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 .
Drawings
The drawing as submitted by Applicant on 09/15/2023 has been accepted.
Disposition of Claims
Claims 1-31 are pending in the instant application. No claims have been added. Claims 11, 17-23, 25, and 28-29 have been cancelled. Claims 1-10, 12-16, 24, 26, 27, 30, and 31 have been amended. The rejection of the pending claims is hereby made non-final.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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, 12-16, 24, 26, 27, 30, and 31 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Reid et al (US 2017/0233804).
Regarding claim 1, the prior art discloses a method of determining a relationship between a target sequence of polymer units in a target polymer and a reference sequence of polymer units, wherein the method comprises: receiving a measured target signal comprising signal levels measured by a measurement system from parts of the target polymer ordered along the target sequence (see at least paragraph [0212] to Reid et al); segmenting the measured target signal into segments and deriving a sequence of target signal symbols, each target signal symbol representing a quantised signal level derived from the signal levels of a respective segment (see at least paragraph [0338] to Reid et al); and using a sequence of reference signal symbols representing quantised signal levels of a sequence of modelled reference signal levels predicted by a measurement system model to be measured from the reference sequence of polymer units by the measurement system, comparing(see at least paragraph [0279] to Reid et al).
Regarding claim 2, the prior art discloses the method according to claim 1, wherein the sequence of target signal symbols are run-length compressed before the step of comparing the sequence of target signal symbols with the sequence of reference signal symbols (see at least paragraph [0030] to Reid et al).
Regarding claim 3, the prior art discloses the method according to claim 1, wherein the sequence of reference signal symbols are run-length compressed before the step of comparing the sequence of target signal symbols with the sequence of reference signal symbols (see at least paragraph [0013] to Reid et al).
Regarding claim 4, the prior art discloses the method according to claim 1, wherein the step of segmenting the measured target signal into segments comprises detecting transitions in the signal level of the measured target signal and segmenting the measured target signal into segments defined between the transitions (see at least paragraph [0015] to Reid et al).
Regarding claim 5, the prior art discloses the method according to claim 4, wherein the step of segmenting the measured target signal into segments further comprises smoothing the measured target signal prior to detecting transitions in the signal level of the measured target signal (see at least paragraph [0183] to Reid et al).
Regarding claim 6, the prior art discloses the method according to claim 5, wherein the step of smoothing the measured target signal is performed by total-variation de-noising (see at least paragraph [0186] to Reid et al).
Regarding claim 7, the prior art discloses the method according to claim 1, wherein the step of deriving a sequence of target signal symbols comprises: deriving an average signal level from the signal levels of each segment; deriving the target signal symbols by quantising the average signal levels in respect of each segment (see at least paragraph [0229] to Reid et al).
Regarding claim 8, the prior art discloses the method according to claim 1, wherein the target signal symbols and the reference signal symbols represent quantised signal levels with a quantisation providing equal populations in each symbol (see at least paragraph [0019] to Reid et al).
Regarding claim 9, the prior art discloses the method according to claim 1, further comprising deriving the sequence of reference signal symbols from the reference sequence, the modelled reference signal levels of the reference signal symbols being predicted by the measurement system model to be measured from the reference sequence by the measurement system (see at least paragraph [0030] to Reid et al).
Regarding claim 10, the prior art discloses the method according to claim 9, further comprising: receiving a measured reference signal comprising signal levels measured by a measurement system from parts of a reference polymer ordered along the reference sequence (see at least paragraph [0013] to Reid et al); and estimating the reference sequence from the measured reference signal using the measurement system model, the reference sequence used in the step of deriving the sequence of reference signal symbols from the reference sequence being the estimated reference sequence (see at least paragraph [0038] to Reid et al).
Regarding claim 12, the prior art discloses the method according to claim 1, wherein the reference sequence of polymer units corresponds to an entirety or a region of a reference polymer (see at least paragraph [0013] to Reid et al).
