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
Claims 1-4, 7-10, 12-13, 15-21 & 25 are under examination on the merits.
Claims 5-6, 11, 14, 22-24 & 26-27 are canceled.
Priority
Claims 1-4, 7-10, 12-13, 15-21 & 25 receive the U.S. effective filing date 22 Dec 2022.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code [p.27, ¶3]. 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.
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 1-4, 7, 18-21 & 25 are rejected under 35 U.S.C. 101 because the claimed invention is directed to natural phenomena (i.e. diagnosing a genotype or a product of nature) without significantly more.
The claims recite a method for characterizing a Cannabis plant via genetic screening for QTL impacting flower to leaf ratio. This is fundamentally a genotype identification/detection method (i.e. establishing the presence of endogenous alleles using molecular markers).
The identification/classification of genetic variants through DNA sequence analysis falls within the category of abstract ideas recognized by the USPTO as patent-ineligible under Alice Corp. v. CLS Bank, [573 U.S. 208, 217, 110 USPQ2d 1976, 1981 (2014)] specifically as:
1. a mental process (classification/identification),
2. claim to fundamental biological principles (DNA sequence variation), and,
3. mathematical algorithms (PCR amplification & amplicon size detection).
Applicant attempts to integrate this into a practical application, reciting ‘genotyping at least one plant’ for SNP markers provided in Table 2. No additional steps are recited following the determination of presence/absence of endogenous markers or QTL in claims.
Regarding claims 1-2, 7 & 18; the specification establishes that the detected markers and QTL are endogenous and characterized from various extant germplasm, presented as “a diverse population of Cannabis” [p.25, ¶5]. The specification establishes that Applicant is retroactively describing DNA sequences of plants previously selected or identified for particular flower to leaf ratios [p.25, ¶6]. The specification establishes that Applicant is not generating mutants or otherwise genetically engineering plants to invent the markers, genes, or QTL that result in the described phenotypes.
In the case of claims 3 & 4; the abstract idea does not amount to significantly more because Applicant is utilizing routine genotyping methods to determine presence/absence of a sequence, and correlating its presence to a particular phenotype. Such correlation methods are conventional in marker-assisted plant breeding and used to describe biodiversity, generally. The claims do not improve upon genotyping technology, detection methodology or otherwise technologically differ from standard genetic diagnosis. Furthermore, the core inventive concept of identifying or ‘selecting’ which plants carry the endogenous QTL, and thus display favorable phenotypic characteristics, is fundamentally a mental classification process.
In the case of claims 19-21; these are dependent from rejected claim 18 and thus are also rejected.
Regarding claim 25; it recites a Cannabis plant with QTL influencing flower to leaf ratio. A Request for Information under 37 CFR § 1.105 is attached to this Office action which requests information on the source material used by Applicant [see below]. The current evidence of record shows such a plant is likely a product of nature, however, response to the 105 should shed light on this. This judicial exception is not integrated into a practical application because reciting a plant possessing a naturally occurring QTL or genetic polymorphism does not add meaningful limitation as it is merely a nominal characterization of existing biodiversity. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because they are simply a recitation of naturally occurring genetic polymorphism that leads to the various observable differences in floral architecture of various Cannabis plants.
The claim is drawn to a plant having one of the genetic polymorphisms listed in Table 2, which are an assortment of SNPs associated with floral architecture. Looking to the specification, it is clear that Applicant performed a standard genetic mapping experiment, or diagnosis, using a panel of different existing Cannabis varieties [p.25, ¶5; p.27, ¶2]. Applicant does this through analysis of an unstructured association analysis panel and several structured mapping populations.
However, all genetic polymorphisms and associated QTL are necessarily derived from the existing parental material(s) used, absent evidence to the contrary. This means that parental material, which Applicant describes as a representative sample of Cannabis biodiversity (i.e. a diverse population of Cannabis displaying variation in flower to leaf ratio), reasonably possesses all SNP markers listed and the QTL they are linked to. These are endogenous markers and QTL.
