DETAILED ACTION
DETAILED ACTION
Notice of Pre-AIA or AIA Status and New Examiner
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Please note that the examiner for this application has changed. Please address future correspondence to Robert T. Crow (Art Unit 1683) whose telephone number is (571) 272-1113.
Continued Examination Under 37 CFR 1.114
3. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 15 December 2025 has been entered.
Amendments and Status of the Claims
4. This action is in response to papers filed 15 December 2025 in which claims 39-40, 44, 49, and 57 were amended, claims 1-2, 4-6, 10, 18, 21-24, 27, 31-32, 37, and 43 was canceled, and new claims 58-69 were added. All of the amendments have been thoroughly reviewed and entered.
All previous objections and/or rejections not reiterated below are withdrawn in view of the amendments.
Applicant’s arguments have been thoroughly reviewed and are addressed following the rejections necessitated by the amendments.
Claims 39-41, 44-45, 48-49, and 57-69 are under prosecution.
5. This Office Action includes objections and rejections.
Claim Objections
6. Claims 39 and 40 are each objected to because of the following informalities: claims 39 and claim 40 each contain the recitation “the one or more microorganism,” which appears to be a typographical error. Appropriate correction is required.
Claim Rejections - 35 USC § 112
7. 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.
8. Claims 39-41, 44-45, 48-49, and 57-69 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.
This is a new matter rejection.
A. Claim 39 (upon which claims 40-41, 44-45, 48-49, and 58-63 depend) and claim 57 (upon which claim 64-69) depend each recite vaginal samples. While the parent 371 specification discusses generic “genital” samples, the parent 371 specification des not discuss the claims species of “vaginal” samples. Thus, the limitation constitutes new matter.
B. Claim 39 (upon which claims 40-41, 44-45, 48-49, and 58-63 depend) and claim 57 (upon which claim 64-69 depend) each recite a substantially cylindrical container. The parent 371 specification only discusses test-tubes as substantially cylindrical containers. Thus, because the parent 371 specification does not support the full scope for the generic container, the limitation constitutes new matter.
9. 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.
10. Claims 39-41, 44-45, 48-49, and 57-69 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.
A. Claim 39 (upon which claims 40-41, 44-45, 48-49, and 58-63 depend) and claim 57 (upon which claim 64-69 depend) are indefinite in each of the following:
I. The term “remote” in claim 39 (upon which claims 40-41, 44-45, 48-49, and 58-63 depend) and claim 57 is a relative term which renders the claim indefinite. The term “remote” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
II. The recitation “the sample container” in part B of each of claims 37 and 57, which lacks antecedent basis in the pervious recitation of a “substantially cylindrical container.”
III. The recitation “the microorganism portion,” which lacks antecedent basis because there is no previous recitation of a “microorganism portion.”
B. Claim 41 is indefinite in the recitation “the nucleic acid sequencing,” which lacks antecedent basis in the previous recitation of “sequencing nucleic acid material.”
C. Claim 49 is indefinite in the recitation “the tip portion,” which lacks antecedent basis because there is no previous recitation of a “tip portion.”
D. The term “complex” in 58 is a relative term which renders the claim indefinite. The term “remote” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
E. Claims 59 and 66 each recite sodium and sulfuric acid as drying agents. It is unclear how sodium, which is pyrophoric, can be used as a drying agent. In addition, it is unclear how sulfuric acid is compatible with nucleic acid samples, as DNA is degraded by strong acid.
F. Claim 62 is indefinite in the recitation “the device,” which lacks antecedent basis in the previous recitation of a “sample collection device.”
G. Claim 68 is indefinite in each of the following:
I. The recitation “the plurality of elongated fibers,” which lacks antecedent basis because claim 57 does not recite a “plurality of elongated fibers.”
II. The recitation “the tip portion,” which lacks antecedent basis because there is no previous recitation of a “tip portion.”
