disease in a subject, which is a law of nature or natural phenomenon that exits in nature. The claims 29, 34-35 in combination with claim 1 do not include any additional elements that are sufficient to amount to significantly more than the judicial exception because the additional steps (amplifying, quantitating) which do not add significantly more to the claimed method. The additional steps are not themselves natural laws, but neither are they sufficient to transform the nature of the claims because they consist of well-understood, routine, conventional activity already engaged in by the scientific community. The additional steps consist of well-understood, routine, conventional activity already engaged in by the scientific community (Vigneault et al. (US 2016/0032282); Davis (WO 2018/069484); Gliddon et al. Immunology, Vol. 153(2), page 171-178, (2018); Squires et al. Scientific Reports, Vol. 5, 11643, page 1-11, (2015)). The additional steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately. The Court has made clear that to transform an unpatentable law of nature into a patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words "apply it." Essentially, appending conventional steps specified at a high level of generality, to laws of nature, natural phenomena, and abstract ideas cannot make those laws, phenomena, and ideas patent-eligible. This judicial exception is not integrated into a practical application because the judicial exception is not markedly different from the natural phenomenon because the claims recite the abstract idea of determining by a computer processing. It is noted that a judicial exception itself, such as an abstract idea, cannot be considered to meet the criteria of "significantly more" than a judicial exception. The Courts decision rested upon an examination of the particular claims in light of the Court's precedents, specifically Bilski, Flook and Diehr. The Court repeated the longstanding exceptions (laws of nature, natural phenomena, and abstract ideas) to categories of patent eligibility defined in 35 U.S.C. § 101. In conducting the analysis, the Court addressed the "machine-or-transformation" test explained in Bilski with a reminder that the test is an "important and useful clue" to patentability but that it does not trump the "law of nature" exclusion. A claim that recites a law of nature or natural correlation, with additional steps that involve well-understood, routine, conventional activity previously engaged in by researchers in the field is not patent-eligible, regardless of whether the steps result in a transformation. On the other hand, reaching back to Neilson, the Court pointed to an eligible process that included not only a law of nature (hot air promotes ignition) but also several unconventional steps involving a blast furnace) that confined the claims to a particular, useful application of the principle. For all the above, the claims are rejected under 35 USC 101.
Conclusion
No claims are allowable.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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