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 .
Status of Claims
Applicant’s amendment filed 07/03/2025 is acknowledged. Claims 1, 7, 11, 14, 19-20, 24, 27, 36, 47, and 51-52 have been amended. Claims 2-6, 9-10, 12-13, 15-18, 21-23, 25-26, 28-35, 37-46, and 49-50 have been cancelled. Claims 1, 7-8, 11, 14, 19-20, 24, 27, 36, 47-48, and 51-52 are pending in the instant application and the subject of this non-final office action.
Claim Objections
Claim 11 is objected to because of the following informalities: The claim recites “0.1millimolar”; the limitation lacks space between the number and unit. Appropriate correction is required.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP 2111.
Regarding claims 11, 14, and 36, the specification fails to define the term “about”. The term was interpreted to encompass 10% plus or minus the stated value for the purposes of interpretation.
Claim Rejections - 35 USC § 112(a)
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.
Claim 36 is 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 reducing transversion of one or more nucleotides of cell-free nucleic acids by at least about 50% compared to a corresponding control composition lacking hypotaurine at 47 degrees C for 16-72 hours, does not reasonably provide enablement for such a reaction that takes place for about 8 hours. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Regarding claim 36, the applicant’s disclosure lacks sufficient detail to enable one of ordinary skill in the art to use the full scope of the claimed invention, as required under 35 U.S.C. 112(a). See MPEP 2164.01(a) for the factors considered.
In the instant case, the disclosure provides the working example of hybrid capture conducted on a thermal cycler at 47 degrees C (para [0143]), wherein the relative reduction in G>T errors is noted to be reduced to 16% from 57% of all errors and the background error rate is noted to be reduced by about 50% (para [0144]). The artisan would understand that the error rates would be approximately 0.16*.50x and 0.57*1x, such that the reduction in G>T errors (transversions of one or more nucleotides) would be about 14% of the original value, i.e., a reduction of 86%.
However, while the specification provides a wide range of potential times that might be utilized by the artisan, from 5 minutes (para [0080]) to 72 hours (para [0081]), in general, and fails to provide any specific direction for the species of heterologous antioxidant moiety hypotaurine.
Indeed, in contrast to the 8 hours claimed, in the working example, the guidance given in the working example for hypotaurine is that the capture steps were conducted at 47 degrees C, wherein a compatible hybrid capture kit is the SeqCap EZ Choice from NimbleGen. The manual for this product (Roche. SeqCap EZ & HyperCap User Guide v2.3 [Internet]. Pleasanton (CA): Roche Sequencing Solutions, Inc.; 2018 [cited 2025 Sep 24]. Available from: https://diagnostics.roche.com/content/dam/diagnostics/se/pdfer-p%C3%A5-webbplatsen-redigerade/pdfer-sekvensering/SE-DIA-OWP-SeqCap_EZ_HyperCap_UGuide_v2.3.pdf) recommends incubating for 16-20 hours (pg. 28, step 22) and up to 72 hours but states that shorter times require guidance from technical support (pg. 46, Hybridizing the Sample Library).
The prior art fails to teach hypotaurine utilized at 47 degrees C for any particular length of time in the context of reducing transversions.
The invention is in the class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
Therefore, while the specification supports a relative reduction in transversions of one or more nucleotides upon subjecting cell-free nucleic acids to temperatures at about 47 degrees C, it is not enabled for the time period of 8 hours given the unpredictability in the field, the lack of specific guidance for hypotaurine and the contrasting guidance in the referenced capture method, and the lack of relevant prior art.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 19 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Regarding claim 19, the claim merely adds the additional nomenclature of “a nucleic acid analysis sample” to the cell-free nucleic acids. As all of the structures required are the same as claim 1, the claim fails to further limit the subject matter of the claim upon which it depends.
For this reason, claim 19 does not meet the requirements of 112(d).
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, 7-8, 11, 14, 19-20, 24, 27, 47-48, and 51 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exceptions without significantly more. The claim(s) recite(s) natural phenomenon. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
The following three inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter?
Yes, the claims 1, 7-8, 11, 14, 19-20, 24, 27, 47-48, and 51 are directed to natural products.
Step 2A, prong 1. Does the claim recite a law of nature, a natural phenomenon, or an abstract idea (recognized judicial exceptions)?