H. Claim 69 is indefinite in the recitation “the device,” which lacks antecedent basis in the previous recitation of a “sample collection device.”
Claim Rejections - 35 USC § 103
11. 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.
12. 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.
13. Claims 39, 41, 57-60, and 63-66 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (PCT International Application Publication No. WO 2015/112352 A2, published 30 July 2015) and Hostettler et al. (U.S. Patent Application Publication No. US 2011/0127177 A1, published 2 June 2011).
Regarding claim 39, Apte et al. teach methods comprising characterizing a microbiome in a subject (i.e.,. a human; paragraph 0003) comprising providing a kit to a remote location (Abstract), wherein the kit includes a substantially cylindrical container (i.e. a tube) containing a collection element comprising a support body and a collection portion (i.e., a swab; paragraph 0005 and Figure 4b). Apte et al. also teach the swab is used to obtain a vaginal or fecal sample (paragraph 0008), which is then received in a sample container (paragraph 0010) and further received from the collection site, followed by sequencing the nucleic acid material to generate a microbiome sequence dataset, identifying the microorganisms therein, generating an analysis therefrom, and communicating (i.e., transmitting) the analysis to the subject (i.e., individual; Abstract). Apte et al. further teach the methods have the added advantage of allowing identification of a number of health and disease related states (paragraph 0003). Thus, Apte et al. teach the known techniques discussed above.
While Apte et al. teach the kit facilitates drying (i.e., lyophilization; paragraph 0016) of the sample, and that the collection element (i.e., swab) is in the substantially cylindrical container (i.e., tube; Figure 4b), Apte et al. do not teach the drying agent is within the sample collection device.
However, Hostettler et al. teach methods wherein test tube 40 comprises a sample collection device, in the form or swab 19 (paragraph 0043), contained therein, wherein the test tube 40 further comp0rises drying agent 46 (Figure 3 and paragraph 0049). Hostettler et al. further teach the methods have the added advantage of being more rapid and effective at drying samples (paragraph 0007). Thus, Hostetter et al. teach the known techniques discussed above.
It is also noted that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C. Thus, any order of steps is an obvious variant of the steps of the cited prior art.
MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, counsel’s mere arguments cannot take the place of evidence in the record.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantages of allowing identification of a number of health and disease related states as explicitly taught by Apte et al. (paragraph 0003) and providing more rapid and effective drying of samples as explicitly taught by Hostetter et al. (paragraph 0007). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because the known techniques of the cited prior art predictably result in methods and devices suitable for sample collection.
Regarding claim 41, the method of claim 39 is discussed above. Apte et al. teach the sequencing is whole genome sequencing (paragraph 0052).
Regarding claim 57, Apte et al. teach methods comprising characterizing a microbiome in a subject (i.e.,. a human; paragraph 0003) comprising providing a kit to a remote location (Abstract), wherein the kit includes a substantially cylindrical container (i.e. a tube) containing a collection element comprising a support body and a collection portion (i.e., a swab; paragraph 0005 and Figure 4b). Apte et al. also teach the swab is used to obtain a vaginal or fecal sample (paragraph 0008), which is then received in a sample container (paragraph 0010) and further received from the collection site, followed by sequencing the nucleic acid material to generate a microbiome sequence dataset, identifying the microorganisms therein, generating an analysis therefrom, and transmitting the analysis to the subject (i.e., individual; Abstract). Apte et al. further teach the methods have the added advantage of allowing identification of a number of health and disease related states (paragraph 0003). Thus, Apte et al. teach the known techniques discussed above.
While Apte et al. teach the kit facilitates drying (i.e., lyophilization; paragraph 0016) of the sample, and that the collection element (i.e., swab) is in the substantially cylindrical container (i.e., tube; Figure 4b), Apte et al. do not teach the drying agent is within the sample collection device.
