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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 02/15/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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 1-6, 12 and 13 are rejected under 35 U.S.C. 102a1 as being anticipated by Hollenbeck et al. (US 2013/0100462 A1 – hereafter ‘462).
‘462 discloses a system for determining the position of a microplate ([0007]) that includes the following limitations for claim 1:
“A patterned flow cell”: ‘462 discloses a microplate (microplate 170; Fig. 1; [0037]) that is being interpreted as the patterned flow cell of the instant application.
“a substrate”: ‘462 discloses a surface (surface 103; Fig. 2) that supports the samples sites ([0038]) and is being interpreted as the substrate of the instant application.
“a plurality of sample sites in a non-fiducial region of the substrate, wherein the plurality of sample sites is arranged in a periodic pattern”: ‘462 discloses a plurality of biosensors or sample sites (Fig. 2; biosensor 102; [0038]) that are being interpreted in a non-fiducial region and are arranged in a periodic pattern.
“a plurality of sample site-based fiducials comprise an arrangement of sample sites and blank regions formed linearly in a first dimension associated with a scan direction of the patterned flow cell.”: ‘462 discloses a plurality of fiducials (fiducials 169) that are being interpreted as located in as the scan location ([0039]; fiducial 169; Fig. 2) and include blank areas that are linearly formed in a scan direction.
For claim 2, ‘462 discloses that the pattern is a rectilinear patter (Fig. 2).
For claim 3, the blank spots of ‘462 are spots where a sample could be located (Fig. 2).
For claim 4, this appears to be drawn to the intended use of the claimed device and therefore does not structurally define the claimed invention over the prior art. See MPEP §2114. It should be noted that ‘462 scans the sites in a sinusoidal scan path ([0072]) and therefore a plot of brightness versus site location would correspond to a sinusoidal waveform.
For claim 5, it appears that this claim is drawn to the image captured of the flow cell. It should be noted that the image detection system has not been claimed within claim 1 or 5, however, the arrangement of the fiducials and blank spaces of ‘462 (Fig. 2; fiducials 169) would form a column of pixels on a CCD.
For claim 6, the fiducials are being interpreted as being in pairs with a blank spot between the pairs (Fig. 6; fiducial 169).
‘462 discloses a system for determining the position of a microplate ([0007]) that includes the following limitations for claim 12:
“A patterned flow cell”: ‘462 discloses a microplate (microplate 170; Fig. 1; [0037]) that is being interpreted as the patterned flow cell of the instant application.
“a substrate”: ‘462 discloses a surface (surface 103; Fig. 2) that supports the samples sites ([0038]) and is being interpreted as the substrate of the instant application.
“a plurality of sample sites in a non-fiducial region of the substrate, wherein the plurality of sample sites is arranged in a periodic pattern”: ‘462 discloses a plurality of biosensors or sample sites (Fig. 2; biosensor 102; [0038]) that are being interpreted in a non-fiducial region and are arranged in a periodic pattern.
“a plurality of fiducials provided on the substrate in a first dimension associated with a scan direction of the patterned flow cell, wherein each fiducial comprise a plurality of features that are separated by one or more blank regions, wherein each feature is contiguous across one or more columns of the periodic pattern.”: ‘462 discloses a plurality of fiducials (fiducials 169) that are being interpreted as located in as the scan location ([0039]; fiducial 169; Fig. 2) and include blank areas that are linearly formed in a scan direction. These features are being interpreted as being contiguous across the columns.
For claim 13, ‘462 discloses that the biosensor (biosensor 102; Fig. 2) is reflective and this is being interpreted as the reflective feature ([0041]).
Therefore, ‘462 meets the limitations of claims 1-6, 12 and 13.
Claim Rejections - 35 USC § 103
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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 14 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Hollenbeck et al. (US 2013/0100462 A1 – hereafter ‘462) in view of Viecell et al. (WO 2018/144582 A1 – hereafter ‘582).
‘462 (Hollenbeck) differs from claims 14 and 15 regarding the fluorescent feature. It should be noted that this feature, in light of the specification, is being interpreted as either a dye or a fluorescent probe.
‘582 (Viecell) discloses a molecular analysis system (Abstract) that for claims 14 and 15 discloses using a fluorescent material ([0011]) as the fluorescent feature where this feature operates at two different wavelengths ([0011]) which can be used, for example, to separate and distinguish the four common nucleotides by color ([0090]).
Therefore, it would have been obvious to one of ordinary skill in the art to employ the fluorescent dye of ‘582 within ‘462 in order to identify a nucleic acid. The suggestion for doing so at the time would have been able to separate and distinguish the four common nucleotides by color ([0090]).
Allowable Subject Matter
Claims 7-11 and 16-17 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.
The following is a statement of reasons for the indication of allowable subject matter: For claim 7, the prior art fails to teach or fairly suggest where the sample site-based fiducials comprise, within a column pixel, a pattern of sample sites having a first value of a geometric parameter, sample sites have a second value of the geometric parameter and one or more blank regions.
Claims 8 and 9 would be allowable for the same reasons as claim 7.
For claim 10, the prior art fails to teach or fairly suggest the flow cell where the sample site-based fiducials comprise a multi-column fiducial, wherein each column of the multi-column fiducial comprises a patter of sample sites having a first value of geometric parameter, sample sites having a second value of the geometric parameter, and one or more blank regions.
Claim 11 would be allowable for the same reasons as claim 10.
For claim 16, the prior art fails to teach or fairly suggest the flow cell where each fiducial comprises a pair of bar-shaped features each formed lengthwise in a second dimension perpendicular to the first dimension and corresponding to a cross-sample direction perpendicular to the scanning direction associated with the patterned flow cell.
Claim 17 would be allowable for the same reasons as claim 16.
The closest prior art is Hollenbeck et al. (US 2013/0100462 A1) discloses a biosensor and optical reader that uses reference sites; however, Hollenbeck does not teach or fairly suggest the sample sites and reference sites having different geometric parameters .
Claim18-20 allowed.
The following is an examiner’s statement of reasons for allowance: For claim 18, the prior art taken either singly or in combination fails to teach or reasonably suggest the following limitation when taken in context of the claim as a whole a sequencing instrument that includes the following limitations: a sample stage configured to support a flow cell; an objective lens, a photodetector, and a light source configured to operate in combination to image the flow cell when present on the sample stage; and a controller configured to perform operations comprising: advancing the flow cell when undergoing an imaging operation along a linear scan path; imaging a patterned surface of the sample container as it is advanced along the linear scan path, wherein the patterned surface comprises: a plurality of sample sites arranged in a periodic pattern, wherein a subset of the sample sites are sample site-based fiducials comprising an arrangement of sample sites and blank regions formed linearly in a first dimension associated with a scan direction of the patterned flow cell; determining a current feature pattern of the flow cell based on the sample-site based fiducials; comparing the current feature pattern with an expected feature pattern; and adjusting one or both of a location of the sample stage or a speed at which the sample stage is moved based upon the comparison of the current feature pattern with the expected feature pattern.
Claims 19 and 20 would be allowable for the same reasons as claim 18.
The closest prior art is Hollenbeck et al. (US 2013/0100462 A1) discloses a biosensor and optical reader that uses reference sites; however, Hollenbeck does not teach or fairly suggest the sample sites and reference sites having different geometric parameters .
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
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Moll et al. (US 2013/0203627 A1) discloses a system for obtaining a pane of serologic assay results rapidly using a small volume of samples.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL L HOBBS whose telephone number is (571)270-3724. The examiner can normally be reached Variable, but generally 8AM-5PM M-F.
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/MICHAEL L HOBBS/Primary Examiner, Art Unit 1799