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 .
Claims 1-17 are pending and currently under examination. Claims 1-2, 5-7, 11-12 are amended. Claims 14-17 are new.
Response to Amendment
The Amendment filed 4/16/26 has been entered. Claims 1-17 are pending. Applicant’s amendments to claims 1-2, 5-7, 11-12 have overcome the 112(b) rejections previously set forth in the Non-Final Office Action mailed 1/27/26.
Response to Arguments
Applicant’s arguments, see pages 6-8, filed 4/22/26, with respect to the rejections of claims 1-13 under 35 USC 103 have been fully considered are found unpersuasive, and the rejections documented in the Non-Final mailed 1/27/26 have been revised to address claim amendments and new claims 14-17 filed 4/16/26 in this Final Office Action. More detailed responses to Applicant’s arguments are provided at the end of each maintained rejection.
Claim Rejections - 35 USC § 103
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.
Claims 1-15 and 17 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Callahan et al. (2019; WO 2019/209597 A1; FOR citation N in PTO-892 filed 1/27/26).
This 103 rejection is necessitated by claim amendments and new claims 14-15 and 17.
Relevant to claims 1 and 17, Callahan et al. teaches "The method provided herein is especially useful in isolating biomolecules from stool samples. Analysis of biomolecules (e.g., nucleic acids) from stool samples allows detection of bacterial and viral infectious agents…" (page 7, lines 17-19).
Relevant to claims 1, 3, 5, and 17, Callahan et al. teaches "A lytic reagent may also include one or more detergents, including nonionic, cationic, anionic (sodium dodecyl sulfate) or zwitterionic detergents. Exemplary detergents include sodium dodecyl sulfate (SDS)… polyoxyethylene sorbitan monolaurate" (page 13, lines 5-10).
Relevant to claims 1, 4, 6, 14, and 17, Callahan et al. teaches "The concentration of an individual detergent in the lytic reagent may be in the range of 0.001 to 15%" (page 13, lines 17-18).
Relevant to claims 1 and 17, Callahan et al. teaches "In addition to one or more relatively mild chaotropic agents, a lytic reagent may further comprise one or more phosphates… Exemplary phosphates include… trisodium phosphate" (page 12, lines 1-15).
Relevant to claim 2 and 17, Callahan et al. teaches "After a sample is collected, the sample is typically lyzed to release biomolecules for subsequent isolation or detection. Sample lysis according to the method disclosed herein uses a lytic reagent that comprises, consists essentially of, or consists of one or more relatively mild chaotropic agents and one or more phosphates (and optionally water)" (page 8, lines 21-25).
Relevant to claims 7 and 15, Callahan et al. teaches "The concentration of a phosphate in a lytic reagent may be 0.05 to 0.5M, preferably 0.1 to 0.2M. The final concentration of phosphate in a lysate (i.e., the mixture of a sample and the lytic reagent) may be 0.01 to 0.4M, preferably 0.1 to 0.2M" (page 12, lines 20-23).
Relevant to claim 8, Callahan et al. Abstract teaches "The present disclosure provides methods for isolating nucleic acids from a sample… Compositions and kits useful in such methods are also disclosed."
Further relevant to claim 8, Callahan et al. teaches "In a related aspect, the present disclosure provides a kit for preparing a lysate from a sample that comprises (a) the lytic reagent described above" (page 17, lines 26-28).
Further relevant to claim 8, Callahan et al. teaches "The kit may further comprise one or more of the following components:… one or more vessels or containers (e.g., collection tubes)" (page 20, line 28 - page 21, line 12).
Relevant to claims 9-10, Callahan et al. teaches "Sample lysis may be performed by physical disruption, chemical lysis, enzymatic lysis, or a combination thereof. Depending on a given sample type and organisms present in the sample, different sample disruption methods may be used. For example, although human cells and viral capsids are easily lysed by salts or detergents, bacterial spores or oocysts require more aggressive chemical, enzymatic or physical methods… Chemical lysis includes the use of a lytic reagent comprising one or more chaotropic agents" (page 23, lines 21-30).
Relevant to claim 10, Callahan et al. teaches "The isolated DNA may be analyzed or used in any application, including PCR, qPCR" (page 35, lines 1-2).
Further relevant to claim 10, Callahan et al. teaches "The method provided herein is especially useful in isolating biomolecules from stool samples. Analysis of biomolecules (e.g., nucleic acids) from stool samples allows detection of bacterial and viral infectious agents…" (page 7, lines 17-19).
Relevant to claims 11-12, Callahan et al. teaches "A lytic reagent may also include one or more detergents, including nonionic, cationic, anionic (sodium dodecyl sulfate) or zwitterionic detergents. Exemplary detergents include sodium dodecyl sulfate (SDS)… polyoxyethylene sorbitan monolaurate" (page 13, lines 5-10).
