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 .
Claims Status
Claims 82-93 & 95-98 filed on 08/11/2026 are pending. Claim 94 is withdrawn from consideration as being drawn to a non-elected invention. Claims 86, 87, & 95 are currently under examination directed to the elected species of binding assay in claim 86, of equilibrium binding assay in claim 87, and of flow cell in claim 95 (see response dated 02/17/2026). The cancellation of claims 99-101 without prejudice or disclaimer in the reply filed on 08/11/2026 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 103
Claim(s) 82-84, 86, 88, 90, 92, 93, & 95-98 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gan (Gan, Yamanaka, Kojima, & Nakano; Biotechnol. Prog., Vol. 24, pages 1107-1114, September 2008), as cited in the IDS dated 02/23/2023, in view of Green (United States Patent Application Publication US 2015/0018236 A1), as cited in the IDS dated 02/23/2023.
Regarding claim 82, it is noted that the recitation of “performed on the same instrument” is broad and is not further defined in the instant specification and therefore instrument is given its broadest reasonable interpretation to encompass a specialized physical device or tool designed and used to conduct experiments, take precise measurements, and gather data.
Gan teaches a method for coupling protein to its coding DNA on magnetic microbeads comprising biotinylated reverse primers (immobilized oligonucleotides) linked to beads (solid surface) (providing a solid surface comprising a plurality of immobilized oligonucleotides) and nucleic acid templates that encode for proteins (library of nucleic acids encoding a plurality of polypeptides), amplifying the nucleic acid templates (library of nucleic acids encoding polypeptides) with the bead linked reverse primer (immobilized oligonucleotides) (generating a process nucleic acid molecule suing an immobilized oligonucleotide and a nucleic acid molecule wherein the process nucleic acid encodes a polypeptide and is immobilized on the solid surface), then expressing proteins in an emulsion creating a bead-DNA-protein complex (expressing the polypeptide from the processed nucleic acid molecule), labeling the bead-DNA-protein complexes with a fluorescent labeled antibody and then assaying through flow cytometry (performing an assay on the polypeptide to identify one or more properties of the polypeptide), followed by an additional round of screening comprising selection and sequencing of samples (performing an assay on the polypeptide and sequencing performed on the same bead system instrument designed to take precise measurements and gather data) (abstract lines 1-16; pg. 1108 column 1 1st full paragraph lines 1-21; pg. 1108 column 2 1st full paragraph lines 1-14; pg. 1109 paragraph bridging column 1 & 2 lines 1-4; pg. 1109 column 2 1st full paragraph lines 1-17; pg. 1110 column 2 1st full paragraph lines 1-18; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 1). Gan also teaches that the proteins are directly linked on the ends of the nucleic acid templates linked to beads (processed nucleic acid) and thus both genes and proteins are displayed in a gene protein complex (linking properties of polypeptide to processed nucleic acid) (pg. 1108 column 1 1st full paragraph lines 3-9).
Gan does not teach that the processed nucleic acid molecule is specifically sequenced to identify a processed nucleic acid molecule sequence.
Green teaches a method for screening and identifying polypeptides that provide a biological response in a living cell comprising the use of an emulsion system comprising obtaining a population of nucleic acid molecules comprising sequences that encode different polypeptides (nucleic acid molecules encoding a plurality of polypeptides), incubating the encoding nucleic acid molecules (processing nucleic acid molecule) under conditions that permit expression of polypeptides (expressing the polypeptide from processed nucleic acid molecule), and testing cells for biological response to polypeptides and isolating encoding nucleic acid molecules associated with polypeptides to analyze the biologically active polypeptide in which candidate polypeptides remain associated with their coding nucleic acid sequences (processed nucleic acid molecules) through beads and emulsion system so that active polypeptides can be identified by sequencing of the coding nucleic acid sequences (sequencing processed nucleic acid molecules to identify a processed nucleic acid molecule sequence and linking one or more properties of the polypeptide to the process nucleic acid molecule sequence) (paragraph [0008] lines 1-14; paragraph [0011] lines 1-18; paragraph [0111] lines 1-9). Green also teaches that this method provides the ability to effectively screen a vast diversity of sequences and a highly efficient method to identify polypeptides (paragraph [0008] lines 1-4; paragraph [0111] lines 21-27).
Gan and Green are considered to be analogous to the claimed invention because they are all in the same field of analysis and identification of polypeptides through nucleic acid libraries. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of coupling protein to its coding DNA on magnetic microbeads comprising labeling and assaying bead-DNA-protein complexes through flow cytometry, followed by an additional round of screening comprising selection and sequencing of samples (performing assay on polypeptide and sequencing performed on same instrument to take precise measurements and gather data) in Gan to incorporate the specific sequencing of coding nucleic acid sequences (processed nucleic acid molecules) to identify polypeptides and link one or more properties of a polypeptide to the processed nucleic acid molecule sequence as taught in Green because Green teaches that doing so would provide a highly efficient method to identify polypeptides and effectively screen a vast amount of sequences.
