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 .
Election/Restrictions
Applicant’s election without traverse of Group II in the reply filed on 4/24/25 is acknowledged.
Priority
Applicant states that this application is a continuation or divisional application of the prior-filed application. A continuation or divisional application cannot include new matter. Applicant is required to delete the benefit claim or change the relationship (continuation or divisional application) to continuation-in-part because this application contains the following matter not disclosed in the prior-filed application: “wherein the isolated nucleic acid sample is obtained from at least one selected from stool, excreta, dejecta, stercus, feces and gut mucosa of the subject”. See claim 11. While the parent application, as originally filed teaches DNA isolation from fecal samples (Example 1) it does not teach gut mucosa. Gut mucosa is distinct from feces as it is the specialized lining of the digestive tract, not feces. As such, the effective filing date of this claim, which has basis in the originally filed claims of the instant specification, is the actual filing date of this application: 2/18/2022.
Response to remarks
The response argues that there is basis in the disclosure for the sample being “gut mucosa.” The sections cited on pages 2 and 8 are silent as to sample. The section cited on page 5 teaches that the gut microbiome refers to all the genetic information of microorganisms existing in the body, particularly the intestines, but is silent as to the more specifically claimed “gut mucosa.” The sections cite on pages 19, 20, 22, and 23 do not make suggestions as to where the sample should be taken, and do not teach or suggest a “gut mucosa” sample. The position is maintained.
Applicant argues that “gut mucosa” is supported by the provisional because the provisional application describes providing an isolated nucleic acid sample for detecting a gut-microbiome subspecies and diagnosing AD.
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 6 and 11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural law without significantly more.
The method claim(s) recite(s) the relationship between the relative of certain subspecies F06 of F. prausnitzii in a sample and that the subject has atopic dermatitis or is in a high-risk group for atopic dermatitis. This correlation is a natural correlation.
The claims further recite “recognizing, in the sequence reads, a nucleotide sequence” which is a mental process abstract idea since it reasonably encompasses the review of data.
The claims set forth “determining a relative abundance” which describes a mathematical process abstract idea because determining a relative abundance is determining a ratio.
The claims also recite “determining” that the subject as atopic dermatitis or is in a high risk group which is a mental process abstract idea, because the determining could be accomplished in the mind.
The claims also recite “when the relative abundance of the subspecies…is higher than that of a normal group” which sets forth a comparing of an obtained value and that of a “normal group” which is a mathematical concept abstract idea as well as a mental process abstract idea since the process is simple enough that it could be carried out in the mind.
These judicial exceptions are not integrated into a practical application because the claims do not apply or use the judicial exceptions in any way. The providing, amplifying and sequencing steps are pre-solution data gathering steps. The final “providing information” step fails to integrate the judicial exception because it does not apply or use it in any way.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception the providing, amplifying and sequencing steps are pre-solution data gathering recited at a high level of generality. The claims do not require particular probes or primers provided that the V1-V2 region is amplified. The steps are necessary to apply the judicial exceptions. Furthermore, recognizing a species of bacteria by recognizing a nucleotide sequence in a sample could be accomplished by PCR amplification and subsequent sequencing were methods that were well established, routine, and conventional at the time of the invention. Sequencing the V1-V2 regions of 16S rRNA genes in an isolated nucleic acid sample was also routine, as evidenced by Thomas which teaches sequence the 16S gene see p. 1492 and following. See Also MPEP 2106.05(d)II which discusses laboratory techniques the courts have recognized as well-understood, routine, and conventional. Finally, with regard to the newly added step directed to providing information, merely presenting the results of a process otherwise unpatentable under section 101 is insufficient to establish eligibility under the statute. See FairWarning IP, LLC v. Iatric Sys., Inc., (Fed. Cir. Oct. 11, 2016) (claim unpatentable despite recitation of the step: "providing notification if [an] event has occurred").
Response to Remarks
The response argues that the claimed amplification and sequencing operations cannot be practiced in the mind. This is not disputed; these are treated as steps “in addition” to the judicial exceptions in the analysis.
The response points out that the V1-V2 region distinguish the F06 clade. However, the relationship between certain nucleic acid content (here a version of the V1-V2 region) and AD is the judicial exception, so the claim essentially instructs one skilled in the art to use conventional techniques (amplifying and sequencing) to gather the necessary data to apply the exception. This is not more than the exceptions themselves. The judicial exceptions are not integrated because the claim does not apply or use them in any way, it merely sets them forth along with general instructions about how to gather the data necessary to practice them.
Applicant argues that the specific combination provides significantly more than the judicial exceptions. Applicant argues that “recognition of the closed exact-and-variant F06 signature set” and “subspecies-level quantification” was not well established. These steps are embodied in the claims in judicial exceptions. It is the steps in addition to the judicial exceptions that were routine, as evidenced by the review article Thomas et al., and as discussed in MPEP 2106.05(d).
The rejection is maintained.
Claim Rejections - 35 USC § 102
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.
Claim(s) 11 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Song et al. (J Allergy Clin Immunol, Vol 137; Number 3; pages 852-860; available online 10/1/2015).
Song et al. teach the claimed methods. See Abstract, methods and materials, and results. Figure 2B, C and E3.
Applicant cannot rely upon the certified copy of the foreign priority application to overcome this rejection because a translation of said application has not been made of record in accordance with 37 CFR 1.55. When an English language translation of a non-English language foreign application is required, the translation must be that of the certified copy (of the foreign application as filed) submitted together with a statement that the translation of the certified copy is accurate. See MPEP §§ 215 and 216.
Response to Remarks
Claim 11 is rejected because it does enjoy the benefit of priority to the 9/21/16 filing date, as discussed previously in this Office action.
Conclusion
Previously set forth rejections were overcome by amendment to the claims.
Claims which have basis to the parent application are free of the prior art. Regarding Claim 6, the prior art does not teach determining the relative abundance of subspecies F06 which includes SEQ ID NO: 1 or SEQ ID NO: 2, or one of the variants recited in part (ii) and (iv) fo claim 6, in a sample, and providing information that a subject has atopic dermatitis or is in a high-risk group.
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 Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571)-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/ Primary Examiner, Art Unit 1682