Thus, Applicant’s claim as written would include extant Cannabis strains and populations, and existing biodiversity for the species which is a product of nature. Applicant does not indicate active mutagenesis, genetic engineering, or any other synthetic or inventive steps were taken to generate the recited polymorphisms or their claimed QTL. The trait which they describe as a selection target is not novel, and is an established trait evaluated and considered by growers when selecting particular Cannabis varieties for production [see discussion Overgrow.com Forum; attached NPL_CalyxToLeafRatio_OvergrowForum_2025], which would also reasonably select underlying, causative QTL and linked markers.
The judicial exception described above is not integrated into a practical application because the claims are merely diagnosing genetic predisposition to a particular trait. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because no active method steps are included beyond diagnosis of a marker/QTL. The claims do not recite specific improvements in detection hardware or use of non-conventional detection(s), the practical application is the known and common use of molecular markers, and the specification does not demonstrate unexpected results beyond what would be predicted from known marker-assisted selection techniques.
Absent an additional active method step, ‘a Cannabis spp. plant’ which comprises endogenous markers and QTL for such traits is a product of nature. Claims do not indicate Applicant is actively generating mutations impacting the gene, genetically modifying or otherwise performing any active step beyond routine characterization or diagnosing of endogenous genetic markers. Thus, this claim is not directed to significantly more than a product of nature.
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 1-4, 7-10, 12-13, 15-21 & 25 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.
Claim 17 recites the limitation “wherein the branch number QTL is selected" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 17 depends from claim 8, which does not introduce or recite ‘a branch number QTL’.
Because of this, claim 17 is rejected.
Claims 1-2, 4, 7-8, 10, 13, 16-18, 21, & 25 incorporate an external reference. The claims recite genetic polymorphisms referenced in Table 2, ‘context sequence’ in Table 4, and/or primer pairs in Table 5.
Claims are to be as complete as possible without incorporating essential details by reference. The genetic sequences limiting the claims are essential material because one would need to know the specific SEQ ID NOs referenced to fully understand the scope of the claims and avoid infringement. Because the values referenced in the claims rely on information described only in tables having various, optional sequences to choose from this is an improper incorporation by reference.
Because the scope of the claims varies depending on which optional sequences are chosen from reference tables presented, claims 1-2, 4, 7-8, 10, 13, 16-18, 21, & 25 are rejected. Their dependent claims 3, 9, 12, 15 & 19-20 are therefore also rendered indefinite and rejected for incorporation by reference.
The term “a flower to leaf ratio trait of interest” in claims 8, 10, 13, 18-20 & 25 is a relative term which renders the claim indefinite. The term “a flower to leaf ratio trait of interest” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree [p.4, ¶3], and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claim language is drawn to a phenotypic value (i.e. flower to leaf ratio) but does not tell the reader what that value is beyond saying it is ‘of interest’. This is subjective language, or a relative term, which does not indicate clear trait values, whether it requires an increased value, decreased value, or any other informative detail on limiting values. The claims reciting this language refer to Table 2 in the specification as characterizing the ratio ‘of interest’ and associated polymorphisms.
Referring to Table 2, the only phenotypic information provided (i.e. flower to leaf ratio) is that of three columns providing different mean values for flower to leaf ratio for each different polymorphic marker [Specification, p.30]. Applicant does not indicate if the values depicted represent a range bound by the high and low values provided (i.e. a desired phenotypic range), if the trait value ‘of interest’ represents an increase or decrease from alternative reference values, or how the ratio ‘of interest’ is defined considering there are approximately equivalent phenotypic values presented for different allelic configurations (i.e. trait values are not distinctly determined by markers).
One reading such claims could interpret “a flower to leaf ratio trait of interest” to be specific to example values or ranges presented in Table 2 of the specification, or alternately, could interpret them broadly to mean any value of flower-to-leaf ratio since what is ‘of interest’ is subjective to the researcher and their particular germplasm or breeding goals. No definite quantitative value or limitation is provided to inform the reader objectively what phenotypes or ratio value(s) are being claimed. No specific flower-to-leaf ratio is recited by the claims or defined by the specification.