Yes, Koukourakis (Koukourakis MI, et al. Circulating Plasma Cell-free DNA (cfDNA) as a Predictive Biomarker for Radiotherapy: Results from a Prospective Trial in Head and Neck Cancer. Cancer Diagn Progn. 2023 Sep 3;3(5):551-557.) teaches that cfDNA is DNA released by tissues (pg. 551, col 2, para 1) and exists in plasma (Abstract). Nishimura (Nishimura T, et al. Hypotaurine Is a Substrate of GABA Transporter Family Members GAT2/Slc6a13 and TAUT/Slc6a6. Biol Pharm Bull. 2018;41(10):1523-1529) teaches that hypotaurine circulates in plasma (Abstract). Therefore, the composition of cell-free nucleic acids reads on, at least, mammalian plasma.
It is noted that while the cell-free nucleic acids of claim 1 are “isolated”, product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. See MPEP 2106.04(b). In the instant case, “isolated DNA” has been identified by the courts as an example of natural phenomena, and thus “isolated cell-free nucleic acids” are held not to be markedly different than cell-free nucleic acids. See Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 589-91, 106 USPQ2d 1972, 1978-79 (2013).
Claim 27 recites “mixing” isolated cell-free nucleic acids and hypotaurine. As above, isolated cell-free nucleic acids lack encompass both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from the naturally occurring counterpart. The mixing merely enables the provision of the product on claim 1, and reads on bodily processes that produce, for example, plasma (i.e., mixing by any means). See MPEP 2106.04(c)(I)(C).
Step 2A, prong 2. Is the judicial exception(s) integrated into a practical application?
Regarding claims 1, 7-8, 11, 14, 19-20, 24, no, the claims are directed to a composition comprising only natural products or those not markedly different from natural products and fail to effect a particular transformation of the natural products. See MPEP 2106.05(c) and 2106.04(d).
It is noted that claim 20 requires an additional probe, with the intended use of capturing a nucleic acid molecule from the pool comprising the cell-free nucleic acids. No structures are recited that require it be anything other than a natural product (i.e., a sequence that may also be found in, for example, plasma).
Regarding claim 27, as mentioned above, the claim encompasses the natural production of, for example, plasma. Thus, the claim fails to integrate the natural products into a practical application.
Regarding claims 47-48, the claims are directed to the source of the nucleic acids, specifying that they are from a natural source. It therefore fails to integrate the limitations into a practical limitation.
Regarding claim 51, the claim encompasses “capturing” the cell-free nucleic acids via one or more nucleic acids probes prior to, concurrent with, or subsequent to the mixing. The only structure required of the probes is that they be a nucleic acid. Broadly interpreted, “capturing” encompasses hybridization. There is no limit on timing placed so the claim merely recites structural features of a product (i.e., a probe capable of capturing/hybridizing to cell-free nucleic acids in the mixture of claim 27). Thus, the claim encompasses the natural product without integrating it into a practical application.
Step 2B. Does the claim amount to significantly more?
Regarding claims 1, 7-8, 19, and 24, the claims are directed directly to the products/a particular source of the products (claims 1, 19, and 24) or to an inherent property of the products (claims 7-8). The claims fail to add more than the judicial exception.
Regarding claim 11, the claim fails to amount to significantly more because the listed concentrations of hypotaurine encompass those known in the art for mammalian plasma (Nishimura, pg. 1523, col 2, para 2: “Hypotaurine…concentration is 0.1 mM in fetal plasma of mouse and bovine”). Thus, there is no particular transformation.
Regarding claim 14, the claim does not amount to significantly more because the listed concentrations encompass those known in the art for mammalian plasma. Koukourakis teaches
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plasma cfDNA levels between 0.09-19.40 ng/uL (Results, para 1) and that circulating cfDNA can range in size from 100 to 800 bp (pg. 551, col 2, para 1). While Koukourakis does not explicitly teach a molarity, it teaches a molarity in the range by teaching the concentration and the length of the cfDNA, evidenced by Bioline (Bioline. Weight to Molar Quantity (for nucleic acids) [Internet]. Meridian Bioscience; [cited 2025 Sep 24]. Available from: https://www.bioline.com/media/calculator/01_07.html.), for example 100 bp with a 19.4 ng/uL concentration is about a 299 nM concentration of cell-free nucleic acids. Thus, there is no particular transformation.
