DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 June 3, 2026 has been entered.
Election/Restrictions
3. In light of the amendments, the restriction requirement among species, as set forth in the Office action mailed on October 3, 2023, has been reconsidered The restriction requirement is hereby withdrawn. Claims 77-82, 84, 85, 87, 92-98, and 100, directed to non-elected species are no longer withdrawn from consideration.
In view of the above noted withdrawal of the restriction requirement, applicant is advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application.
Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Status of the Claims
Claims 75, 76-90, 92-104, 106-111, and 113-114 are under examination.
Claim Rejections - 35 USC § 112
4. 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.
5. Claims 75, 76-90, 92-104, 106-111, and 113-114 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.
Instant claims 75 and 90 are amended to recite the limitation “using threshold number of miscalculations” in step (j) and step (f) respectively. This limitation is not found in the specification nor in the claims as originally filed. While specification contains a teaching of “detecting a threshold point in each gene that minimizes the number of misclassifications” (Specification, page 26, paragraph [0095]), it is unclear if this is equivalent to the limitation. Thus, the claims contain 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, at the time the application was filed, had possession of the claimed invention.
Claim Rejections - 35 USC § 112
6. 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.
7. Claims 77-82, 92-98, and 100 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.
Claim 77 recites the limitation “said nucleic acid sample”. It is unclear if the limitation is intended to refer to the first nucleic acid sample or the subsequent nucleic acid sample. Instant claim 78 is also rejected for depending from claim 77.
Claim 79 recites the limitation "said regulatory elements" in line 1. There is insufficient antecedent basis for this limitation in the claim. This term was not mentioned previously in the instant claim or in the claim from which it depends. It is unclear to what the limitation refers.
Claim 80 recites the limitation “wherein said computer processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required.
Claim 81 recites the limitation “wherein said computer processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required. Instant claim 82 is also rejected for depending from claim 81.
Claim 92 recites the limitation “said nucleic acid sample”. It is unclear if the limitation is intended to refer to the first nucleic acid sample or the subsequent nucleic acid sample. Instant claim 93 is also rejected for depending from claim 92.
Claim 94 recites the limitation "said regulatory elements" in line 1. There is insufficient antecedent basis for this limitation in the claim. This term was not mentioned previously in the instant claim or in the claim from which it depends. It is unclear to what the limitation refers.
Claim 95 recites the limitation “wherein said processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required.
Claim 96 recites the limitation “wherein said processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required.
Claim 97 recites the limitation “wherein said processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required. Dependent claim 98 is also rejected for depending from claim 97.
Claim 100 recites the limitation “wherein said processing of said plurality of aligned sequence reads”. It is unclear if “said plurality of aligned sequence reads” refers to the “first plurality of aligned sequence reads” or the “subsequent plurality of sequence reads”. Clarification via clearer claim language is required.
Withdrawn Rejections
8. Applicant’s arguments and amendments, filed June 3, 2026, with respect to the rejection made under 35 U.S.C. §101 have been fully considered and are persuasive. The ordered combination of the additional elements is not well-understood, conventional or routine. The rejection made under 35 U.S.C. §101 is withdrawn. Furthermore, the amendments to the claims are sufficiently patentably distinct from the claims in co-pending application 16/937,287. The double patenting rejection is withdrawn.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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