Because the scope of the claims varies based on this subjective interpretation of what constitutes “a flower to leaf ratio of interest”, and Applicant does not objectively define the phenotype being referenced as a limitation, claims 8, 10, 13, 18-20 & 25 are rejected.
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 1-4, 7-10, 12-13, 15-21 & 25 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
All method claims are drawn to production of specific phenotypes utilizing QTL linked to specific SNPs characterized in Applicant’s germplasm. As such, all claims require starting materials (i.e. identified germplasm or breeding lines) that possess the claimed markers and corresponding linked QTL regions to be selected.
Since the starting materials or sources of markers and linked QTLs are essential to the claimed invention, these must be obtainable by a repeatable method set forth in the specification or otherwise readily available to the public.
Applicant indicates the material source of the recited markers and phenotypes is a “diverse population of Cannabis displaying variation in flower to leaf ratio, including hemp-types and resin-types” [p.25, ¶5]. Applicant goes on to state initial screening of this unspecified group of material was subsequently used to generate 24 F2 populations, which indicates approximately 24-48 specific parental lines were identified/used to contribute the claimed markers and linked QTL.
The specification does not disclose the identity of any of these starting materials and does not disclose a repeatable process to obtain the same seed or plants produced by claimed methods. It is not apparent if such germplasm is readily available to the public.
Enablement requires deposit of starting materials or characterized lines possessing the claimed markers and validated (i.e. linked) QTL that confer the claimed phenotypic effects, or, resulting progeny able to be used as source germplasm.
If a deposit of these seeds is made and accepted under the terms of the Budapest Treaty, then an affidavit or declaration by the Applicant, or a statement by an attorney of record over his or her signature and registration number, stating that the seeds will be irrevocably and without restriction or condition released to the public upon the issuance of a patent would satisfy the deposit requirement made herein.
If a deposit has not been made and accepted under the Budapest Treaty, then in order to certify that the deposit meets the requirements set forth in 37 CFR 1.801-1.809, Applicant may provide assurance of compliance by an affidavit or declaration, or by a statement by an attorney of record over his or her signature and registration number showing that:
(a) during the pendency of the application, access to the invention will be afforded to the Commissioner upon request;
(b) all restrictions upon availability to the public will be irrevocably removed upon granting of the patent;
(c) the deposit will be maintained in a public depository for a period of 30 years or 5 years after the last request or for the enforceable life of the patent, whichever is longer; and
(d) the viability of the biological material at the time of deposit will be tested (see 37 CFR 1.807).
In addition, the identifying information set forth in 37 CFR 1.809(d) should be added to the specification. See 37 CFR 1.801 - 1.809 [MPEP 2401-2411.05] for additional explanation of these requirements.
Claims 1-4, 7-10, 12-13, 15-21 & 25 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 claims contain 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.
Independent claims 1, 8 & 18 are drawn to methods of characterizing or producing a Cannabis plant with a particular phenotypic value for flower to leaf ratio. Claim 25 is drawn to such a Cannabis plant with a defined phenotype. This limits the invention to methods reliably able to produce a specific flower to leaf ratio of interest via detection of one of Applicant’s listed SNPs provided in Table 2. Claims depending from 8 & 18 also include this limitation.
However, flower to leaf ratio is admitted by Applicant to be a quantitative, or polygenic, trait [p8, ¶3; p.28, ¶2]. Complex, quantitative traits are known by plant breeders to be the result of interactive effects of multiple genes (i.e. loci) as well as being conditioned by environmental effects and therefore require validation of their effectiveness [p.186, col.1, ¶1 in Collard, Euphytica (2005) 142: 169–196; Published 2 Feb 2005]. Applicant reports the individual effects of QTL linked to singular SNP markers but does not describe a method whereby one can achieve a specific value for this trait, in any and all Cannabis plants, via selection of a singular SNP absent details of specific genetic background(s) or particular environmental conditions.