However, Hostettler et al. teach methods wherein test tube 40 comprises a sample collection device, in the form or swab 19 (paragraph 0043), contained therein, wherein the test tube 40 further comp0rises drying agent 46 (Figure 3 and paragraph 0049). Hostettler et al. further teach the methods have the added advantage of being more rapid and effective at drying samples (paragraph 0007). Thus, Hostetter et al. teach the known techniques discussed above.
It is also reiterated that the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results. Thus, any order of steps is an obvious variant of the steps of the cited prior art.
Applicant is again cautioned to avoid merely relying upon counsel’s arguments in place of evidence in the record.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantages of allowing identification of a number of health and disease related states as explicitly taught by Apte et al. (paragraph 0003) and providing more rapid and effective drying of samples as explicitly taught by Hostetter et al. (paragraph 0007). In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because the known techniques of the cited prior art predictably result in methods and devices suitable for sample collection.
Regarding claim 58, the method of claim 39 is discussed above. Apte et al. teach the sample comprises a complex community of microorganisms; namely, the sample comprises multiple microorganisms (paragraph 00117 and Figure 15A).
Regarding claims 59-60, the method of claim 39 is discussed above Hostetter et al. teach the drying agent is substantially composed of silica (paragraph 0011).
Regarding claim 63, the method of claim 57 is discussed above. Apte et al. teach the nucleic acid material is from a microorganism present in the microbiome of a subject (Abstract).
Regarding claim 64, the method of claim 57 is discussed above. Apte et al. teach the sequencing is whole genome sequencing (paragraph 0052).
Regarding claim 65, the method of claim 57 is discussed above. Apte et al. teach the support body (i.e., the body of the swab) comprises a longitudinal extension, in the form of an elongated shaft relative to the end (Figure 4b), as do Hostettler et al. (Figure 3).
Regarding claim 66, the method of claim 57 is discussed above Hostetter et al. teach the drying agent is silica (paragraph 0011).
14. Claims 40, 62, and 69 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (PCT International Application Publication No. WO 2015/112352 A2, published 30 July 2015) and Hostettler et al. (U.S. Patent Application Publication No. US 2011/0127177 A1, published 2 June 2011) as applied to claims 39 and 57 above, and further in combination with Bajaj et al. (U.S. Patent Application Publication No. US 2014/0179726 A1, published 26 June 2014).
Regarding claims 40, 62, and 69, the methods of claims 39 and 57 are discussed above in Section 13.
While Apte et al. teach gut sample (paragraph 0005), neither Apte et al. nor Hostettler et al. teach the fecal sample is representative of microorganisms in the gut.
However, Bajaj et al. teach methods wherein fecal (i.e., stool) samples are taken to characterize (i.e., obtain a signature of) the gut microbiome of a patient, which has the added advantage of assessing the presence or risk of development of encephalopathy in a patient with liver disease (paragraph 0010). Thus, Bajaj et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art with those of Bajaj et al. to arrive at the instantly claimed methods with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in methods having the added advantage of assess in the presence or risk of development of encephalopathy in a patient with liver disease as explicitly taught by Bajaj et al. (paragraph 0010). In addition, it would have been obvious to the ordinary artisan that the known techniques Bajaj et al. could have been combined with the cited prior art with predictable results because the known techniques of Bajaj et al. predictably result in methods useful for assessing disease states, which is a stated goal of Apte et al. (paragraph 0003).
15. Claim 44-45 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (PCT International Application Publication No. WO 2015/112352 A1, published 30 July 2015) and Hostettler et al. (U.S. Patent Application Publication No. US 2011/0127177 A1, published 2 June 2011) as applied to claim 39 above, and further in combination with Triva (U.S. Patent Application Publication No. US 2012/0171712 A1, published 5 July 2012).
Regarding claim 44, the method of claim 39 is discussed above in Section 13.
The previously cited prior art does not teach the swab terminates in a non-absorbent surface.
