Prosecution Insights
Last updated: October 25, 2026
Application No. 18/242,825

METHODS OF ANALYZING NUCLEIC ACIDS

Non-Final OA §DOUBLEPATENT
Filed
Sep 06, 2023
Priority
May 29, 2015 — provisional 62/168,281 +4 more
Examiner
BOESEN, CHRISTIAN C
Art Unit
Tech Center
Assignee
Illumina Inc.
OA Round
1 (Non-Final)
76%
Grant Probability
Favorable
1-2
OA Rounds
5m
Est. Remaining
97%
With Interview

Examiner Intelligence

Grants 76% — above average
76%
Career Allowance Rate
490 granted / 645 resolved
+16.0% vs TC avg
Strong +21% interview lift
Without
With
+21.1%
Interview Lift
resolved cases with interview
Typical timeline
3y 7m
Avg Prosecution
29 currently pending
Career history
664
Total Applications
across all art units

Statute-Specific Performance

§101
8.8%
-31.2% vs TC avg
§103
30.3%
-9.7% vs TC avg
§102
17.2%
-22.8% vs TC avg
§112
26.1%
-13.9% vs TC avg
Black line = Tech Center average estimate • Based on career data from 645 resolved cases

Office Action

§DOUBLEPATENT
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 . DETAILED ACTION This Non-Final Office Action is responsive to the communication received 9/6/2026. Claims 1-14 and 18-23 are pending. Claims 1-14 and 18-23 are under examination in this Office Action. Double Patenting 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 1-14 and 18-23 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-19 of U.S. Patent Number 10640809. Although the conflicting claims are not identical, they are not patentably distinct from each other because the present claim 1 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids, wherein the library of double-stranded nucleic acids comprises complementary DNA (cDNA) prepared from RNA; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to double-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species and claim 1 in U.S. Patent Number 10640809 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a transposase that preferentially binds to double-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species. Therefore, the present claims are obvious in view of the claims of U.S. Patent Number 10640809. Claims 1-14 and 18-23 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-16 of U.S. Patent Number 11339422. Although the conflicting claims are not identical, they are not patentably distinct from each other because the present claim 1 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids, wherein the library of double-stranded nucleic acids comprises complementary DNA (cDNA) prepared from RNA; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to double-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species and claim 1 in U.S. Patent Number 11339422 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to double-stranded nucleic acids, wherein the nucleic acid binding protein does not comprise double stranded DNA nuclease activity; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species, wherein separating comprises immobilizing the binding protein to a solid support. Therefore, the present claims are obvious in view of the claims of U.S. Patent Number 11339422. Claims 1-14 and 18-23 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-22 of U.S. Patent Number 11795578. Although the conflicting claims are not identical, they are not patentably distinct from each other because the present claim 1 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids, wherein the library of double-stranded nucleic acids comprises complementary DNA (cDNA) prepared from RNA; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to double-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species and claim 1 in U.S. Patent Number 11795578 is drawn to a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to single-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species. Therefore, the present claims are obvious in view of the claims of U.S. Patent Number 11795578. Closest Prior Art The following is the closest prior art: Dorange et al. (10/22/2015) PCT International Patent Application Publication WO 2015/160895 A2 cited in the 9/6/2023 IDS (hereinafter referred to as "Dorange") represents the closest prior art. Dorange teaches a method for the detection of rare target nucleic acids by extracting nucleic acids from a sample, denaturing and renaturing and treating with duplex specific nuclease and nucleic acid sequencing (see claim 1 and pages 3 to 30). Dorange does not explicitly teach a method of analyzing rare nucleic acid species comprising: (a) providing a library of double-stranded nucleic acids, wherein the library of double-stranded nucleic acids comprises complementary DNA (cDNA) prepared from RNA; (b) denaturing the library; (c) renaturing the library under conditions sufficient to renature abundant nucleic acid species, wherein a portion of the library comprising less abundant nucleic acid species does not renature; (d) contacting the library with a nucleic acid binding protein that preferentially binds to double-stranded nucleic acids; and (e) separating renatured abundant nucleic acid species from the less abundant nucleic acid species. Conclusion No claim is allowed. Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Christian Boesen whose telephone number is 571-270-1321. The Examiner can normally be reached on Monday-Friday 9:00 AM to 5:00 PM. If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. 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 . /CHRISTIAN C BOESEN/Primary Examiner, Art Unit 1684
Read full office action

Prosecution Timeline

Sep 06, 2023
Application Filed
Oct 12, 2023
Response after Non-Final Action
Oct 05, 2026
Non-Final Rejection mailed — §DOUBLEPATENT (current)

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Study what changed to get past this examiner. Based on 5 most recent grants.

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Prosecution Projections

1-2
Expected OA Rounds
76%
Grant Probability
97%
With Interview (+21.1%)
3y 7m (~5m remaining)
Median Time to Grant
Low
PTA Risk
Based on 645 resolved cases by this examiner. Grant probability derived from career allowance rate.

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