DETAILED ACTION
Status of the Claims
Claims 84-85, 87, 94, 97, 104, 106-109, 112-119, and 121-122 are currently pending and examined herein.
Claims 1-83, 86, 88-93, 95-96, 98-103, 105, 110-111, and 120 are canceled.
Claims 84, 106, 112, and 117 have been amended.
Claims 121-122 are new.
The following Office Action is in response to Applicant’s communication dated 04/06/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Withdrawn Rejection(s)/Objection(s)
The objection to the Abstract as being too short and not descriptive enough is withdrawn in light of the new Abstract submitted by Applicant on 04/06/2026.
The rejection of claims 84-85, 87, 94, 104, and 106-110 under 35 U.S.C. 112(a) as failing to comply with the written description requirement is withdrawn in light of persuasive arguments presented by Applicant in the 04/06/2026 response.
The rejection of claims 110 and 120 under 35 U.S.C. 112(b) as being indefinite is withdrawn in light of the claims being canceled by Applicant.
Modified Claim Rejections - 35 USC § 101
Necessitated by Amendments
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 84-85, 87, 94, 97, 104, 106-109, 112-119, and 121-122 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
Independent claim 84 recites a collection of polynucleotides sized 125-200 base pairs in length, comprising a plurality of background polynucleotides (each corresponding to a primary polynucleotide) and a first, second, and third primary polynucleotide each comprising a variation compared with a corresponding background polynucleotide, wherein each primary polynucleotide corresponds to a genomic nucleic acid region, wherein each variation in each position of the primary polynucleotide corresponds to a single position in the genomic nucleic acid region, and wherein the primary polynucleotide regions (and primary polynucleotide positions) are offset 1-30 bases from one another. Figure 1A from the disclosure is instructive:
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It is also noted that independent claim 84 (as well as independent claim 112) use the term “comprising”, which is inclusive or open-ended and does not exclude additional, unrecited elements or method steps, as stated in MPEP 2111.03. In other words, since the claims specify that “each primary polynucleotide comprises a variation compared to a corresponding background polynucleotide”, then each primary polynucleotide may comprise multiple or many insertions, deletions, fusions, duplications, frameshifts, repeat expansions, and/or substitutions, and still be encompassed by the broadest reasonable interpretation of the claims.
The broadest reasonable interpretation of the claim encompasses embodiments that are either naturally occurring, or are non-naturally occurring but lacking markedly different characteristics as compared to their naturally occurring counterparts, and therefore are “product of nature” judicial exceptions as per MPEP 2106.04(c).
As an initial matter, as noted in MPEP 2106.04(c), it has been well established that by the courts that isolated portions of a genome (including single-stranded DNA) differ from their naturally occurring counterpart merely by being merely being isolated from flanking genomic DNA regions, and that such isolation does not render them patent eligible. See, e.g., Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591-94, 106 USPQ2d 1972, 1979-81 (2013) (comparing isolated BRCA1 genes and BRCA1 cDNA molecules to naturally occurring BRCA1 gene), Roche Molecular System, Inc. v. CEPHEID, 905 F.3d 1363, 1371, 128 USPQ2d 1221, 1227 (Fed. Cir. 2018) (comparing claimed primers to "their corresponding nucleotide sequences on the naturally occurring DNA"), and/or University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 760, 113 USPQ2d 1241, 1241 (Fed. Cir. 2014) (comparing single-stranded nucleic acid to the same strand found in nature, even though "single-stranded DNA cannot be found in the human body"). Furthermore, the mere combining of naturally occurring materials (and/or of materials which are not naturally occurring but lack markedly different characteristics as compared to their naturally occurring counterparts) is generally not enough to render such a mixture as patent eligible, especially where there is no evidence that mixing creates a fundamentally new material. See, e.g., Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127 (1948) and MPEP 2104.04. Therefore, if a series of naturally occurring DNA sequences were identified whose isolated portions thereof would read on the limitations of claim 84, then it would support a conclusion that even of a mixture of said isolated portions would not be patent eligible based on the above reasonings.
As disclosed by Ciosi et al. (EBioMedicine, 2019, 48:568-580 plus supplementary materials), several variations in exon one of the HTT gene occur in nature that differ in the number of CAG/CAA repeats present (e.g., as per Fig. 2 and Table 1 of Ciosi). Isolated portions of these repeats (with or without sequences before or after said repeats) that are within the length requirements of the claim (i.e., 125-200 base pairs) from different people/alleles could form a collection that would possess all of the structural limitations of the claim and therefore support a rejection under 35 U.S.C. 101 for the claim.
