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
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(s) 1, 2, 6-12, 20, 26 and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 20170107562 A1) in view of Ramsey (US 20190094212 A1).
Regarding claim 1, Rothberg teaches excitation energy delivered to a luminescent marker (par 27) exciting, with excitation light from at least one excitation source, one or more reference dye molecules that, the luminescent markers are used to identify single molecules as they are incorporated during the synthesis of a biomolecule (par 10) during the exciting with the excitation light, are attached to respective biomolecules of the sample a target nucleic acid molecule can be immobilized to a solid support such as a reaction chamber (par 105) bound to a surface of a respective single chamber of one or more chambers of the integrated device; and luminescent labels on nucleotides sequencing determine luminescent lifetime of the molecules (par 131) where luminescent markers can be in the form of luminescent labels, such as dyes (par 97) obtaining a signal emitted by the one or more reference dye molecules in response to the excitation light; and distinguishing a single molecule and distinguishing a molecule from a plurality of molecules (par 132) and determining, based on the signal emitted by the one or more reference dye molecules, the measure of quantitative loading of the sample, wherein the measure of quantitative loading of the sample comprises a number of the respective biomolecules wherein each single molecule identified is immobilized on a bottom surface of a sample well (claims 19 and 20) bound to the surface of the respective single chamber of the one or more chambers; and outputting the number of respective biomolecules bound to the surface of the single chamber of the one or more chambers, performing sequencing after a biological sample is processed in preparation for detection (par 279) subsequent to determining the measure of quantitative loading of the sample, performing sequencing to determine an identity of the respective biomolecules being bound to the surface of the respective single chamber. It is noted that paragraph 112, for instance, of Rothberg teaches that the target volume can be configured to confine a single molecule or complex. If a signal is emitted the number is 1, if it is not, the number is zero. This identifies the quantitative loading of the chamber as either 1 or zero. Paragraph 337 has further discussion of wells that hold only a single molecule. Paragraph 306 further discusses the detection of a single molecule.
Rothberg fails to teach the exciting is photobleaching and determining a number of photobleaching steps reflected by the signal emitted by the one or more reference dye molecules; determining, based on the number of photobleaching steps reflected by the signal, whether the respective single chamber contains zero, one, or more than one reference dye molecules therein and the determination of the quantitative loading is based upon the number of reference dye molecules therein.
Ramsey teaches incorporating time-domain encoding with photobleaching kinetics to decode different population or molecular recognition elements (Ramsey, par 95) and multiple Defined Events that can be photobleaching for multiplexed analysis to identify targets of a respective single sample (Ramsey, par 121) and there may be zero, one or multiple analyte molecules per well (Ramsey, par 168).
Therefore, it would have been obvious to one of ordinary skill in the art at the effective filing date of the claimed invention to have modified the method of Rothberg to include the photo bleaching kinetics of Ramsey because “time-domain encoding can unlock additional multiplexing levels that are unattainable by conventional decoding methods” (Ramsey, par 95).
Regarding claim 2, Rothberg teaches a luminescent lifetime and luminescent intensity of a molecule can be determined from a plurality of photons that are emitted sequentially (par 91).
Regarding claim 6, Rothberg teaches some sample wells may contain no samples and a percentage of sample wells with a single molecule (par 337).
Regarding claim 7, Rothberg teaches determining the number of sample wells that contain a single molecule, so that single-molecule analysis can be carried out for a large number of single molecules (par 337).
Regarding claim 8, Rothberg teaches configuring sample wells to confine a single molecule allowing measurements to be performed on the single molecule (par 306).
Regarding claim 9, Rothberg teaches only processing the sample wells where photons are detected (Fig. 2 “Processed data”, par 118-119).
Regarding claim 10, Rothberg teaches determining the number of sample wells that contain a single molecule, so that single-molecule analysis can be carried out for a large number of single molecules (par 337).
Regarding claims 11 and 12, Rothberg teaches a protecting molecule which is an oligonucleotide that attaches to a luminescent label and one or more nucleotides (par 209). Oligonucleotides would reversibly attach to the nucleotides in the same manner as in the instant case (see paragraph 62 of the Specification).
