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 .
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 31-39 are rejected under 35 U.S.C. 103 as being unpatentable over Collins (WO 2016/134191 A1).
With respect to Claim 31, Collins’191 shows a method of controlling an average minimum center-to-center distance between one or more analytes, comprising:
exposing a plurality of analytes deposited on a surface to a gas-liquid interface to form a monolayer of analytes deposited across said surface (paragraph [00216]-[00217] monolayers can be made that cover some or all the array, different samples are deposited at different locations, paragraph [00231] and [00416] using air-water interface),
wherein said plurality of analytes are treated with a repellant or attractive substance (paragraphs [00116] and [00253] solid support will be divided by chemical means, such as having hydrophobic or hydrophyllic regions that repel or attract material deposited on the substrate), and
wherein said plurality of analytes is deposited on said surface at an average center-center-to-center distance of less than about 500nm (paragraph [00123], [00218] and [00250] deposited at concentrations of on average 0.1 nm, 1 nm, 5 nm, 10 nm, 50 nm, 100 nm, 200 nm).
With respect to Claim 32, Collins’191 shows the method of claim 31, wherein said surface is patterned or non-patterned (paragraphs [00230], [00247], [00256] arrangement of the spots should be in regular pattern and out of line spots).
With respect to Claim 33, Collins’191 shows the method of claim 31, wherein said gas-liquid interface comprises an air-water interface (paragraph [00416] air-water).
With respect to Claim 36, Collins’191 shows the method of claim 31, wherein said plurality of analytes comprises a plurality of concatemers (figure 78 and paragraph [0069] Sequence repetitively probed on lambda concatemer (arrow)).
With respect to Claim 37, Collins’191 shows the method of claim 31, further comprising contacting said plurality of analytes with a plurality of probes, wherein a probe of said plurality of probes comprises a detectable label, wherein said probe binds to an analyte of said plurality of analytes (paragraph [00427]-[00429] Reprobing linearised molecules: In some embodiments of the invention, it may be necessary to remove one or more bound probes before binding of further probes, Probes would be preferentially labelled with large nanoparticles or microspheres to be able to be easily detected by epi-fluorescence microscopy).
With respect to Claim 38, Collins’191 shows the method of claim 37, further comprising imaging said surface with an optical unit to detect one or more optical signals from said probe bound to said analyte of said plurality of analytes (paragraphs [0030] and [00324] reading first and second labels on the substrate in first and second imaging channels that correspond to the first and second labels, members of the array encompassing the field of view).
With respect to Claim 39, Collins’191 shows the method of claim 31, wherein said plurality of analytes comprise one or more nucleic acid molecules (paragraph [00297] target nucleic acids are captured on the substrate surface at multiple points).
With respect to Claim 40, Collins’191 shows the method of claim 31, wherein said repellant or attractive substance comprises zwitterionic features.
Claim 40 is rejected under 35 U.S.C. 103 as being unpatentable over Collins (WO 2016/134191 A1) in view of Bommarito et al. (US 2011/0097814 A1).
With respect to Claim 40, Collins’191 does not specifically show the method of claim 31, wherein said repellant or attractive substance comprises zwitterionic features.
Bommarito’814 shows the method of claim 31, wherein said repellant or attractive substance comprises zwitterionic features (paragraph [0091] The probes may be positively charged, negatively charged, or zwitterionic depending on the pH of the environment).
At the time of the invention, it would have been obvious to one of ordinary skill in the art before the effective filling date of the claim invention to modify Collins’191 to include wherein said repellant or attractive substance comprises zwitterionic features method taught by Bommarito’814. The suggestion/motivation for doing so would have been to improve the system’s ability to be able to obtain the desired pH below the isoelectric point of a probe (paragraph [0091])
Allowable Subject Matter
Claims 1-10 are allowed.
The following is an examiner’s statement of reasons for allowance: none of the references either singularly or in combination teach or fairly suggest a method for determining a relative position of analytes deposited on a surface of a densely packed substrate, comprising: (a) providing a substrate comprising a surface, wherein said surface is patterned or unpatterned and comprises a plurality of analytes deposited on said surface at discrete locations; (b) performing a plurality of cycles of probe binding and signal detection on said surface, wherein a cycle of said plurality of cycles comprises: (i) contacting said plurality of analytes with a plurality of probes from a probe set, wherein a probe of said plurality of probes comprises a detectable label, wherein said probe binds to an analyte of said plurality of analytes; (ii) introducing said plurality of analytes to a solution comprising erythorbic acid; and (iii) imaging said surface with an optical unit to detect one or more optical signals from said probe bound to said analyte.