Relevant to claims 11-12, Callahan et al. teaches "The concentration of an individual detergent in the lytic reagent may be in the range of 0.001 to 15%" (page 13, lines 17-18).
Relevant to claims 11-12, Callahan et al. teaches "In addition to one or more relatively mild chaotropic agents, a lytic reagent may further comprise one or more phosphates… Exemplary phosphates include… trisodium phosphate" (page 12, lines 1-15).
Relevant to claims 11-12, Callahan et al. teaches "The concentration of a phosphate in a lytic reagent may be 0.05 to 0.5M, preferably 0.1 to 0.2M. The final concentration of phosphate in a lysate (i.e., the mixture of a sample and the lytic reagent) may be 0.01 to 0.4M, preferably 0.1 to 0.2M" (page 12, lines 20-23).
Relevant to claim 13, Callahan et al. teaches "The term 'biological sample' as used herein refers to a sample obtained from or produced by a biological subject, including but are not limited to, organs, tissues, cells, body fluid (e.g., blood, blood plasma, serum, cerebrospinal fluid, or urine), swab samples" (page 7, lines 10-13).
Further relevant to claim 13, Callahan et al. teaches "The kit may further comprise one or more of the following components:… one or more vessels or containers (e.g., collection tubes)" (page 20, line 28 - page 21, line 12).
The skilled artisan would recognize that the Callahan et al. "collection tubes" can be combined with the "swab samples" biological inputs within the disclosed kit, and furthermore, would recognize the need for aseptic packaging, as the skilled artisan would find it obvious in order to not introduce unintended contaminants.
Callahan et al. does not teach a specific embodiment having all the claimed elements. That being said, however, it must be remembered that "[w]hen a patent simply arranges old elements with each performing the same function it had been known to perform and yields no more than one would expect from such an arrangement, the combination is obvious." KSR v. Teleflex, 127 S.Ct. 1727, 1740 (2007) (quoting Sakraida v. AG. Pro, 425 U.S. 273, 282 (1976)). "[W]hen the question is whether a patent claiming the combination of elements of prior art is obvious," the relevant question is "whether the improvement is more than the predictable use of prior art elements according to their established functions." (Id.). Addressing the issue of obviousness, the Supreme Court noted that the analysis under 35 USC 103 "need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ." KSR at 1741. The Court emphasized that "[a] person of ordinary skill is... a person of ordinary creativity, not an automaton." Id. At 1742.
Consistent with this reasoning, it would have been prima facie obvious to have selected various combinations of various disclosed elements — including ionic detergents, non-ionic detergents, phosphate compounds, and kits — for compositions and methods for extracting nucleic acid(s) from pathogens, to arrive at compositions "yielding no more than one would expect from such an arrangement."
Applicant’s Arguments and Response to Applicant’s Arguments
Applicant argues that “the presently claimed composition does not require any chaotropic agent and is not defined in terms of a chaotropic-based lysis system, but instead is defined by a specific combination of detergents and salts. The Office Action does not provide any articulated reasoning explaining why a person of ordinary skill in the art would have been motivated to omit the chaotropic agent from Callahan’s system while retaining phosphates, nor does it establish a reasonable expectation of success for such a modification” (Remarks 4/16/26, page 7, paragraph 2).
The Examiner respectfully disagrees with these assertions. The presently claimed composition in claim 1 is not as defined or exclusionary as the applicant argues. Per MPEP 2111.03(I):
The transitional term "comprising", which is synonymous with "including," "containing," or "characterized by," is inclusive or open-ended and does not exclude additional, unrecited elements or method steps (emphasis added).
As such, claim 1 composition containing the recited elements does not require reasoning explaining motivation for including or excluding other elements such as those used by Callahan et al.
The Applicant further argues that “Callahan broadly lists various classes of detergents (including ionic and non-ionic detergents” and “does so only in a generic manner, without teaching any specific combination of detergent types or any defined relationship between their concentrations”, citing that the “claims, however, require a structured and narrowly defined combination” that would rely upon “impermissible hindsight reconstruction” (Remarks 4/16/26, page 7, paragraph 3).
The Examiner respectfully disagrees with these assertions.
As discussed above, the composition of claim 1 is not a structured or narrowly defined combination, and instead recites concentrations and reagent amounts previously disclosed within Callahan et al.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Applicant argues that “claim 1 recites Na3PO4 and/or NaHCO3” and that the Office Action and Callahan et al. omission of NaHCO3 is not explained for “as to why a person of ordinary skill in the art would have selected NaHCO3 for use in the claimed composition” (Remarks 4/16/26, page 8, paragraph 1).
