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 .
Application Status
Claim amendments were filed 01/06/2026. Claims 1, 3-4, 6-9, 14, 16, 19-20, 22-24, 29, 33, 44-45,67 are pending and currently under examination in this office action.
Any objection or rejection not reiterated herein has been overcome by Applicant’s amendments and is therefore withdrawn.
Claim Rejections - 35 USC § 112 in view of amendments
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 23, 44 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for SEQ ID Nos 1,2,4-5, does not reasonably provide enablement for .90 identity to these sequences. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims. This is a scope of enablement rejection.
Claims 3-4, 6-9, 14, 16, 19-20, 22 depend from claim 1, and as such, are rejected for the same scope issue. Claims 24, 33, depend from claim 23, and as such, are rejected for the same scope issue. Claims 45, and 67 depend from claim 43 and as such, are rejected for the same issue.
The test of enablement is whether one skilled in the art could make and use the claimed invention from the disclosure in the specification alone or in combination with information known in the art, without undue experimentation (see MPEP 2164.01(a)), (United States v. Telectronics., 8 USPQ2d 1217 (Fed. Cir. 1988)). Whether undue experimentation is needed is not based upon a single factor but rather is a conclusion reached by weighing many factors. These factors were outlined in Ex parte Forman, 230 USPQ 546 (Bd. Pat. App. & Inter. 1986) and again in: In re Wands, 8 USPQ2d 1400 (Fed. Cir. 1988). The most relevant factors are addressed below:
Nature of the Invention: Claims 1, 23 and 44 are directed to a method (claim 1) of processing a sample to detect Legionella species, and a kit for detecting Legionella (claim 23) and method amplifying Legionella in/from a subject (claim 44).
This method involves contacting the sample with primers that amplify ssrA and primers that amplify 16S rRNA and detecting one or more amplification products to identify Legionella species or Legionella pneumophila, wherein the first forward primer comprises an oligonucleotide having 90% sequence identity to SEQ ID NO: 1, reverse primer, 90% identity to SEQ ID NO: 2 and wherein the second forward primer comprises an oligonucleotide having at least 90% sequence identity to SEQ ID NO: 4, and a second reverse primer, at least 90% sequence identity to SEQ ID NO: 5.
The kit (claim 23) includes primer pairs with at least 90% sequence identity to SEQ ID NO: 1-2,4 and 5.
Claim 44 is directed to a method for selecting a symptomatic subject and amplifying Legionella using primers with at least 90% sequence identity to SEQ ID NO: 1-2,4 and 5.
Breadth of the Claims: The claims explicitly recite particular SEQ ID Nos for multiple primer sequences (SEQID Nos: 1-2, 4-5 are disclosed), then broaden this sequence scope substantially to include, for each SEQ ID NO:, a genus of any and all primers with 90% similarity to a given recited SEQ ID NO: (primer sequence). The genus of possible species for a given primer is very large and thus unpredictable.
The claimed primer sequences range in size from 18 to 22 base pairs. In, for example, a 20 base pair primer, 90% similarity means that two sites may vary out of 20. With 3 nucleotide options per site (that differ from the nucleotide found in the SEQID at a site) there are 9 alternative (32) combinations of alternate nucleotides for two sites. There are 190 combinations (20 pick 2), or ways to arrange two sites out of 20 sites. 190 site combinations X 9 nucleotide variants would result in 1710 unique primers with 90% similarity to a 20 base pair SEQ ID, which constitutes a large genus.
For SEQ ID NO: 1, one of the bases is also degenerate (allows more than one nucleotide), and this additional variation is not considered to contribute to the above variation, such that when degenerate sites are considered the number of unique sequences will increase further.
Teachings in the Specification (Direction Provided and Working Examples):
Direction: In addition to the above variants, the Specification teaches that the term “specific”, in reference to the primer, means that the sequence of the primer has at least 12 bases of sequence identity with the nucleic acid to be amplified. This high-level recitation allows for a large amount of variation, if for example 12 bases of identity to a sequence is met: where those particular 12 bases is not defined; in a 20 base primer, this allows for 8 potential sites to vary; or for more sites to vary if the primer is longer. So .90 SEQ ID, means 2 of those 8 sites can vary, or (8 pick 2) =28 with three nucleotide options for each of the two sites, or 252 possible primers, which is a large genus.
The specification also indicates “higher levels of identity are preferred” with up to (a recitation of) varied percent matches, including 75% to 98% [0060], with an exemplary primer pair, SEQID NO: 4 and 5, for 16S rRNA in a Table [0099], with no alternate or additional sequences provided to represent these genera.
The recitation indicates “under the stringent hybridization or washing conditions” the primer is capable of hybridizing to the target of interest and not to the non-targets, which would require experimentation to determine.