Collins’191 shows methods of detecting a genetic variation in a genetic sample from a subject. Collins’191 do not include all the detailed combined limitations included in the claim including a method for determining a relative position of analytes deposited on a surface of a densely packed substrate, comprising: (a) providing a substrate comprising a surface, wherein said surface is patterned or unpatterned and comprises a plurality of analytes deposited on said surface at discrete locations; (b) performing a plurality of cycles of probe binding and signal detection on said surface, wherein a cycle of said plurality of cycles comprises: (i) contacting said plurality of analytes with a plurality of probes from a probe set, wherein a probe of said plurality of probes comprises a detectable label, wherein said probe binds to an analyte of said plurality of analytes; (ii) introducing said plurality of analytes to a solution comprising erythorbic acid; and (iii) imaging said surface with an optical unit to detect one or more optical signals from said probe bound to said analyte, therefore this claim is allowable.
Bommarito’814 shows a detection device for detecting an analyte in a test sample, and optionally for sample preparation. Bommarito’814 do not include all the detailed combined limitations included in the claim including a method for determining a relative position of analytes deposited on a surface of a densely packed substrate, comprising: (a) providing a substrate comprising a surface, wherein said surface is patterned or unpatterned and comprises a plurality of analytes deposited on said surface at discrete locations; (b) performing a plurality of cycles of probe binding and signal detection on said surface, wherein a cycle of said plurality of cycles comprises: (i) contacting said plurality of analytes with a plurality of probes from a probe set, wherein a probe of said plurality of probes comprises a detectable label, wherein said probe binds to an analyte of said plurality of analytes; (ii) introducing said plurality of analytes to a solution comprising erythorbic acid; and (iii) imaging said surface with an optical unit to detect one or more optical signals from said probe bound to said analyte, therefore this claim is allowable.
Staker et al. (US 2018/0274028 A1): shows in paragraph [0049] identifying a plurality of densely packed analytes immobilized on a surface of a substrate, comprising: providing a substrate comprising a surface, wherein the surface comprises a plurality of analytes immobilized on the surface at discrete locations; performing a plurality of cycles of probe binding and signal detection on said surface, (each cycle comprising: contacting said analytes with a plurality of probes from a probe set, wherein said probes comprise a detectable label, wherein each of said probes binds specifically to a target analyte; and imaging a field of said surface with an optical system to detect a plurality of optical signals from individual probes bound to said analytes); determining a peak location from each of said plurality of optical signals from images of said field from at least two of said plurality of cycles; overlaying said peak locations for each optical signal and applying an optical distribution model at each cluster of optical signals to determine a relative position of each detected analyte on said surface with improved accuracy. Staker do not include all the detailed combined limitations included in the claim including a method for determining a relative position of analytes deposited on a surface of a densely packed substrate, comprising: (a) providing a substrate comprising a surface, wherein said surface is patterned or unpatterned and comprises a plurality of analytes deposited on said surface at discrete locations; (b) performing a plurality of cycles of probe binding and signal detection on said surface, wherein a cycle of said plurality of cycles comprises: (i) contacting said plurality of analytes with a plurality of probes from a probe set, wherein a probe of said plurality of probes comprises a detectable label, wherein said probe binds to an analyte of said plurality of analytes; (ii) introducing said plurality of analytes to a solution comprising erythorbic acid; and (iii) imaging said surface with an optical unit to detect one or more optical signals from said probe bound to said analyte, therefore this claim is allowable.
Claim 34-35 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Any comments considered necessary by applicant must be submitted no later than the payment of the issue fee and, to avoid processing delays, should preferably accompany the issue fee. Such submissions should be clearly labeled “Comments on Statement of Reasons for Allowance.”
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to IRIANA CRUZ whose telephone number is (571)270-3246. The examiner can normally be reached 10-6.
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, Akwasi M. Sarpong can be reached at (571) 270-3438. 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.
/IRIANA CRUZ/Primary Examiner, Art Unit 2681