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 Objections
Claim 39 is objected to because of the following informalities: typo “regents” should be changed to --reagents--. The phrase “the single molecule array” should be amended to --the singe molecule protein array-- for consistency. Appropriate correction is required.
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.
Claim 39 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 39 line 8 recites “a controller coupled to the fluidic system”. The claim previously recites “a first fluidic system”. The same terminology should be used throughout the claims for clarity.
Claim 39 line 10 recites “such that an elapsed time between delivering affinity reagents to the flowcell unit and detection of binding of affinity reagents to one or more proteins on the single molecule array is substantially equivalent”. This confusing and indefinite since the claim only requires one flowcell unit and does not identify the interval that must be equivalent of the reference against which equivalence is measured. The current claim language provides material different interpretations; equivalence among different affinity reagent cycles, equivalence among separate delivery events within a cycle, equivalence for different proteins, or equivalence to an unstated target interval. Thus, this claim is indefinite. Claim 20 expressly identifies the comparator as each flowcell, and that is how claim 39 will be interpreted. Nevertheless, clarification is required.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 20, 21, 25-27 and 34 are rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Gordon et al., (US 2010/0323350; hereinafter “Gordon”).
Regarding claim 20, Gordon discloses a method for analyzing a plurality of analytes, comprising:
“providing a plurality of flowcell units in a flowcell device, each flowcell unit having an array of analytes disposed therein”. Gordon discloses a plurality of smaller flow cells mounted on a moveable support and configured to move to a plurality of stations, wherein at least some stations are reagent-delivery stations. Gordon further discloses that the flow cells are used for nucleic-acid sequencing, and therefore include analytes subjected to sequencing reactions. See paras. [0005], [0010]-[0011], [0026]-[0028], and Fig. 61,
“performing an interrogation reaction process on the arrays of analytes in each of a subset of flowcell units in the plurality of flowcell units by passing one or more interrogation reagents through each subset of flowcell units”. Gordon discloses reservoirs containing nucleic-acid sequencing reagents, reagent-delivery stations, and a sequencing protocol in which reagents are delivered to flow cells. See paras. [0007], [0010]-[0011], [0015], and [0027] et seq.,
“serially detecting a result of the interrogation reagents on the analytes in the arrays in each of a plurality of subsets of the flowcell units”. Gordon discloses an imaging station and movement of the flow cells among the protocol stations. Gordon teaches that multiple flow cells are run in parallel at different stages of the protocol and that a second flow cell may be imaged while a first flow cell undergoes chemistry steps. See paras. [0018]-[0022], [0026]-[0028], and Figs. 60-61,
“repeating the performing and detecting steps on each subset of the plurality of flowcell units”, Gordon discloses performing a plurality of cycles in which protocol steps are repeated. See paras. [0010] and [0016]., and
“wherein the performing steps and the detecting steps are staged such that an elapsed time between completion of the performing step and beginning of the detecting step for any flowcell unit is substantially equivalent.” Gordon discloses staged operation in which multiple flow cells are at different protocol stages, and the imaging station is kept fully utilized rather than intermittently idle. Gordon further discloses cycling the flow cells through stations and comparative timing arrangements for the flow cells. See paras. [0017]-[0022], and Figs. 60-61.
Regarding claim 21, Gordon teaches “wherein between each of the performing steps and the detecting steps, a wash reagent is introduced into each of the flowcell units to carry out a washing step.” Gordon discloses a reservoir set having at least one reservoir containing nucleic-acid sequencing reagents and at least one reservoir containing wash buffer. Gordon discloses a sequencing protocol having washing steps within the station sequence before imaging. See paras. [0007]-[0015], and [0024]-[0028], and Fig. 61.
Regarding claim 25, Gordon teaches “wherein the plurality of flow cell units comprises at least 4 flowcell units,” and serially performing the same interrogation reaction and serially detecting results in the at least four flowcell units. Gordon discloses a plurality of smaller flow cells, typically including 2, 4, 8, 10, 16, or 20 flow cells and a carousel having fixtures for locating the plurality of flow cells. Gordon moves the respective flow cells through the same reagent-delivery and imaging stations. See paras. [0005], [0026]-[0028], and Fig. 61.
