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
1. The Applicant’s response to the office action filed on December 15, 2025 is acknowledged.
Status of the Application
2. Claims 1-10, 12-28 and 30-35 are pending under examination. Claims 11 and 29 were canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive in-part for the following reasons.
Claim Rejections - 35 USC § 112-Withdrawn
3. The rejection of claims under 35 USC 112(b) has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 102-Maintained
4. 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.
Claims 1-10, 12-28 and 30-35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. (US 2018/0335424).
Chen et al. teach a method of claim 1, for lysing a fixed sample, wherein the fixed biological sample comprises crosslinks between nucleic acid molecules and protein molecules due to fixation, the method comprising:
(a) lysing the fixed biological sample, wherein lysis involves digestion with a proteolytic enzyme (para 0530-0561, 0211-0213, 0299-0307);
(b) heating the lysed sample to reverse crosslinks (para 0530-0561, 0298-0307);
(c) adding a proteolytic enzyme and performing a proteolytic digestion (para 0530-0561, 0298-0307).
With reference to claim 2, Chen et al. teach that the method comprises (d) purifying nucleic acids from the lysed sample (para 0530-0561);
With reference to claim 3-6, Chen et al. teach that the lysis step(a) comprises a lysis mixture comprising the fixed biological sample and a lysis composition comprising proteolytic enzyme, wherein the proteolytic enzyme is a protease, the lysis mixture is heated to assist digestion by the proteolytic enzyme for 30 minutes and completed is 120 min or less and the step (b) comprises heating the lysed sample to a temperature of at least 80 C (para 0306-0307).
With reference to claims 7-10, 34-35, Chen et al. teach that the method comprising performing at least one enzymatic treatment step different from a proteolytic digestion between step (b) and step (c), wherein the enzymatic treatment involves an uracil DNA glycosylase at elevated temperature (para 0298-0307, 0530-0561).
With reference to claim 12-14, Chen et al. teach salt concentration in the enzymatic treatment is< 500 mM or in a range of 10 mM to 500mM and the lysis mixture has a pH in the range of 6 to 9.5 and the lysis composition comprises a salt, detergent and a buffering agent (para 0530-0561).
With reference to claim 15-20, Chen et al. teach that the lysis composition comprises a reactive compound reacts with the fixative, wherein the lysis composition has a mono or divalent salt in a concentration of at least 15mM a non-ionic or anionic detergent, and buffering agent comprises a reactive compound or a buffering agent (para 0530-0561).
With reference to claim 21-22, 30-31, Chen et al. teach that the nucleic acids comprise DNA or the fixed biological sample comprises a cell-containing sample and the step(d) comprises binding nucleic acids with a solid phase and eluting nucleic acids and/or method further comprises analyzing the purified nucleic acids amplifying the
nucleic acids and /or performing next generation sequencing method, wherein the sequencing method comprises attaching unique molecular identifier (UMI) sequence to the DNA molecules, each DNA molecule comprises a different UMI; amplifying DNA molecules attached to the UMI and sequencing the DNA molecules (para 0298-0314, 0545-0551).
With reference to claim 23, 28, Chen et al. teach that the method comprises (a) lysing the fixed biological sample, wherein lysis involving digestion with a proteolytic enzyme, the lysis step comprises preparing a lysis mixture comprising the fixed biological sample and a lysis composition comprising the proteolytic enzyme, wherein the lysis mixture is incubated for at least 30 min at an elevated temperature between 35-750 C; (b) heating the lysed sample to reverse crosslink, at a temperature range of 80-1100 C; (c) adding a proteolytic enzyme and performing digestion comprising incubating for at least 5 min at elevated temperature between 35-750 C, wherein incubation of step (c) is shorter than the incubation in step (a) and the temperature is higher than in step (a) (para 0298-0307, 0530-0546).
With reference to claim 24-27, Chen et al. teach that the fixed biological sample is a solid fixed biological sample and the method comprises at least one enzymatic treatment step different from digestion step between step (b) and step(c), wherein the enzymatic treatment step comprises a DNA glycosylase and a ribonuclease, and performed at an elevated temperature and completed in 30 min or less (0295-0307,
0031, 0091, 0530-0561).
With reference to claim 32-33, Chen et al. teach that the proteolytic enzyme in step (c) is a proteinase K (para 0299, 0545). For all the above the claims are anticipated.
Response to Arguments:
With reference to the rejection of claims under 35 USC 102(a)(1) as being anticipated by Chen et al., the Applicant’s arguments and the amendment have been fully considered and found unpersuasive. The Applicant’s argue that Chen does not teach lysis comprising a proteolytic enzyme citing different portions of the Chen et al. document other than the Examiner cited portions. The Applicant’s arguments were found unpersuasive. Chen et al. teach lysis comprising proteolytic enzyme or proteinase K in Examiner cited paragraphs 545, 551. The Applicant cited paragraph 0220 indicates a cell lysis using a detergent, an enzyme such as lysozyme, said para indicates enzymes such as lysozyme, where in ‘such as’ indicates as an example of an enzyme in cell lysis. Further, the broader scope of lysosome contains proteolytic enzymes or proteases, which do not exclude the proteolytic enzymes as used in para 545, 551 taught by Chen. Further, the Applicant’s arguments drawn to lysing cells by sonication, the arguments were fully considered and unpersuasive because as discussed above, in addition to cell lysis by sonication, Chen also teaches enzymatic lysis or fragmentation of cells (para 0239) which includes proteinase K (para 545, 551) and anticipates the claims. For all the above, the rejection has been maintained and restated to address the amendment.
5. The rejection of claims under 35 USC 102(a)(1) as being anticipated by Fraser et al., has been withdrawn in view of the Applicant’s arguments.
Conclusion
No claims are allowable.
THIS ACTION IS MADE FINAL. 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 SURYAPRABHA CHUNDURU whose telephone number is (571)272-0783. The examiner can normally be reached 8.00am-4.30pm.
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.
Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681