However, Triva teaches methods using swabs having non-absorbent material on the end, which as the added advantage of allowing quantitative release of the sample (paragraph 0017). Thus, Triva teaches the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art with those of Triva to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantage of allowing quantitative release of the sample as explicitly taught by Triva (paragraph 0017). In addition, it would have been obvious to the ordinary artisan that the known techniques Triva could have been combined with the cited prior art with predictable results because the known techniques of Triva predictably result in methods useful for collecting samples.
Regarding claim 45, the method of claim 44 is discussed above. Hostettler et al. teach the drying agent 46 is in container 40 (Figure 3 and paragraph 0049).
16. Claims 48-49 and 67-68 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (PCT International Application Publication No. WO 2015/112352 A1, published 30 July 2015) and Hostettler et al. (U.S. Patent Application Publication No. US 2011/0127177 A1, published 2 June 2011) as applied to claims 39 and 57 above, and further in combination with Triva (U.S. Patent Application Publication No. US 2012/0150088 A1, published 14 June 2012; hereafter “Triva2”).
Regarding claims 48-49 and 67-68, the methods of claims 39 and 57 are discussed above in Section 13.
The previously cited prior art does not teach the swab comprises elongated fibers.
However, Triva2 teaches methods using swabs having fibers with a long nap (i.e., the elongated fibers of claims 48 and 67; paragraph 0021). The fibers are also hydrophilic (i.e., claims 49 and 68; Abstract), and have the added advantage of allowing rapid absorption of the specimen to be collected (paragraph 0003). Thus, Triva2 teaches the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art with those of Triva2 to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantage of allowing rapid absorption of the specimen to be collected as explicitly taught by Triva2 (paragraph 0003). In addition, it would have been obvious to the ordinary artisan that the known techniques Triva2 could have been combined with the cited prior art with predictable results because the known techniques of Triva2 predictably result in methods useful for collecting samples.
17. Claim 61 rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (PCT International Application Publication No. WO 2015/112352 A1, published 30 July 2015) and Hostettler et al. (U.S. Patent Application Publication No. US 2011/0127177 A1, published 2 June 2011) as applied to claim 39 above, and further in combination with Sangha (U.S. Patent Application Publication No. US 2012/0220042 A1, published 30 August 2012).
Regarding claim 61, the method of claim 39 is discussed above in Section 13.
The previously cited prior art does not teach the drying agent is in a packet.
However, Sangha teaches methods wherein swab 14 is stored in a tube, in the form of a desiccant chamber, having packets of desiccant 36 therein (Figure 4 and paragraph 0045), which have the added advantage of achieving early stabilization of specimens (Abstract). Thus, Sangha teaches the known techniques discussed above. It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art with those of Sangha to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantage of achieving early stabilization of specimens as explicitly taught by Sangha (Abstract). In addition, it would have been obvious to the ordinary artisan that the known techniques Sangha could have been combined with the cited prior art with predictable results because the known techniques of Sangha predictably result in methods useful for collecting samples.
Response to Arguments
18. Applicant's arguments filed 15 December 2025 (hereafter the “Remarks”) have been fully considered but they are not persuasive for the reasons discussed below.
A. Regarding Applicant’s arguments with respect to new matter presented on pages 6-7 of the Remarks, the examiner has provided a detailed analysis of new matter above.
B. Applicant argues on pages 7-8 of the Remarks that the instant claims reflect the technological advance of dry sample preservation for whole genome sequencing.
However, as noted in the rejections above, Apte et al. explicitly teach the kit facilitates drying (i.e., lyophilization; paragraph 0016) of the sample, and that the sequencing is whole genome sequencing (paragraph 0052).
C. Applicant’s remaining arguments have been considered but are moot in view of the new rejections necessitated by the amendments.
Conclusion
19. No claim is allowed.
20. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert T. Crow whose telephone number is (571)272-1113. The examiner can normally be reached M-F 8:00-4:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at 571-272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Robert T. Crow
Primary Examiner
Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683