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 .
Applicant's amendments and remarks, filed 02/24/2026, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1, 3-4, 6-10, 13,15, 17,21-22, 25, 27, 29, 31-32 and 41 are allowed.
Claims 5, 11-12, 14, 16, 18-20, 23-24, 26, 28, 30, 33-40 and 42-49 were canceled.
Priority
Applicant’s claim for the benefit of priority under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. The instant application claims the benefit of priority to US National Stage Application claiming priority to PCT/US2020/049751, filed 09/08/2020.
Withdrawn Rejections
The rejection of claims 1-4, 6-10, 13, 15, 17, 21, 22, 25, 27, 29, 31-32, 41 under 35 U.S.C. 101 is withdrawn in view of applicant’s amendments (directed to stratifying and training the claimed noise model) and arguments [Remarks, pages 11-13].
The rejection of claims 1-4, 6-10, 13, 15, 17, 21, 22, 25, 31-32, 41 under 35 U.S.C. 103(a) as being unpatentable over Shen et al. (US20190073445A1; Pub. Date: 03/07/2019) is withdrawn in view of applicant’s amendments and arguments [Remarks, page 14].
The rejection of claims 27 and 29 under 35 U.S.C. 103(a) as being unpatentable over Shen et al. (US20190073445A1; Pub. Date: 03/07/2019), as applied to claims 1-4, 6-10, 13, 15, 17, 21, 22, 25, 31-32, 41, above, and further in view of Vogelstein et al. (WO2019/067092) is withdrawn in view of applicant’s amendments and arguments [Remarks, page 14].
Claim rejections - 35 USC § 112, 2nd Paragraph
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.
The following rejections are necessitated by amendment.
Claims 1, 3-4, 6-10, 13,15, 17,21-22, 25, 27, 29, 31-32 and 41 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1, 32, 41 is/are also rejected due to said dependency.
Claims 1, 32, 41 recite “stratifying the…sequence reads into a…plurality of read tiers include at least two of following: (1) a double-stranded, stitched read tier, (2) a double-stranded, unstitched read tier, (3) a single-stranded, stitched read tier, or (4) a single-stranded, unstitched read tier.” In each case, it is unclear as to the metes and bounds of the terms “stitched” and “unstitched” such that the artisan would know how to avoid infringement. A review of the specification teaches a sequence processer classifying reads a stitched or unstitched based on determining that an overlap (e.g., of a given number of nucleotide bases) between the first and second reads is greater than a threshold length (e.g., a threshold number of nucleotide bases) [0085]. However, this is not a limiting definition and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Moreover, this disclosure clearly suggests these conditional limitations are the result of a presently unclaimed computer classification process and Applicant is reminded that claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. See MPEP 2111.04. Clarification is requested via amendment.
Claims 1, 32, 41 recite “determining, for each read tier, the one or more noise parameters by inputting stratified sequencing depth of the read tier to the noise model specific to the read tier.” This limitation is confusing and problematic because the previous step already requires “iteratively adjusting values of the one or more noise parameters based on the noise distribution…” (i.e. the noise parameters are already known at that point). As such, it is unclear in what way the “determining” step further limits the claimed method because “the noise parameters” have already been determined. If applicant intends for the determining step to be somehow directed to “applying” the noise model that was trained in the previous step, this is not what is presently reflected in the claims. If, on the other hand, applicant intends for the second noise parameters to be different from the first recited noise parameters, this is also not clearly reflected in the claims as written. Clarification is requested via amendment.
Claims 1, 32, 41 recite “generating, for each read tier, an output of the noise model specific to the read tier based on the one or more noise parameters In this case, it is unclear what is meant by “one or more noise parameters the stratified sequencing depth of the read tier.” This phrase appears to be a run-on phrase that is grammatically incorrect. Clearly something is missing. Clarification is requested via amendment.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619
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