Regarding claim 83, Gan teaches hybridizing biotinylated reverse primers (immobilized oligonucleotides) linked to beads (solid surface) to nucleic acid templates that encode for proteins (library of nucleic acids encoding a plurality of polypeptides) to amplify the nucleic acid templates (nucleic acid molecules) (hybridizing an immobilized oligonucleotide to a nucleic acid molecule) (pg. 1108 column 1 1st full paragraph lines 1-21; pg. 1109 column 2 1st full paragraph lines 1-17; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 1).
Regarding claim 84, Gan teaches that the proteins are directly linked on the ends of the nucleic acid templates linked to beads (processed nucleic acid) (pg. 1108 column 1 1st full paragraph lines 3-9).
Regarding claim 86, Gan teaches labeling and assaying the bead-DNA-protein complexes through flow cytometry comprises assaying and determining the relative binding activity (assay comprises a binding assay) (pg. 1110 column 2 1st full paragraph lines 1-18).
Regarding amended claim 88, Gan teaches screening the bead-DNA-protein complexes with flow cytometry in two rounds (second round of flow cytometry screening assay comprises performing an additional assay on the polypeptide) (pg. 1111 paragraph bridging column 1 & 2 lines 20-34).
Regarding claim 90, Gan teaches screening the bead-DNA-protein complexes with flow cytometry in two rounds (first and second round of flow cytometry screening assay (assay and additional assay) performed sequentially) (pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 5).
Regarding claim 92, Gan teaches screening the bead-DNA-protein complexes with flow cytometry in two rounds in which the second round comprises using a lower amount of input nucleic acid template, different gating, and selection of 13 specific samples for further sequencing (first and second round of flow cytometry screening assay (assay and additional assay) are performed under varying conditions) (pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 5).
Regarding claim 93, Gan teaches labeling and assaying the bead-DNA-protein complexes with a fluorescent labeled antibody through flow cytometry (performing the assay comprises fluorescent imaging) (pg. 1110 column 2 1st full paragraph lines 1-18; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 4; Figure 5).
Regarding claim 95, Gan teaches labeling and assaying the bead-DNA-protein complexes with a fluorescent labeled antibody through flow cytometry (solid surface comprises a flow cell) (pg. 1110 column 2 1st full paragraph lines 1-18; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 4; Figure 5).
Regarding claim 96, Gan teaches that around 0.5x106 nucleic acid molecules were used as the nucleic acid templates (library of nucleic acids) for the different mutants (library of nucleic acids comprises at least 1x105 nucleic acid variants) (pg. 1110-1111 paragraph bridging pg. 1110 & 1111 lines 10-27).
Regarding claim 97, Gan teaches the protein (polypeptide) comprises antibodies (plurality of polypeptides comprises a library of antibodies or binding fragments) (pg. 1109 paragraph bridging column 1 & 2 lines 1-4; pg. 1109 column 2 1st full paragraph lines 1-5; Figure 1).
Regarding claim 98, Green teaches the library of polypeptides comprises antigens (plurality of polypeptides comprises a library of antigens) (paragraph [0047] lines 1-4 & 19-21).
Claim(s) 85 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gan (Gan, Yamanaka, Kojima, & Nakano; Biotechnol. Prog., Vol. 24, pages 1107-1114, September 2008), as cited in the IDS dated 02/23/2023, and Green (United States Patent Application Publication US 2015/0018236 A1), as cited in the IDS dated 02/23/2023 as applied to claims 82-84, 86, 88, 90, 92, 93, & 95-101 above, and further in view of Khatwani (Khatwani et al.; Bioorganic & Medicinal Chemistry, Vol. 20, pages 4532-4539, May 2012).
The teachings of Gan and Green with respect to claims 82 & 84 are discussed above.
Regarding amended claim 85, Gan and Green does not teach covalently linking the polypeptide to the processed nucleic acid molecule.
Khatwani teaches a method of covalently linking protein (polypeptide) to oligodeoxynucleotides (nucleic acid molecules) through a click reaction (abstract lines 1-9; pg. 4534 column 2 1st full paragraph lines 1-10). Khatwani also teaches that this method is a simple and versatile method to covalently link proteins to nucleic acids compared to methods comprising copper (abstract lines 13-14).