Regarding claim 26, Gordon teaches “wherein the plurality of flow cell units comprises at least 6 flowcell units,” and serial performance and detection in the at least six flowcell units. Gordon discloses configurations containing 8, 10, 16, or 20 flow cells, each of which includes at least six flow cells. Gordon moves the flow cells through the same reagent-delivery and imaging stations. See paras. [0005], [0026]-[0028], and Fig. 61.
Regarding claim 27, Gordon teaches “wherein the plurality of flow cell units comprises at least 12 flowcell units,” and serial performance and detection in the at least twelve flowcell units. Gordon discloses configurations containing 16 or 20 flow cells, each of which includes at least twelve flow cells. Gordon moves the flow cells through the same reagent-delivery and imaging stations. See paras. [0005],[0026]-[0028], and Fig. 61.
Regarding claim 34, Gordon teaches “wherein the step of performing an interrogation reaction in a first subset of flowcell units is carried out concurrently with the step of detecting the result of an interrogation reaction in a second subset of flowcell units.” Gordon discloses that multiple flow cells are run in parallel at different stages in the protocol and that a second flow cell may be imaged while a first flow cell undergoes analysis steps. See paras. [0018]-[0022], and Fig. 60.
Claims 20, 21, and 34 are rejected under 35 U.S.C. 102(a)(1)/(a)(2) as being anticipated by Stone et al. (US 20150045234 Al; hereinafter “Stone”- already of record).
Regarding claim 20, Stone discloses a method for analyzing a plurality of analytes, comprising:
“providing a plurality of flowcell units in a flowcell device, each flowcell unit having an array of analytes disposed therein.” Stone discloses a flow cell containing a plurality of channels. Stone illustrates a four-lane flow cell 2020 having channels that are fluidically manipulated and optically detected. The channels are individually addressable through fluid lines, valves, a reagent manifold, and syringe pumps. See paras. [0047]-[0051], and Fig. 9.,
“performing an interrogation reaction process on the arrays of analytes in each of a subset of flowcell units in the plurality of flowcell units by passing one or more interrogation reagents through each subset of flowcell units.” Stone discloses fluidic manipulation of a first subset of channels and delivery of reagents from reagent tray 2035 through reagent manifold 2030 to the flow-cell channels. See paras. [0047] et seq., and Fig. 9.,
“serially detecting a result of the interrogation reagents on the analytes in the arrays in each of a plurality of subsets of the flowcell units.” Stone discloses optical detection for a second subset of channels while fluidic manipulation is carried out on a first subset. Stone further discloses alternating channel sets undergoing fluidic steps and detection steps in respective sequencing cycles. See paras. [0047]-[0048],
“repeating the performing and detecting steps on each subset of the plurality of flowcell units.” Stone discloses that the alternating channel sets can undergo fluidic and detection steps and that the steps can be repeated several times. See para. [0047], and
“wherein the performing steps and the detecting steps are staged such that an elapsed time between completion of the performing step and beginning of the detecting step for any flowcell unit is substantially equivalent.” Stone teaches a staggered configuration in which a more rapid sequencing run results if the time for fluidic manipulation is about the same as the time for detection. Stone further teaches changing the staggered pattern when the timing of detection and fluidic steps differs. See para. [0048].
Regarding claim 21, Stone teaches a reagent cartridge having wash reservoirs corresponding to reagent reservoirs, with wash buffer drawn into reagent sippers from the wash reservoirs. Stone further discloses that washes can be carried out between various delivery steps of a sequencing-by-synthesis cycle performed on a flow cell. See paras. [0058], [0070] et seq., and Fig. 8.
Regarding claim 34, Stone teaches performing an interrogation reaction in a first subset of flowcell units concurrently with detecting a result in a second subset. Stone expressly discloses that fluidic manipulations can be carried out on a first subset of channels while optical detection occurs for a second subset of channels. See para. [0047] et seq.
