DETAILED ACTION
Applicant's response, filed 23 Feb. 2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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
Claims 1-9, 11, 13, 15-27 are cancelled.
Claims 10, 12, and 14 are pending.
Claims 10, 12, and 14 are rejected.
Priority
The effective filing date of the claimed invention is 08 Oct. 2013.
Claim Interpretation
Claim 10 recites “(c) fragmenting the isolated nucleic acid from the microbiome stool sample and performing whole-genome shotgun sequencing on the fragmented nucleic acid to sequence one or more sets of nucleic acid octamers selected from the group consisting of:….”. Therefore, claim 10 involves performing whole-genome shotgun sequencing on nucleic acid isolated from a stool sample. Given whole-genome shotgun sequencing sequences all nucleic acid fragments in the genome, by definition, the limitation “to sequence one or more sets of nucleic acid octamers” is interpreted to recite an intended result of performing whole-shotgun sequencing on the isolated nucleic acid octamers. See Kaiser et al. (Whole genome shotgun sequencing guided by bioinformatics pipelines- an optimized approach for an established technique, 2003, Journal of Biotechnology, pg. 121-133; previously cited) at FIG. 1, in which the entire genome is fragmented into pieces and then sequenced.
Claim 14 similarly recites “wherein said method sequences all of the sets i) to xvii) of the octamers in the microbiome stool sample”. As discussed above for claim 10, the limitation regarding which octamers are sequenced is interpreted as an intended result of performing whole-genome shotgun sequencing on the nucleic acid of the stool sample. It is inherent that all octamers present “in the microbiome stool sample” are necessarily sequenced in whole-genome shotgun sequencing (see Kaiser above).
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.
Claim 14 is rejected under 35 U.S.C. 112(d) 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.
Claim 14 recites “The method of claim 10, wherein said method sequences all of the sets i) to xvii) of the octamers in the microbiome stool sample”. As discussed above in claim interpretation, claim 14 does not serve to further limit the actual process of performing whole-genome shotgun sequencing, and instead only recites the intended result of the active step of “performing metagenomic whole-genome shotgun sequencing on the fragmented nucleic acid” in claim 10. MPEP 2111.04 I states a "‘whereby clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited.’" Id. (quoting Minton v. Nat’l Ass’n of Securities Dealers, Inc., 336 F.3d 1373, 1381, 67 USPQ2d 1614, 1620 (Fed. Cir. 2003)). Therefore, the limitation of claim 14 does not have patentable weight, and claim 14 fails to further limit the claimed subject matter of claim 10, from 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.
Claim Rejections - 35 USC § 101
The rejection of claims 11, 15-27, and 26-27 under 35 U.S.C. 101 in the Office action mailed 22 Aug. 2025 has been withdrawn in view of the cancellation of these claims received 23 Feb. 2026.
The rejection of claims 10-12 and 14 under 35 U.S.C. 101 in the Office action mailed 22 Aug. 2025 has been withdrawn in view of claim amendments received 23 Feb. 2026. As presently recited, the claims are directed to a method of sequencing and do not recite a judicial exception. The claims do not require detecting (e.g. by analyzing sequencing) the recited octamers, and instead only require performing whole-genome shotgun sequencing on the fragmented nucleic acid with the intended result of sequencing the one or more sets of octamers.
Claim Rejections - 35 USC § 103
The rejection of claims 10-12, 14, 18-20, 22, and 26-27 under 35 U.S.C. 103 as being unpatentable over Baran (2012) in view of Morgan (2012) in the Office action mailed 22 Aug. 2025 has been withdrawn in view of claim amendments and cancellations received 23 Feb. 2026. However, after further consideration of the claims, a new grounds of rejection under 35 U.S.C. 102 is set forth below.
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(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 10, 12, and 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Morgan (2012), as evidenced by Kaiser (2003). This rejection is newly recited and necessitated by claim amendment.
Cited references:
Morgan et al., Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment, 2012, Genome Biology, 13(R79), pg. 1-18; cited in IDS filed 17 July 2023; previously cited; and
Kaiser et al. (Whole genome shotgun sequencing guided by bioinformatics pipelines- an optimized approach for an established technique, 2003, Journal of Biotechnology, pg. 121-133; previously cited).
Morgan discloses a method for analyzing the gut microbiome in inflammatory bowel disease (Abstract), which comprises the following steps:
Morgan discloses (a) collecting fecal samples from subjects having inflammatory bowel disease, including ulcerative colitis (UC) or Crohn’s disease (CD) (pg. 2, col. 2, para. 2).
Morgan discloses (b) extracting DNA from the fecal samples (i.e. isolating microbiome nucleic acid from the stool sample) (pg. 2, col. 2, para. 2; pg. 7, col. 1, para. 4).
