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 .
Response to Amendment
The amendment filed 01/22/2026 is acknowledged. Regarding the Office action mailed 10/22/2025, the rejections set forth therein are withdrawn in part, and maintained in part. The maintained portion of the rejections are reiterated below, modified as needed to address any amendments. Applicant’s remarks will be addressed following the rejections.
Claim Rejections - 35 USC § 112
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.
Claims 1-20 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.
The term “relatively high-complexity” in claim 1 is a relative term which renders the claim indefinite. The term “relatively high-complexity” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
The specification notes that "Reads with low complexity sequences may contain stretches of homopolymer nucleotides or simple sequence repeats." (paragraph 0070) However, this does not constitute a limiting definition by which one of ordinary skill in the art may distinguish between “high-complexity sequence context” and “non-high-complexity sequence context”. The specification also states (paragraph 0114):
"Subsequent tests are for low complexity genomic context of a deletion. For example, low complexity analysis may be performed by calculating entropy of kmer distributions for kmers of length 1-5, within the range of ~60bp to the left and to the right (~120bp total). In other cases, different parameters may be used in the filter, i.e. different functions than entropy, different sizes of sequence regions, and different size of kmers. If a sequencing read is determined to have a repetitive environment, the read is discarded at 172. If a read passes the filter by not having a repetitive environment, the read is retained at 128 for further filtering and processing."
This discussion does not provide any sort of numerical value (of entropy of kmer distributions, e.g.) that determine whether a sequence context is “high-complexity”. The term “repetitive environment” is also not helpful, since “repetitiveness” is also somewhat relative. For example, one might argue that GATCGATC is a repetitive sequence, while others might argue that repetitiveness requires 4 iterations: GATCGATCGATCGATC. Similarly, some might argue that a repeat must be exactly matching: GAATTCGAATTC. Others might argue that some mismatches would still constitute “repetitiveness”: GAATTCGAAATC. Some might argue that a simple mononucleotide sequence constitutes “repetitive”: AAAAAAAAA. Others might argue that repetitiveness excludes such sequence and requires at least a dinucleotide repeating unit: ACACACAC.
Because the term “relatively high-complexity” is not defined and different people could come to different conclusions regarding what is and is not “relatively high-complexity” sequence context, the claim is vague and indefinite. Claims 2-20 depend ultimately from claim 1 and are rejected for the same reason.
Claim 15 is 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.
The term “relatively elevated” in claim 15 is a relative term which renders the claim indefinite. The term “relatively elevated” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. There is no frame of reference provided for the term “relatively elevated” (relatively elevated compared to what?).
Response to Arguments
The arguments filed 01/22/2026 merely indicate that the amendments “provide the requested clarifications under 35USC112, second paragraph.” For those portions of the rejection maintained above, they do not. In addition, the amendment to claim 15 raises a new issue of indefiniteness, resulting in a new, separate rejection of that claim.
Conclusion
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 SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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, GARY BENZION can be reached at 571-272-0782. 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.
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
Prosecution Insights