Regarding claim 20, Rothberg teaches excitation energy delivered to a luminescent marker (par 27) exciting, with light from at least one excitation source, one or more reference dye molecules, a protecting molecule which is an oligonucleotide that attaches to a luminescent label and one or more nucleotides (par 209). Oligonucleotides would reversibly attach to the nucleotides in the same manner as in the instant case (see paragraph 62 of the Specification). the one or more reference dye molecules being attached to respective secondary biomolecules which reversibly binds to respective biomolecules of the sample, a target nucleic acid molecule can be immobilized to a solid support such as a reaction chamber (par 105) the respective biomolecules being bound to a surface of a chamber of a plurality of chambers of the integrated device; and luminescent labels on nucleotides sequencing determine luminescent lifetime of the molecules (par 131) where luminescent markers can be in the form of luminescent labels, such as dyes (par 97) obtaining a signal emitted by the one or more reference dye molecules in response to the excitation light; identifying a molecule can be done by recording for each detected luminescence the time duration between the luminescence and the prior pulse of excitation energy (par 27) determining a pulsing pattern of the one or more reference dye molecules; determining the measure of quantitative loading of the sample based on the pulsing pattern of the one or more reference dye molecules, distinguishing a single molecule and distinguishing a molecule from a plurality of molecules (par 132), the system is also set up to detect which wells contain one, zero, or two or more samples (par 294) wherein the measure of quantitative loading of the sample comprises a percentage of the plurality of chambers containing at least a single biomolecule and wherein each single molecule identified is immobilized on a bottom surface of a sample well (claims 19 and 20) of the sample bound to a surface of a respective one or the plurality of chambers; and outputting the percentage of the plurality of chambers containing at least a single biomolecule preforming sequencing after a biological sample is processed in preparation for detection (par 279) subsequent to determining the measure of quantitative loading of the sample, performing sequencing to determine an identity of the respective biomolecules being bound to the surface of the respective single chamber.
Rothberg fails to teach the exciting is photobleaching and determining a number of photobleaching steps reflected by the pulsing pattern of the one or more reference dye molecules; determining, based on the number of photobleaching steps reflected by the signal, whether the respective single chamber contains zero, one, or more than one reference dye molecules therein and the determination of the quantitative loading is based upon the number of reference dye molecules therein.
Ramsey teaches incorporating time-domain encoding with photobleaching kinetics to decode different population or molecular recognition elements (Ramsey, par 95) and multiple Defined Events that can be photobleaching for multiplexed analysis to identify targets of a respective single sample (Ramsey, par 121) and there may be zero, one or multiple analyte molecules per well (Ramsey, par 168).
Therefore, it would have been obvious to one of ordinary skill in the art at the effective filing date of the claimed invention to have modified the method of Rothberg to include the photo bleaching kinetics of Ramsey because “time-domain encoding can unlock additional multiplexing levels that are unattainable by conventional decoding methods” (Ramsey, par 95).
Regarding claim 26, modified Rothberg teaches wherein the photobleaching the one or more reference dye molecules comprises exciting, with the excitation light, the one or more reference dye molecules such that the one or more reference dye molecules emit the signal in response to the excitation light, for a duration until the one or more reference dye molecules are photobleached (Ramsey, par 95).
Regarding claim 27, modified Rothberg teaches wherein the photobleaching the one or more reference dye molecules comprises exciting, with the excitation light, the one or more reference dye molecules such that the one or more reference dye molecules emit the signal in response to the excitation light, for a duration until the one or more reference dye molecules are photobleached (Ramsey, par 95).
Claim(s) 21 and 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg and Ramsey as applied to claim 20 above, and further in view of Tamamura et al. (US 20100075434 A1).
Regarding claim 21, Rothberg and Ramsey teach the method of claim 20 but do not appear to explicitly disclose wherein: the respective secondary biomolecules binds to the respective biomolecules of the sample once per pulsing period; the pulsing pattern comprises one or more pulses or no pulses; and the measure of quantitative loading is determined based on a number of the one or more pulses received during a pulsing period.
However, Tamamura teaches tag-probe complexes to be reacted at desired timing and reversibly bonded suitable for use with pulse-chase analysis (Tamamura, par 116).
Therefore, it would have been obvious to one of ordinary skill in the art at the effective filing date of the claimed invention to have modified the method of Rothberg to include the timing and reversibly bonded tagging of Tamamura because it automatically arranges the fluorescent dye (Tamamura, par 117).
Regarding claim 23, Rothberg teaches testing for single molecules and sample wells with no sample (par 337).
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Regarding applicant’s argument that Ramsey does not describe the use of photobleaching information to determine a measure of quantitative loading is not found persuasive. Paragraph 95 of Ramsey teaches using photobleaching kinetics to decode different populations, paragraph 121 teaches to use defined events which are based on photobleaching to determine changes from the array and to detect when the events occur for the assay and paragraph 168 teaches that there can be zero, one or multiple analytes per well. Based upon these paragraphs in Ramsey, one of ordinary skill in the art would have determined the number of photobleaching steps (defined events), determine the number of photobleaching events and whether a single chamber comprises zero, one or multiple dye molecules (there are zero, one or multiple analytes in each well which are detected using the defined events) and determine the quantitative loading based on the number of reference dye molecules (the assay is performed based on the defined events and this analysis would be due to the number of dyes (analytes) which would represent the quantitative loading of the device).
Conclusion
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 MATTHEW D KRCHA whose telephone number is (571)270-0386. The examiner can normally be reached M-Th 7am-5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Elizabeth Robinson can be reached at (571)272-7129. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MATTHEW D KRCHA/ Primary Examiner, Art Unit 1796