Claim 85 recites the library of claim 84, wherein the variation is derived from genomic sequences, which is consistent with the HTT gene being derived from human genomic sequences, and therefore does not make the claim patent eligible.
Claims 87 and 112 limit the relative amounts of the primary polynucleotides in the library or collection, and for similar reasoning as presented in Funk Bros., such a precise combination would still not make the claimed invention patent eligible.
Regarding claim 94, which recites the polynucleotide library of claim 84, wherein the variation of each primary polynucleotide includes a modification to a tumor suppressor gene or an oncogene, it is noted that as per Altinoz et al. (Clin Transl Oncol, 2016, 18:9–17) the oncogenic driver AR gene comprises CAG trinucleotide expansions (e.g., as per the Abstract).
Regarding claim 97, the inclusion of the instructions and packaging, while not being naturally occurring, do not make the claim patent eligible. See MPEP 2106.04(c)(I)(A), which states:
Where the claim is to a nature-based product in combination with non-nature based elements (e.g., a claim to "a yogurt starter kit comprising Lactobacillus in a container with instructions for culturing Lactobacillus with milk to produce yogurt"), the markedly different characteristics analysis should be applied only to the nature-based product limitation. For instance, for the yogurt starter kit example, the Lactobacillus would be analyzed for markedly different characteristics. The container and instructions would not be subject to the markedly different characteristics analysis as they are not nature-based products, but would be evaluated as additional elements in Prong Two (and Step 2B if needed) if it is determined that the Lactobacillus does not have markedly different characteristics from any naturally occurring counterpart and thus is a product of nature exception.
The present instructions and packaging correspond to the instructions and container of this example, and therefore only need be considered as potential “additional elements”, as below.
Claims 87, 104, 107-108, and 113-115, and 117-119, and 121-122 depend from claims 84 and 112, respectively, and further recite limitations as to the number, ratios, origins, and nature of variations in the pluralities of polynucleotides, but since these are all found in nature, they do not represent markedly different characteristics.
Claim 106 adds a fourth and fifth primary polynucleotide, which can also be deemed patent ineligible for similar reasoning, at least because the Ciosi reference discloses many, many variations found in the HTT gene (e.g., as per Table 1, Fig. 2, and the supplemental materials).
Regarding claims 109 and 116, short tandem repeats and/or microsatellites have been documented in hundreds of thousands of places in the genome in scores of genes, as per Bahlo et al. (F1000Research, 2018, 7:736).
Therefore, it can be reasonably concluded that the analysis for patent eligibility fails Prong One of Step 2A, and the claim must be further analyzed in the Step 2A Prong Two and Step 2B to determine whether the claim as a whole integrates the exception into a practical application or there are additional elements that amount to significantly more than the judicial exception. Relevant considerations for evaluating whether additional elements integrate a judicial exception into a practical application, based on the Supreme Court and Federal Circuit, are discussed at length in MPEP 2106.04(d) and in the Federal Register (Vol. 84, No. 4, from January 7, 2019). In the present case, the only “additional elements” are the instructions and/or packaging in claim 97, and are recited at a high level of generality and constitute routine, conventional, and well-understood elements such that they cannot transform the claim into something patent eligible. See MPEP 2106.04(d).
For further information, please see the latest revision of MPEP § 2104-2106 {Patent Subject Matter Eligibility Under 35 U.S.C. 101}, including MPEP § 2106.04 {Eligibility Step 2A: Whether a Claim is Directed to a Judicial Exception} and 2106.05 {Eligibility Step 2B: Whether a Claim Amounts to Significantly More}, as well as any additional guidance on Subject Matter Eligibility, provided on the USPTO website at
https://www.uspto.gov/patent/laws-and-regulations/examination-policy/subject-matter-eligibility.
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Response to Arguments
The 04/06/2026 remarks argue: claims are patent eligible.
In response, it is noted that the rejections above have been altered to address all amendments to the claims.
Conclusion
No claims are allowed.
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 JEREMY FLINDERS whose telephone number is (571)270-1022. The examiner can normally be reached M-F 10-6:00 EST.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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