Regarding claim 20, as discussed in step 2A prong 2, the limitation requires an additional probe but does not require further structures beyond what could be found in the natural product as the design is an intended use. Thus, the claim fails to recite significantly more than the judicial exception.
Regarding claims 27, 47-48, and 51, as discussed in step 2A, prong 2, the limitations are directed to natural products and the process steps merely recite the structures of the product, as discussed. Therefore, the claims fail to recite significantly more than the judicial exception.
Claim Rejections - 35 USC § 103
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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 7-8, 11, 14, 19-20, 24, 27, 47-48, and 51-52 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dhingra (WO 2018/231818 A1; as cited in the IDS dated 01/24/2024) in view of Donnelly (Donnelly ET, et al. Glutathione and hypotaurine in vitro: effects on human sperm motility, DNA integrity and production of reactive oxygen species. Mutagenesis. 2000 Jan;15(1):61-8; as cited in the IDS dated 08/12/2024), as evidenced by Bioline (Bioline. Weight to Molar Quantity (for nucleic acids) [Internet]. Meridian Bioscience; [cited 2025 Sep 24]. Available from: https://www.bioline.com/media/calculator/01_07.html.)
Regarding claims 1 and 19, Dhingra teaches a composition prepared by a method (claim 21) comprising providing a first plurality of polynucleotides and at least one damage-mitigating reagent (claim 1). Dhingra teaches that the first plurality of polynucleotides may comprise cell-free nucleic acids (para [00264]; instant claim 19, wherein “a nucleic acid analysis sample” is a matter of nomenclature as only the structures of instant claim 1 are required) and that the nucleic acids may be isolated (para [0039-40]).
Dhingra teaches that the compositions and systems may be utilized to reduce nucleic damage during exposure to reactive oxygen species (para [0044]; [00374]).
Dhingra fails to teach that the damage-mitigating reagent may be hypotaurine.
Donnelly rectifies this by teaching that supplementation of 10 mM hypotaurine in vitro (pg. 63, Effect of glutathione and hypotaurine supplementation in vitro (10 mM) on H2O2-induced DNA damage in human sperm) significantly protected against H2O2-induced DNA damage and ROS production (Abstract; pg. 66, col 2, para 1; pg. 66, col 2, para 4, spanning pg. 67), wherein H202 is a key ROS (pg. 61, col 2, para 1).
Therefore, it would have been obvious to one of ordinary skill in the art at the time of filing to simply substitute hypotaurine as a damage-mitigating reagent in the composition of Dhingra, as the function of hypotaurine as a ROS damage-mitigating reagent was known in the art and one of ordinary skill could have substituted damaging-mitigating reagent for the other with predictable, and the results would have been predictable as would be expected to perform the same function in a cell-free composition. The artisan would have been so motivated by the significant protection against the relevant DNA damage taught by Donnelly.
Regarding claims 7 and 8, in the composition of Dhingra in view Donnelley, Dhingra teaches that the reduced nucleic acid damage comprises reduced transversions selected from A> T, T > A, C > T, T > C, A> C, C > A, G > T and T > G (para [0014], [0050]).
Further, the specification recites that hypotaurine inherently reduces G>T transversions in a cfDNA hybrid capture reaction (para [0048-49]).
Regarding claim 11, in the composition of Dhingra in view Donnelley, Dhingra teaches that the presence of the damage mitigating reagent should be at various concentrations ranges between about 0.01 mM and about 100 mM (para [0058]).
As cited in claim 1 above, Donnelly teaches supplementation with 10 mM hypotaurine.
Further, while neither Dhingra nor Donnelly specifically teaches the combination of cfDNA and hypotaurine, such is held to be obvious as matter of routine optimization at least because of the above teachings and the large range claimed.
Regarding claim 14, in the composition of Dhingra in view Donnelley, Dhingra teaches adding 100 ng to 100 ug input DNA into 130 uL (para [00403]) and that the first plurality of polynucleotides comprises fragments of 50-450 bp or about 100-200 bp (para [0095]).