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.
Claim 22 is rejected under 35 U.S.C. 103 as being unpatentable over Gordon in view of Drmanac et al., (US 2017/0175184; hereinafter “Drmanac”).
As discussed above, Gordon discloses the method of claim 21, including sequential reagent delivery, wash-buffer delivery, staged multi-flow-cell operation, and detection.
Claim 22 recites “wherein interrogation reagents for performing the interrogation reaction, and wash reagents for performing the washing step, are introduced into the flowcell device using a plurality of independent fluidic systems.” Gordon discloses separate reagent and wash delivery at respective stations and recognizes a need to avoid cross-contamination between reagent types. See Gordon paras. [0024] et seq. Gordon does not expressly disclose the recited plurality of independent fluidic systems.
Drmanac discloses dedicated syringe pumps that may dispense wash and hybridization buffers directly into funnel ports for each flow cell of a multi-flow-cell instrument. See Drmanac para. [0083]. The dedicated syringe pumps correspond to the claimed independent fluidic-delivery hardware for independently delivering wash and interrogation-related buffers to the flow-cell structures.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use Drmanac’s dedicated-pump fluidic architecture in Gordon's staged multi-flow-cell system to provide independent fluidic delivery for interrogation and wash reagents. Gordon recognizes cross-contamination between reagent types as a design concern, and Drmanac teaches dedicated syringe-pump delivery directly to flow-cell ports. The modification would reduce reagent carryover while preserving Gordon's staged reagent-delivery and imaging arrangement. One of ordinary skill in the art would have had a reasonable expectation of success because both references concern fluidic delivery of reaction and wash materials to multiple flow cells.
Claims 23 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Gordon.
Claim 23 recites “wherein for a given flowcell unit, the detection step is longer than a combined duration of the interrogation reaction and washing steps,” and “a length of time to perform a cycle of interrogation reaction, washing and detection steps is equal to x+y+n(z).” Gordon discloses staged multi-flowcell sequencing and a worked timing comparison in which the imaging step takes twice as long, or more, as any other step. Gordon further teaches selecting the number of flow cells and timing arrangement
to reduce overall cycle time. See paras. [0015] et seq., and Fig. 60.
It would have been obvious to one of ordinary skill in the art at the time of the claimed invention to have used Gordon's disclosed timing relationship using the recited algebraic form. The formula expresses the aggregate time of reaction, washing, and serial detection stages across the number of flow cells. Gordon already discloses and compares the relevant timing relationships. Expressing the disclosed timing relationship as an algebraic equation would have been a routine mathematical formalization of the scheduling arrangement taught by Gordon.
Claim 24 recites “wherein for a given flowcell unit, the detection step is shorter than a combined duration of the interrogation reaction and washing steps,” and “a length of time to perform a cycle of interrogation reaction, washing and detection steps is equal to n(x+y)+z.” Gordon discloses staged multi-flow-cell sequencing and compares timing regimes in which the imaging step and other station steps have different relative durations. Gordon teaches selecting the number of flow cells and staging arrangement based on those relative durations. See paras. [0015]-[0019], and Fig. 60.
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to express the scheduling relationship in the recited algebraic form when reaction and washing steps collectively determine the repeated portion of the cycle time. The formula represents a routine mathematical expression of Gordon's disclosed timing and optimization relationship.
Claims 35-37, as applied to claim 20, are rejected under 35 U.S.C. 103 as being unpatentable over Gordon or Stone.