Exemplary primers for ssrA are disclosed as forward primers with SEQID NO: 1,11,12,13, 14, where SEQID NO: 1 is the sequence presented with a degenerate “R” base, which represents A or G (IUPAC www.bioinformatics.org), and these options, R, A, G are three of the options in this table, with T and C at this site, also recited as the only primer differences for these variants. There is a singular reverse primer presented, SEQID NO:2, absent empirical data [00102]. Aside from this, there are no other examples of a particular primer with 90% similarity to the SEQIDNO’s in claims 1, 23, 44, which is insufficient evidence to consider all of the species of each of these genera predictable or possible to make and use.
Working examples: The specification does not provide any working examples.
The specification teaches a prophetic “Example 1”, without any primer nucleotide sequences recited. Prophetic Example 2 addresses cross-reactivity, and spiking samples, but not the primer genera considered here. The Specification does not clearly demonstrate results produced from multiple species of primers, such as may be found in working examples, or through experimental data and/or recitation of results, or drawings or graphs.
While some partial methods are presented in general descriptive context: e.g. potential Ct values are mentioned [00126][00127], even these references vary in scope (positive Ct is <35 or is <40 [00126], and are disclosed for 40 cycles or for up to 45 cycles [00126], in present tense, such that absent further detail this serves as insufficient guidance for enabling the full scope of the claimed invention for these genera and while Example 1 narrows this scope, it is not a working example but instead prophetic. Thus, disclosure is not optimized, nor clearly reflective of predictability in unpredictable art, within which primer function is unpredictable absent undue experimentation, since the scope of the species comprising these broad functional primer genera, at a minimum mean that this fraction of disclosure still requires extensive experimentation by one or ordinary skill in the art, inclusive of making and testing many species until identifying what conditions work for a given species, if that species will work at all, and inclusive of testing and manipulating multiple, varied experimental parameters. Appropriately detailed working examples, reflective of the breadth of these genera are simply not disclosed for making and using the full scope of the claims, or the numerous species, reflected in the genera of this invention.
Drawings: There are no Drawings to demonstrate enablement or use of/data from experiments with alternate sequences for these primers.
In sum, the specification does not provide sufficient guidance on successful use of variants in amplification, or on amplification efficiency, with particular primer sequence alternatives (species), or provide sufficient functional guidance (e.g. where in the sequences there is/not mismatch tolerance). Nor does the specification provide information on nucleotide positions that could be freely modified or not modified at all, despite that it is well known that successful primer binding and amplification are sensitive to primer sequence variation, particularly at sites that must be conserved.
The guidance in the specification for these genera is largely limited to disclosure of the SEQID Nos, (plus two additional variants at a degenerate site as discussed above, listed in a table) but does not include representative examples across a claimed genus. As such, the amount of experimentation required to overcome unpredictability for use of these primers, would be excessive given the possible number and type of variants and the experimental modifications necessary to test, optimize and use them, or determine they fail as functional primers, specific for their intended purpose.
State of the Prior Art (including level of Predictability in the Art): The state of the art was such that knowledge regarding the effect of primer variation on successful primer binding and amplification was known (e.g. Green, M. Optimizing primer and probe concentrations for use in real-time PCR assays, 2018, Cold Spring Harb Protoc, 825-835; Wu, J-H. et al Quantitative effects of position and type of single mismatch on single base primer extension 2009 Jour Micrb methods 77 267-275.). Green addressed the need for primer optimization to determine efficiency, sensitivity and reproducibility, though plot comparison (Abstract) which indicates the primers would need to be designed, generated, purchased and tested. Green also points to the labor of comparative empirical work that is required for real-time PCR primers (Pg 826 para 1). Green points to several issues known to affect successful primer use and actually state explicitly before starting the time-consuming process of designing primers, it is worth searching literature for a validated assay, though even then it is necessary to validate the assay in your own hands, particularly with respect to amplification efficiency and sensitivity limits (Pg 830, para 3). They recite necessary requirements for primers and also point out “despite all attempts to optimize the reaction conditions, many primer sets fail to amplify the desired template, and accordingly a new set of primers must be designed and tested” (Pg 832, para 2). Wu addressed how just a single base pair that is a mismatch at the primer binding site can affect PCR efficacy, to a large degree (Abstract). Bustin (Bustin, S. qPCR primer design revisited, 2017, Biomol. Detect Quantif. 14:19-28) literally states “primers are arguably the single most critical components of any PCR assay, as their properties control the exquisite specificity and sensitivity that make this method uniquely powerful. Consequently, poor design, combined with failure to optimize reaction conditions is likely to result in reduced technical precision and false positive or negative detection of amplification targets.” (Abstract).
Quantity of experimentation needed to make or use the invention based upon the disclosure
Given the general unpredictability associated with primer design and successful use in amplification as shown by the art, and the lack of guidance or teachings in the specification regarding how to identify effective species in these genera of primers, the quantity of experimentation associated with making and using effective primers from the large numbers of variants possible (0.90 (SEQID No)) is very high. It is likely not all variants will bind and particularly amplify what is desired, thus the genera each likely display heterogeneous function, where individual species effectiveness is unpredictable and therefore the work necessary to reliably make and/or use the invention is beyond routine experimentation.