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Dhingra teaches that the concentration of nucleic acid molecules comprising cell-free nucleic acids in the composition is between about 10 nM and about 10 mM by teaching the mass range of input DNA, the reaction volume, and the length of the fragments, as cited above, as evidenced by Bioline. While Dhingra does not explicitly teach a molarity of the cell-free nucleic acids in the composition, it is inherently taught because these numbers together comprise molarities within the cited range, as evidenced by Bioline (e.g., for 100 bp [i.e., 0.1 kb] dsDNA, 100 ug in 130 uL is equivalent to about 10 uM).
Regarding claim 20, in the composition of Dhingra in view Donnelley, Dhingra teaches that the composition includes sequencing control nucleic acids prepared by the methods described, wherein the control nucleic acids can include an adapter having a universal capture sequence [i.e., a probe designed to capture the molecule from a pool] (para [00317]).
Regarding claim 24, in the composition of Dhingra in view Donnelley, Dhingra teaches that the first plurality of nucleic acids can comprise cell-free nucleic acids from a biological fluid (para [00264], [00272]) and that the first plurality may be isolated from a healthy source, a diseased source, or an infected source [i.e., a subject] (para [00275]).
Regarding claim 27, Dhingra teaches a method comprising providing a single reaction mixture containing a first plurality of polynucleotides and at least one nucleic acid damage-mitigating reagent (claim 1). Dhingra teaches that the first plurality of polynucleotides may comprise cell-free nucleic acids (para [00264]) and that the nucleic acids may be isolated (para [0039-40]).
A single reaction mixture requires a step of mixing for any embodiments that are not strictly natural products (including those that are not markedly different, such as isolated nucleic acids); thus, by teaching that the nucleic acids may be isolated, Dhingra teaches a step of mixing the plurality of isolated cell-free nucleic acids and the at least one nucleic acid damage-mitigating reagent.
Dhingra teaches that the methods and compositions may be utilized to reduce nucleic damage during exposure to reactive oxygen species (para [0044]; [00374]).
Dhingra fails to teach that the damage-mitigating reagent may be hypotaurine.
Donnelly rectifies this by teaching that supplementation of 10 mM hypotaurine in vitro (pg. 63, Effect of glutathione and hypotaurine supplementation in vitro (10 mM) on H2O2-induced DNA damage in human sperm) significantly protected against H2O2-induced DNA damage and ROS production (Abstract; pg. 66, col 2, para 1; pg. 66, col 2, para 4, spanning pg. 67), wherein H202 is a key ROS (pg. 61, col 2, para 1).
Therefore, it would have been obvious to one of ordinary skill in the art at the time of filing to simply substitute hypotaurine as a damage-mitigating reagent in the method of Dhingra, as the function of hypotaurine as a ROS damage-mitigating reagent was known in the art and one of ordinary skill could have substituted damaging-mitigating reagent for the other with predictable, and the results would have been predictable as would be expected to perform the same function in a cell-free composition. The artisan would have been so motivated by the significant protection against the relevant DNA damage taught by Donnelly.
Regarding claim 47, in the method of Dhingra in view of Donnelly, Dhingra teaches that the first plurality of nucleic acids can comprise cell-free nucleic acids from a biological fluid (para [00264], [00272]) and that the first plurality may be isolated from a healthy source, a diseased source, or an infected source [i.e., a subject] (para [00275]).
Regarding claim 48, in the method of Dhingra in view of Donnelly, Dhingra teaches that the first plurality of nucleic acids may be isolated from a human (para [00270]).
Regarding claims 51 and 52, in the method of Dhingra in view of Donnelly, Dhingra teaches the methods of the invention can further include sequencing the nucleic acids prepared by the method [i.e., subsequent to the mixing] (instant claim 52), wherein the nucleic acids can include a universal capture sequence and attaching the control nucleic acids to a support by binding/hybridizing the universal capture sequence of the control nucleic acids to a capture primer on a support [i.e., capturing the cell-free nucleic acids via one or more probes] (para [00317]).
It is noted that the respective order of steps is obvious, not least because all orders of steps are claimed with regard to the capture probe. See also MPEP 2144(IV)(C).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMMA R HOPPE whose telephone number is (703)756-5550. The examiner can normally be reached Mon - Fri 11:00 am - 7:00 pm.
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/EMMA R HOPPE/ Examiner, Art Unit 1683
/ANNE M. GUSSOW/ Supervisory Patent Examiner, Art Unit 1683
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