Regarding claim 13, the prior art discloses the method according to claim 1, wherein the target sequence of polymer units corresponds to an entirety or a region of the target polymer (see at least paragraph [0063] to Reid et al).
Regarding claim 14, the prior art discloses the method according to claim 1, wherein the reference sequence of polymer units corresponds to a region of a reference polymer that is the same polymer as the target polymer (see at least paragraph [0041] to Reid et al).
Regarding claim 15, the prior art discloses the method according to claim 1, wherein the step of comparing (step Al) the sequence of target signal symbols with the sequence of reference signal symbols is performed using a weight matrix that takes into account differences between the quantised levels represented by the target signal symbols and the reference signal symbols (see at least paragraph [0338] to Reid et al).
Regarding claim 16, the prior art discloses the method according to claim 1, wherein the determined relationship comprises an alignment between the target sequence and the reference sequence (see at least paragraph [0036] to Reid et al).
Regarding claim 24, the prior art discloses the method according to claim 1, wherein the measurement system comprises a nanopore and the measured target signal comprises signal levels measured by the measurement system during translocation of the polymer with respect to the nanopore (see at least paragraph [0152] to Reid et al).
Regarding claim 26, the prior art discloses the method according to claim 24 or 25, further comprising the step of ejecting the polymer from the nanopore during translocation depending upon the measure of similarity (see at least paragraph [0012] to Reid et al).
Regarding claim 27, the prior art discloses the method according to claim 1, wherein the signal levels representing one or more of: ionic current, impedance, a tunnelling property, a field effect transistor voltage and an optical property (see at least paragraph [0134] to Reid et al).
Claims 30 and 31 each contain recitations substantially similar to those addressed above and, therefore, are likewise rejected.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
The examiner has considered all references listed on the Notice of References Cited, PTO-892.
The examiner has considered all references cited in the Information Disclosure Statement submitted by Applicant, PTO-1449.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TALIA F CRAWLEY whose telephone number is (571)270-5397. The examiner can normally be reached on Monday through Thursday; 8:30 AM-4:30 PM EST.
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, Fahd A Obeid can be reached on 571-270-3324. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
The following are suggested formats for either a Certificate of Mailing or Certificate of Transmission under 37 CFR 1.8(a). The certification may be included with all correspondence concerning this application or proceeding to establish a date of mailing or transmission under 37 CFR 1.8(a). Proper use of this procedure will result in such communication being considered as timely if the established date is within the required period for reply. The Certificate should be signed by the individual actually depositing or transmitting the correspondence or by an individual who, upon information and belief, expects the correspondence to be mailed or transmitted in the normal course of business by another no later than the date indicated.
Certificate of Mailing
I hereby certify that this correspondence is being deposited with the United States Postal Service with sufficient postage as first class mail in an envelope addressed to:
Commissioner for Patents
P.O. Box 1450
Alexandria, VA 22313-1450
on __________.
(Date)
Typed or printed name of person signing this certificate:
________________________________________________________
Signature: ______________________________________
Certificate of Transmission by Facsimile
I hereby certify that this correspondence is being facsimile transmitted to the United States Patent and Trademark Office, Fax No. (___)_____ -_________ on _____________. (Date)
Typed or printed name of person signing this certificate:
_________________________________________
Signature: ________________________________________
Certificate of Transmission via USPTO Patent Electronic Filing System
I hereby certify that this correspondence is being transmitted via the U.S. Patent and Trademark Office (USPTO) patent electronic filing system to the USPTO
on _____________.
(Date)
Typed or printed name of person signing this certificate:
_________________________________________
Signature: ________________________________________
Please refer to 37 CFR 1.6(a)(4), 1.6(d) and 1.8(a)(2) for filing limitations concerning transmissions via the USPTO patent electronic filing system, facsimile transmissions and mailing, respectively.
/TALIA F CRAWLEY/ Primary Examiner, Art Unit 3627
Prosecution Insights