Gan, Green, and Khatwani are considered to be analogous to the claimed invention because they are all in the same field of linking polypeptides to nucleic acids. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of linking proteins (polypeptides) on the ends of the nucleic acid templates linked to beads (processed nucleic acid) in Gan to incorporate the covalently linking the proteins to nucleic acids as taught in Khatwani because Khatwani teaches that doing so would provide a simple and versatile method to covalently link proteins to nucleic acids.
Claim(s) 87 & 91 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gan (Gan, Yamanaka, Kojima, & Nakano; Biotechnol. Prog., Vol. 24, pages 1107-1114, September 2008), as cited in the IDS dated 02/23/2023, and Green (United States Patent Application Publication US 2015/0018236 A1), as cited in the IDS dated 02/23/2023 as applied to claims 82-84, 86, 88, 90, 92, 93, & 95-101 above, and further in view of Hulme (Hulme & Trevethick; British Journal of Pharmacology, Vol. 161, pages 1219-1237, February 2010), as cited on the IDS dated 02/23/2023.
The teachings of Gan and Green with respect to claim 82 are discussed above.
Regarding amended claim 87, Gan and Green does not teach that the binding assay comprises an equilibrium binding assay.
Hulme teaches equilibrium binding assays for analysis of ligand binding under equilibrium conditions comprising strategies and experimental designs to appropriately measure binding at equilibrium (abstract lines 1-12; pg. 1220 column 1 3rd full paragraph lines 1-13; pg. 1220 column 2 1st full paragraph lines 1-10). Hulme also teaches that equilibrium binding assays are a straightforward method to analyze data and extract quantitative estimates of rate constant, affinity constants, and cooperativities (pg. 1220 column 1 3rd full paragraph lines 1-13).
Gan, Green, and Hulme are considered to be analogous to the claimed invention because they are all in the same field of analyzing binding activity of polypeptides. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of labeling and assaying the bead-DNA-protein complexes through flow cytometry comprises assaying and determining the relative binding activity in Gan to incorporate the use of an equilibrium binding assay as taught in Hulme because Hulme teaches that doing so would provide a straightforward method to analyze quantitative estimates of rate constant, affinity constants, and cooperativities.
Regarding claim 91, Hulme teaches particular set of equilibrium binding assay conditions lead to an upper limit on apparent affinity measured and that performing these binding assays at different temperatures to further analyze binding (assay performed under varying conditions) (abstract lines 7-9; pg. 1235 column 1 3rd full paragraph lines 1-11).
Claim(s) 89 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gan (Gan, Yamanaka, Kojima, & Nakano; Biotechnol. Prog., Vol. 24, pages 1107-1114, September 2008), as cited in the IDS dated 02/23/2023, and Green (United States Patent Application Publication US 2015/0018236 A1), as cited in the IDS dated 02/23/2023 as applied to claims 82-84, 86, 88, 90, 92, 93, & 95-101 above, and further in view of Elshal (Elshal & McCoy; Methods, Vol. 38, pages 317-323, November 2005).
The teachings of Gan and Green with respect to claims 82 & 88 are discussed above.
Regarding claim 89, Gan teaches assaying the bead-DNA-protein complexes with flow cytometry in two rounds (second round of flow cytometry screening assay comprises performing an additional assay on the polypeptide) (pg. 1111 paragraph bridging column 1 & 2 lines 20-34).
Gan and Green does not teach that the assay and the additional assay are performed simultaneously.
Elshal teaches a method of multiplex bead array assay for the detection of multiple target proteins in 96-well plate formats enabling simultaneous measurement and assaying of multiple target proteins comprising a cytometric (flow cytometry) array (assay and additional assay are performed simultaneously) (abstract lines 1-10; pg. 320 column 1 1st full paragraph lines 1-5; pg. 320 column 1 2nd full paragraph lines 1-8; pg. 320 column 1 3d full paragraph lines 1-3; pg. 323 column 1 1st full paragraph lines 1-5). Elshal also teaches that this multiplex bead array assay provides a high throughput analysis of numerous analytes comprising protein analytes (abstract lines 3-4 & 8-10).
Gan, Green, and Elshal are considered to be analogous to the claimed invention because they are all in the same field of assaying polypeptides through flow cytometry. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of assaying the bead-DNA-protein complexes with flow cytometry in two rounds (assay and additional assay) in Gan to incorporate the performing these rounds of assays simultaneously as taught in Elshal because Elshal teaches that doing so would provide a high throughput analysis of numerous analytes comprising protein analytes.