Contrary to such claim(s), reference to Table 2 actually shows there are multiple QTL, and potential SNPs, that would need to be selected or manipulated collectively or in tandem (i.e. haplotype construction) to arrive at a specific phenotype or cultivar. Several of the allelic profiles shown for the various SNPs assayed by Applicant have approximately equivalent effect on the phenotype of interest. This indicates that manipulation of a single SNP marker for a single QTL, absent the simultaneous manipulation of the other(s), would not necessarily produce the desired Cannabis ideotype.
Further, Applicant does not demonstrate validation of the singular effects of these QTL. To do so they would need to describe comparison of near isogenic lines (NILs), validation of transfer or manipulation of the QTL in different genetic backgrounds, and/or directed mutation and/or knockout of the recited SNP marker(s) with documented phenotypic effects or, preferably, arrival at a specific phenotype ‘of interest’ using marker data alone. None of these are provided by the written description.
Furthermore, because Applicant is silent as to the genetic backgrounds in which the claimed markers and QTL occur, one would have no way of even understanding which germplasm the described SNPs could potentially function in.
Additionally, QTL refer to regions on chromosomes rather than specific point mutations or genes (i.e. functional mutations). Markers genetically or physically linked to such QTL, and not shown to be causative mutations or genes per se, delimit the bounds of these regions or, in the case of haplotypes, characterize intervening DNA sequence. Because of this, and because of the disruptive effect of recombination during meiosis, the accurate selection of a QTL region contributed by donor germplasm requires at the minimum use of two ‘flanking’ molecular markers to determine the bounds of a proscribed QTL, preferably located as physically close to the functional DNA polymorphism as possible. This is acknowledged by Applicant, and reflected in the language of claims 4 & 13 where Applicant describes this well-established and essential feature of marker assisted selection when targeting QTL [see claims 4 & 13].
Despite acknowledging the need to account for regions affected by recombination, rather than points, Applicant’s method claims that use of singular SNPs is able to produce plants with target QTL regions [p.16, ¶1; p.30, Table 2]. Applicant states their method involves selecting these singular SNPs and unspecified but potentially multiple ‘linked’ loci [p.8, ¶3; p.12, ¶6]. Without providing/requiring specific flanking markers, or at least more than one marker to identify each of the encompassed QTL regions, it is unclear how one would reliably transfer or select QTL regions without being able to determine whether they remained intact (i.e. not disrupted via recombination) or how to identify such regions in uncharacterized germplasm.
For these reasons, the written description does not reasonably convey to one skilled in the relevant art that the inventor had possession of the claimed invention. Their disclosure does not support that they are or were able to generate Cannabis with specific flower-to-leaf profiles via selection of their listed singular SNP markers. The specification is merely retroactive description of marker profile in plants previously arrived at via phenotypic means. Lacking validation of use of the singular markers to generate or produce Cannabis plant ideotypes, Applicant does not appear to have been in possession of the claimed methods at the time of filing.
Claim Rejections - 35 USC § 102
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 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)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-4, 7, 18-21 & 25 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by McKernan [U.S. Patent Application Publication US20140057251A1; Published 27 Feb 2014].
Claims are drawn to methods of producing Cannabis plants and resulting Cannabis plants having at least one marker polymorphism associated with QTL that influence flower to leaf ratio. Polymorphic markers included are listed in Table 2.
Search of sequence databases reveals that QTL markers ‘common_3494’ and ‘common_567’ listed in Table 2 have a high level of similarity to sequences reported by McKernan in their PG Pub describing the Cannabis genome [McKernan SEQ ID NO. 334 & 298318]. Applicant’s ‘common_3494’ has 96.2% similarity to McKernan’s reported SEQ ID NO.334 and Applicant’s ‘common_567’ has 100% similarity to McKernan’s reported SEQ ID NO.298318. This indicates that identifying sequences (i.e. markers for these loci) were previously reported in the genome of Cannabis plants. Therefore, Cannabis plants were previously available to the public that necessarily had endogenous QTL variants or polymorphic forms of Applicant’s recited markers. Such plants with these inherent loci, having both flowers and leaves, would have displayed at least a floral phenotype of some form (i.e. “having an increased…decreased…or intermediate flower to leaf ratio QTL”) comprising the trait of flower to leaf ratio that would have been considered in selection as a trait ‘of interest’.