Claim 35 recites that the elapsed times for first and second flowcell units are “no more than 20% different”. Claim 36 recites that the elapsed times are “no more than 10% different”. Claim 37 recites that the elapsed times are “no more than 3% different”. Gordon discloses staged timing intended to keep the imaging station fully utilized, rather than intermittently idle, and teaches cycling flow cells through the respective stations using the disclosed timing arrangement. See paras. [0017]-[0022], and Figs. 60-61. Gordon does not expressly disclose the claimed numerical percentage ranges. However, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to select an elapsed-time variance within the recited 20%, 10%, or 3% ranges as a result effective variable in Gordon's staged system. The relevant objective maintaining utilization of the imaging station through appropriately matched staged operations is expressly taught by Gordon. Optimizing the timing difference among flow cells to obtain predictable improvements in station utilization and overall throughput would have involved routine experimentation.
Regarding claims 35-37, Stone discloses staggered fluidic manipulation and optical detection among respective subsets of channels. Stone teaches that a more rapid sequencing run results if the time for fluidic manipulation is about the same as the time for detection. Stone further teaches changing the staggered configuration to a more appropriate pattern when fluidic and detection timing differ. See paras.
[0047]-[0048]. Stone does not expressly disclose the claimed 20%, 10%, or 3% numerical limits. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to select the claimed percentage differences through routine optimization of Stone's disclosed relative timing parameter. Stone identifies the timing match between fluidic steps and detection steps as affecting overall sequencing speed and teaches modifying the staggered pattern to account for timing differences. Selecting tighter percentage tolerances to improve the efficiency of the staggered operation would have been a predictable result of routine experimentation.
Claims 28-33 and 38 are rejected under 35 U.S.C. 103 as being unpatentable over Gordon in view of Mallick et al. (US 20200158722 Al; hereinafter “Mallick”).
Gordon discloses the staged multi-flowcell, repeated performing and detecting process of claim 20. See Gordon paras. [0010], [0016]-[0022], and Figs. 60-61. Claim 28 recites that the performing and detecting steps are repeated with “at least 50 different interrogation reagents”. Regarding claims 29-31, the respective claims recite “at least 100, at least 200, and at least 300” different interrogation reagents. Gordon does not expressly disclose those reagent quantities.
Mallick discloses protein-analysis methods using affinity-reagent panels. Mallick teaches that the methods may require about 100, 200, 300, 400, or 500 different affinity reagents to identify a target proteome. Mallick further discloses a simulation involving 8,000 trimer-specific affinity reagents. See para. [0118] and Fig. 13. Mallick's disclosure of at least 100 different affinity reagents also encompasses at least 50 different affinity reagents.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to employ Mallick's disclosed affinity-reagent panels in Gordon's repeated staged reagent-delivery and detection cycle. Gordon supplies the multi-flowcell cyclic interrogation architecture, and Mallick supplies the protein-analysis reagent-panel quantities. The combination would use known reagent panels in a known repeated reagent-delivery and detection workflow. One of ordinary skill in the art would have had a reasonable expectation of success because both references disclose repeated application of reagents to analyte-bearing flow-cell or substrate structures followed by detection.
Claim 32 recites that the performing and detecting steps are repeated “at least 50 times with different interrogation reagents or combinations of interrogation reagents”. Claim 33 recites repeating the steps “at least 100 times with different interrogation reagents or combinations of interrogation reagents”. Gordon discloses a protocol that typically involves numerous cycles, including 20 to 100 or more cycles. See para. [0016]. Mallick teaches panels containing 100, 200, or 300 different affinity reagents. See para. [0118] and Fig. 13.
It would have been obvious to one of ordinary skill in the art prior to the effective filing date to apply the respective reagents from Mallick's disclosed panel sequentially through Gordon's repeated cycles. Application of at least 100 different reagents necessarily entails at least 50 and at least 100 repeated reagent-interrogation operations when individual reagents or combinations are delivered in the repeated cycles, timing differences. Selecting tighter percentage tolerances to improve the efficiency of the staggered operation would have been a predictable result of routine experimentation.