Morgan discloses (c) performing whole-genome shotgun sequencing on the extracted DNA (pg. 2, col. 2, para. 2; pg. 15, col. 1, para. 1), which inherently sequences the entire microbiome of the fecal sample, including all octamers present. As discussed above in claim interpretation, since the claim only requires performing shotgun sequencing on the fragmented nucleic acid, the limitation “to sequence one or more sets of nucleic acid octamers” is interpreted as an intended result of performing whole-genome shotgun sequencing on the sample.
While Morgan does not explicitly disclose fragmenting the isolated nucleic acid from the microbiome stool sample, this is inherent in performing whole-genome shotgun sequencing, as evidenced by Kaiser; Kaiser overviews whole genome shotgun sequencing and discloses the shotgun procedure starts by fragmenting the genome into pieces (Abstract; Fig. 1).
Regarding claim 12, Morgan discloses the nucleic acid is DNA (pg. 2, col. 2, para. 2; pg. 15, col. 1, para. 1).
Regarding claim 14¸ Morgan discloses performing whole-genome shotgun sequencing, as discussed above for claim 10, which inherently discloses sequencing all octamers present in the sample. The limitation of claim 14 is interpreted as an intended result of performing the whole-genome shotgun sequencing, which does not have patentable weight. Therefore, claim 14 is rejected for the same reasons discussed above for claim 10.
Therefore, Morgan as evidenced by Kaiser anticipates the claimed invention.
Response to Arguments
Applicant's arguments filed 23 Feb. 2026 regarding 35 U.S.C. 103, as applicable to the new grounds of rejection under 35 U.S.C. 102 set forth above, have fully considered but they are not persuasive.
Applicant remarks that there is not disclosure of the recited set of octamers in the cited art, and therefore, there would not be a reasonable expectation of achieving success in sequencing the claimed sequences of these particular sets of octamers (Applicant’s remarks at pg. 7, para. 2-3).
This argument is not persuasive. As discussed above in claim interpretation, claim 10 only requires “performing metagenomic whole-genome shotgun sequencing on the fragmented nucleic acid to sequence one or more sets of nucleic acid octamers”, which simply recites an intended result of the positively recited step of performing metagenomic whole-genome shotgun sequencing. Performing whole genome shotgun sequencing on DNA extracted from a stool sample, as shown by Morgan, necessarily sequences all octamers present in the DNA sample.
While Applicant states there would not be a reasonable expectation of success in sequencing the claimed sequences because the specific set was not known in the art, knowing which exact sequences are present in a sample prior to sequencing is not a prerequisite for performing shotgun sequencing and sequencing those exact “unknown” sequences. In fact, the purpose of sequencing is to determine which sequence(s) are present in a given sample.
Applicant further remarks the amended claims are not anticipated by the prior art as the Examiner alluded to in the interview summary, because Baran does not disclose a stool sample (Applicant’s remarks at pg. 7, para. 5 to pg. 8, para. 2).
This argument is not persuasive because Baran is not relied upon in the above rejection. Morgan does anticipate the claimed invention for the reasons discussed above. It is noted that in the interview summary mailed 24 Nov. 2025, it was not stated that Baran would anticipate the claimed invention. It was stated that if the claims were amended to only require performing shotgun sequencing (rather than detecting specific octamers from the sequencing data), there would likely be a 102 rejection. Morgan anticipates the method as claimed.
Double Patenting
The provisional rejection of claims 11, 20, 22, and 26-27 on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 8-11, 15-16, 19, 21, and 25-26 of copending Application No. 15/489,658 (reference application) in the Office action mailed 22 Aug. 2025 has been withdrawn in view of the cancellation of these claims received 23 Feb. 2026.
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 10, 12 and 14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 27-38 of copending Application No. 15/489,658 (reference application). Any newly recited portion is necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding instant claim 10, reference claim 31, 32, and 33 disclose the method of obtaining a microbiome sample of a subject, isolating a microbiome of a stool sample of the sample, and using whole genome shotgun sequencing of total DNA isolated from the microbiome sample, which shows steps (a)-(c).
Regarding instant claim 12, reference claim 33 discloses the nucleic acid is DNA.
Regarding instant claim 14, reference claim 31 discloses these octamer sets.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant's arguments filed 23 Feb. 2026 regarding Double Patenting have at pg. 8, para. 3-4 been fully considered but they are not persuasive because they do not present any arguments.
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 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.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAITLYN L MINCHELLA whose telephone number is (571)272-6485. The examiner can normally be reached 7:00 - 4:00 M-Th.
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, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685