The Examiner respectfully disagrees with this assertion. Claim 1, as written, requires a composition that contains:
i. Na3PO4;
ii. Na3PO4 and NaHCO3;
iii. NaHCO3.
The Office Action and Callahan et al. rely upon teachings of compositions of option i. (Na3PO4) to fulfill the claim 1 composition requirements, and thus would not require explanation as to why the skilled artisan would omit the optional compositions of ii. or iii. (Na3PO4 and NaHCO3; NaHCO3).
Applicant argues that “The Office Action does not provide a reasoned explanation as to why a skilled artisan would have combined the specific components and concentration ranges recited in the claims, nor does it explain how such a combination would have been expected to function in the manner required by the claimed invention” (Remarks 4/16/26, page 8, paragraph 2).
The Examiner respectfully disagrees with these assertions. As stated in the above rejection and reiterated from the 1/27/26 Non-Final Rejection, the instant patent “simply arranges old elements with each performing the same function it had been known to perform” from the disclosure of Callahan et al. The skilled artisan is “a person of ordinary creativity, not an automaton” and would find it obvious and reasonable to select previously disclosed elements from the Callahan et al. disclosure to arrive at the instantly rearranged combination of old elements.
Applicant argues that “Claim 17 uses ‘consisting of’ instead of ‘compromising’ so that it is narrower than claim 1 and is thus patentable for at least the same reasons as claim 1” (Remarks 4/16/26, page 5).
The Examiner respectfully disagrees that claim 17 is patentable for “at least the same reasons as claim 1.”
Callahan et al. teaches “a lytic reagent that comprises, consists essentially of, or consists of one or more relatively mild chaotropic agents and one or more phosphates (and optionally water)” (page 8, lines 23-25). Callahan et al. further teaches embodiments wherein "A lytic reagent may also include one or more detergents, including nonionic, cationic, anionic (sodium dodecyl sulfate) or zwitterionic detergents. Exemplary detergents include sodium dodecyl sulfate (SDS)… polyoxyethylene sorbitan monolaurate" (page 13, lines 5-10).
The multiple Callahan et al. embodiments are not considered as teaching away from the instantly claimed composition recited in new claim 17. Instead, as set forth in MPEP 2141.02:
Ascertaining the differences between the prior art and the claims at issue requires interpreting the claim language, and considering both the invention and the prior art references as a whole… A prior art reference must be considered in its entirety, i.e., as a whole, including portions that would lead away from the claimed invention… However, ‘the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed….’ In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004) (emphasis added).
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Callahan et al. (2019; WO 2019/209597 A1; FOR citation N in PTO-892 filed 1/27/26), as applied to claims 1-15 and 17 above, and further in view of Herzer et al. (2008; US 2008/076911 A1).
This 103 rejection is necessitated by new claim 16 filed 4/16/26.
The teachings of Callahan et al. are applied to instantly rejected claim 16 as they were previously applied to claims 1-15 and 17 as rendering obvious a liquid composition. Callahan et al. is silent to specifics regarding NaHCO3. However, these limitations were known in the prior art and taught by Herzer et al.
Herzer et al. paragraph 0054 teaches DNA elution buffers containing sodium bicarbonate (NaHCO3).
Although Callahan et al. does not include sodium bicarbonate within the liquid composition, it would have been prima facie obvious to the skilled artisan. Callahan et al. and Herzer et al. are analogous disclosures within the instant nucleic acid extraction field.
The skilled artisan would have been motivated to combine the analogous art. Callahan et al. page 32, lines 13+ teach that “Methods for sequentially isolating DNA and RNA are known… Preferably, a solid support for binding DNA and a solid support for binding RNA are used” and that the nucleic acid “bound to the solid phase may be washed, and subsequently eluted from the solid phase… DNA elution solution may be a buffer”. Herzer et al. paragraph 0054 teaches the inclusion of sodium bicarbonate within elution buffers for DNA elution.
Thus, the skilled artisan would have been motivated to include the Herzer et al. sodium bicarbonate within the liquid composition/nucleic acid extraction methodologies of Callahan et al. because Callahan et al. teaches that DNA elution buffers for isolating DNA are known and Herzer et al. teaches inclusion of sodium bicarbonate within DNA elution buffers. The skilled artisan would have a reasonable expectation of success based on the disclosures of Callahan et al., and further in view of Herzer et al., as discussed in the preceding paragraphs.
Conclusion
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sarah J Kennedy whose telephone number is (571)272-1816. The examiner can normally be reached Monday - Friday 8a - 5p.
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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