Regarding claim 38, Mallick teaches “wherein the array of analytes comprises a single molecule protein array and the plurality of interrogation reagents comprises a plurality of affinity reagents having affinity to different proteins”. Mallick discloses single protein molecules conjugated to a substrate and spatially separated so that each individual protein molecule has a unique optically resolvable spatial address. Mallick that, in some instances, the substrate is a flow cell. See paras. [0009], [00105}-[0016], [0067], et seq. and Fig. 18. Mallick discloses affinity reagents including antibodies,
antibody fragments, aptamers, and peptides screened for their ability to bind a single protein. Mallick also discloses sequential interrogation of an unknown protein using distinct trimer-specific affinity reagents and identification based on a binding pattern. See paras. [0083] et seq. and Fig. 18.
Claim 39 is rejected under 35 U.S.C. 103 as being unpatentable over Gordon, Mallick in view of Guo et al. (US 20210121882 Al; hereinafter “Guo”).
Regarding claim 39, as discussed above, Mallick discloses “a flowcell unit comprising a single molecule protein array” and “single protein molecules conjugated to a substrate and spatially separated so that each individual protein molecule has a unique optically resolvable spatial address”. See Mallick paras. [0009], [0015]-[0016], [0067], and Fig. 18. Claim 39 further recites “a source of at least 300 different affinity reagents.” Mallick teaches that the disclosed methods may require about 100, 200, 300, 400, or 500 different affinity reagents to identify a target proteome. See Mallick para. [0118] and Fig. 13. Claim 39 further recites “a detection system positioned relative to the flowcell unit to detect binding reactions between the affinity reagents and proteins on the single molecule array.” Mallick discloses optically resolvable spatial addresses for individual protein molecules and sequential affinity-reagent interrogation to identify a protein from its binding pattern. See Mallick paras. [0015]-[0016], [0083], [0134], and Fig. 18.
Claim 39 further recites ‘“a first fluidic system fluidicly coupled to the flowcell unit and configured to access each of the 300 different affinity reagents”. Mallick does not expressly disclose the recited externally coupled fluidic system. Guo discloses a flow-cell device having two or more fluidic adaptors configured to mate with tubing providing fluid communication between capillaries of the flow-cell device and a fluid-control system external to the flow-cell device. Guo discloses a flow-cell cartridge having a chassis, fluidic adaptors, and capillaries. See Guo paras. [0006], [0008], and Figs. 1-2.
Claim 39 further recites “a controller coupled to the fluidic system and detection system, and configured to serially deliver each of a plurality of individual affinity reagents to the flowcell unit, and detect binding” such that the elapsed time between delivery and detection is substantially equivalent. Gordon discloses a moveable support and staged system for moving multiple flow cells among reagent-delivery and imaging stations. Gordon teaches timing the staged sequence to keep the imaging station fully utilized. See Gordon paras. [0010]-[0011], [0017]-[0019], [0022], [0026]-[0028], and Figs. 60-61.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Mallick's protein-identification assay to use Guo's externally fluidically coupled flow-cell structure and Gordon's staged reagent-delivery and detection control arrangement. Guo teaches an external fluid-control interface for providing fluid communication to a flow-cell device and identifies simplified reagent exchange and reduced consumable cost as purposes of the flow-cell structure. Gordon teaches staged scheduling of reagent delivery and detection to improve utilization of the imaging system. The combination would provide fluidic access to Mallick's disclosed affinity-reagent panel and use staged control to serially deliver reagents and detect binding events. One of ordinary skill in the art would have had a reasonable expectation of success because each reference discloses a compatible known function: protein interrogation, fluidic communication with a flow cell, and staged reagent/detection scheduling.
Pertinent Prior Art
The following prior art is hereby made of record. Although the prior art is relied upon, the examiner considers the listed prior art relevant to the applicant’s invention and may be relied upon in a future prior art rejection or as general background information related to applicant’s field of endeavor.
Lawson et al. (US 20080219888) teach providing a plurality of flowcell units in a flowcell device, two or more multi-channel flow cells attached to a common holder, with each flow cell having separate fluidic connections, each flow cell having multiple imaging areas, and a reaction component can be performed on one imaging area while another imaging area is interrogated/imaged.
Conclusion
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/P. Kathryn Wright/Primary Examiner, Art Unit 1798
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