Regarding claims 1-2, 7, 18-19 & 25; McKernan describes use of genomic sequence and polymorphic markers to introduce, or selectively breed, linked Cannabis genes among plants [p.10, ¶91]. McKernan lists allelic (i.e. polymorphic) forms of Applicant’s sequences, obtained via genotyping, for ‘common_3494’ and ‘common_567’.
Regarding claims 3 & 4; McKernan describes the use of PCR based markers to detect polymorphic markers linked to Cannabis genes [p.4, ¶53-54].
Regarding claim 20, McKernan describes the use of genomic sequence and polymorphic markers to genetically engineer Cannabis plants (i.e. via vectors) using markers and linked sequences associated with phenotypes of interest [p.4, ¶51-52].
Because McKernan describes highly similar polymorphic variants of the markers claimed by Applicant as inherently within the Cannabis genome, it is clear that prior to Applicant’s filing plants and germplasm were available to the public with the claimed markers. The markers reported appear to be inherent to various native loci in the Cannabis genome, and thus any plant with any flower to leaf ratio characteristic that could potentially be ‘of interest’ would reasonably have allelic variants of the claimed markers. Any use of Cannabis plants would comprise introducing these loci and any linked polymorphisms and thus, Applicant’s claims 1-4, 7, 18-21 & 25 are anticipated.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
Request for Information under 37 CFR § 1.105
Applicant and the assignee of this application are required under 37 CFR § 1.105 to provide the following information that the examiner has determined is reasonably necessary to the examination of this application.
This request is being made for the following reasons:
Applicant’s claims are drawn to methods and resultant plants requiring germplasm with specific QTL and marker associations. Applicant’s remarks and specification indicate that the source(s) of these QTL is critical to examination of the instant application. The requested information is required to make a meaningful and complete search of the prior art.
In response to this requirement, please provide answers to each of the following interrogatories eliciting factual information:
(i) What specific germplasm, breeding lines, and/or cultivars were used as starting material to identify the claimed markers and their associated QTL?
(ii) What specific germplasm, breeding lines, and/or cultivars were identified as progeny/parents comprising the claimed markers and their associated QTL?
(iii) At or before the time of filing of the instant application or any provisional application to which benefit is claimed, had said germplasm, breeding lines, and/or cultivars used as starting materials or developed as progeny been disclosed, made publicly available, or offered for commercial sale? If so, under what designation/denomination and under what conditions is this material disclosed, made publicly available, or sold and from when to when?
If Applicant views any or all of the above requested information as a Trade Secret, then Applicant should follow the guidance of MPEP § 724.02 when submitting the requested information.
If any part of the response is marked DO NOT SCAN or TRADE SECRET, Applicant is reminded that a cover letter, not so marked, is to be included.
In responding to those requirements that require copies of documents, where the document is a bound text or a single article over 50 pages, the requirement may be met by providing copies of those pages that provide the particular subject matter indicated in the requirement, or where such subject matter is not indicated, the subject matter found in applicant' s disclosure. Please indicate where the relevant information can be found.
The fee and certification requirements of 37 CFR § 1.97 are waived for those documents submitted in reply to this requirement. This waiver extends only to those documents within the scope of this requirement under 37 CFR § 1.105 that are included in the applicant' s first complete communication responding to this requirement. Any supplemental replies subsequent to the first communication responding to this requirement and any information disclosures beyond the scope of this requirement under 37 CFR § 1.105 are subject to the fee and certification requirements of 37 CFR § 1.97.
The applicant is reminded that the reply to this requirement must be made with candor and good faith under 37 CFR § 1.56. Where the applicant does not have or cannot readily obtain an item of required information, a statement that the item is unknown or cannot be readily obtained may be accepted as a complete reply to the requirement for that item.
This requirement is an attachment of the enclosed Office action. A complete reply to the enclosed Office action must include a complete reply to this requirement. The time period for reply to this requirement coincides with the time period for reply to the enclosed Office action.
/Amjad Abraham/SPE, Art Unit 1663