In conclusion, taking into consideration the factors addressed above, including the nature of the invention, the breadth of the claims, the state of the art, the guidance provided by the applicant, including absence of working examples, an undue amount of experimentation would be required to make and use the invention as claimed.
Claims 1, 23 and 44 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 3-4, 6-9, 14, 16, 19-20, 22 depend from claim 1, and as such, are rejected for the same written description issue. Claims 24, 33, depend from claim 23, and as such, are rejected for the same written description issue. Claims 45, and 67 depend from claim 43 and as such, are rejected for the same written description issue.
The claims are directed to four genera of primers, each with 0.90 identity to a primer SEQID NO:, here SEQID NO: 1,2,4,5. While these primers have a function of hybridizing to target and amplifying target, e.g. 16s rRNA, ssrA, and per for example, [0093] where it is disclosed that ssrA may amplify all Legionella species, and 16s rRNA L. pneumophila, the structure that drives this function is not recited / presented in sufficient detail (e.g. sufficient representative species or structure) to indicate possession of these genera. Please see the enablement rejection above, which addressed this in further detail.
As well, [0099] discloses “exemplary primer sequences for amplifying and detecting 16S rRNA” and depicts SEQ ID NO: 4 and 5 as forward and reverse primers, respectively. [00102] recites exemplary primers for amplifying and detecting ssrA target and discloses forward primer SEQID NO: 1, and 11-13 (a degenerate and four options for nucleotides at position 15), and one reverse primer, SEQID NO: 2. [00103] discloses that at least in some embodiments, ssrA will not detect/amplify non-Legionella. The specification does not provide a working example with evidence of possession of a representative number of functional species for these genera.
While the claims are directed to the genera of these four primers, a sufficient representative number of species for which possession is demonstrated, or for which identified common structural features of the primers (e.g. pertinent conserved sites or motifs, or other defined structural feature of primers like mismatch tolerance at particular positions) that allow prediction/determination of which variants will function properly, is not disclosed in such a manner as to demonstrate to one or ordinary skill that the inventor possessed the full scope of the claimed genera. Accordingly, the specification does not adequately convey that the inventor possessed the claimed genera of the primers, with .90 identity to SEQID Nos: 1,2,4,5, at the time of filing and the claims are rejected for a lack of written description.
Response to Remarks:
All remarks have been carefully considered. Those that relate to the Specification objection, 35 U.S.C. § 103, 35 U.S.C. §112b and 35 U.S.C. § 101 rejections also relate to the amendments, in view of which, the rejections were withdrawn and as such are not further discussed here. However, in the Remarks section regarding 35 U.S.C. §112b, applicant presents the amended independent claims 1, 23, and 44, inclusive of the language “at least 90% sequence identity to SEQ ID NO;”. Applicant indicates that support for the multiple functional variants of the primers is found in [0060] disclosing preferred levels of sequence identity, [00102] reciting exact sequences, where SEQID NO1 and 11-14 are disclosed as suitable forward primers with one nucleotide difference in 20, or at least 90% sequence identity. Applicant states this fully supports and enables the “at least 90% sequence identity” phrase.
While the examiner has considered these comments and did read these sections of the specification, the examiner disagrees with the quantity of evidence presented here as being sufficient to enable all of the alternative sequences. The single nucleotide differences presented in SEQID 11-14 are also partly already reflected in the degenerate base of SEQID NO: 1. For the detailed reasons disclosed in the enablement rejection found in this Office action, the preponderance of evidence does not support what the Applicant has pointed to as sufficient to overcome a scope of enablement rejection for these genera of primers.
However, it is important to recognize that, using the phraseology present in the independent claims at present, if the SEQID Nos were recited absent the “at least 90% sequence identity”, the scope of enablement rejection would be withdrawn.
Allowable subject matter: The claims are presently considered free of the art.
Conclusion
Claims 1, 3-4, 6-9, 14, 16, 19-20, 22-24, 33, 44-45, 67 are rejected. Claim 29 is objected to as being dependent upon a rejected base claim (claim 23). However, claim 29 includes additional limitations that appear to place the claim in condition for allowance; specifically, the recitation of the exact sequences {SEQ ID NO:) for each of the primer pairs. Accordingly, claim 29 would be allowable if rewritten in independent form, including the limitations of the base claim, absent the recitation in the base claim referencing oligonucleotides having at least 90% sequence identity to the SEQ ID Nos, found in (a) and (b) of claim 23.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lisa Horth whose telephone number is (703)756-4557. The examiner can normally be reached Monday-Friday 8-4 EST.
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/LISA HORTH/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681