Response to Arguments
The response traverses the rejection. The response asserts that neither Gan nor Green, alone or in combination, teaches, suggests, or discloses all elements of claim 82 as, for example, neither Gan nor Green teaches or discloses “wherein (d) and (e) are performed on the same instrument” as recited in independent claim 82. Further, the response asserts that Gan does not further teach “wherein (d) and (e) are performed on the same instrument” as claimed and that Green does not cure this deficit of Gan, because Green at most teaches performing an assay on a polypeptide and sequencing a nucleic acid molecule on different instruments as, for example, Green provides a screening process where bee venom peptides are assayed followed by peptide isolation, DNA amplification, and DNA sequencing on a separate instrument in example 3. Further, the response asserts that Green discloses performing DNA sequencing on a separate instrument operated by a third party. This argument has been thoroughly reviewed but was not found persuasive. First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Second, Green is recited for teaching a method for screening and identifying polypeptides through isolating encoding nucleic acid molecules associated with polypeptides to analyze the biologically active polypeptide in which candidate polypeptides remain associated with their coding nucleic acid sequences (processed nucleic acid molecules) through beads and emulsion system so that active polypeptides can be identified by sequencing of the coding nucleic acid sequences (sequencing processed nucleic acid molecules to identify a processed nucleic acid molecule sequence and linking one or more properties of the polypeptide to the process nucleic acid molecule sequence) (paragraph [0008] lines 1-14; paragraph [0011] lines 1-18; paragraph [0111] lines 1-9). Therefore, Green is recited for teaching specific sequencing of a processed nucleic acid molecule to identify a processed nucleic acid molecule sequence and not for performing steps (d) and (e) on the same instrument. Further, as discussed and clarified above further, the recitation of “performed on the same instrument” is broad and is not further defined in the instant specification and therefore instrument is given its broadest reasonable interpretation to encompass a specialized physical device or tool designed and used to conduct experiments, take precise measurements, and gather data. Further, Gan teaches labeling the bead-DNA-protein complexes with a fluorescent labeled antibody and then assaying through flow cytometry (performing an assay on the polypeptide to identify one or more properties of the polypeptide), followed by an additional round of screening comprising selection and sequencing of samples (performing an assay on the polypeptide and sequencing performed on the same bead system instrument designed to take precise measurements and gather data) (abstract lines 1-16; pg. 1108 column 1 1st full paragraph lines 1-21; pg. 1108 column 2 1st full paragraph lines 1-14; pg. 1109 paragraph bridging column 1 & 2 lines 1-4; pg. 1109 column 2 1st full paragraph lines 1-17; pg. 1110 column 2 1st full paragraph lines 1-18; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 1). Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of coupling protein to its coding DNA on magnetic microbeads comprising labeling and assaying bead-DNA-protein complexes through flow cytometry, followed by an additional round of screening comprising selection and sequencing of samples (performing assay on polypeptide and sequencing performed on same instrument to take precise measurements and gather data) in Gan to incorporate the specific sequencing of coding nucleic acid sequences (processed nucleic acid molecules) to identify polypeptides and link one or more properties of a polypeptide to the processed nucleic acid molecule sequence as taught in Green because Green teaches that doing so would provide a highly efficient method to identify polypeptides and effectively screen a vast amount of sequences.
The response also asserts that a person of ordinary skill in the art would not be motivated to modify Gan or Green to arrive at the claimed methods with a reasonable expectation of success as Gan relates to the use of bead-DNA complexes and analysis via a flow cytometer in which the beads with signals were collected and the genes were amplified for the next round of screening and thus Gan identifies positive hits and selectively collects those for future screening by performing PCR on the collected DNA from positive hits, removing them from the instruments and purifying and, as discussed above, Green similarly discloses a PCR step on positive hits prior to sequencing using a third party. Further, the response asserts that, a person of skill in the art, even if motivated to perform assays of Gan and sequence the positive hits, would have no reason to perform sequencing using Gan’s flow cytometer/FACS machine such that assaying and sequencing would be performed on the same instrument and, if anything, Green’s disclosure of providing DNA to a sequencing company would motive an artisan to remove the hits from the flow cytometer and send those nucleic acids to a specialized service or apparatus. Further, the response asserts that such modification to performing sequencing using the flow cytometer or FACS of Gan would have no reasonable expectation of success, as it is wholly unclear from the references how an artisan would even attempt to sequence nucleic acids using the flow cytometer. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed and clarified above further, the recitation of “performed on the same instrument” is broad and is not further defined in the instant specification and therefore instrument is given its broadest reasonable interpretation to encompass a specialized physical device or tool designed and used to conduct experiments, take precise measurements, and gather data. Further, Gan teaches labeling the bead-DNA-protein complexes with a fluorescent labeled antibody and then assaying through flow cytometry (performing an assay on the polypeptide to identify one or more properties of the polypeptide), followed by an additional round of screening comprising selection and sequencing of samples (performing an assay on the polypeptide and sequencing performed on the same bead system instrument designed to take precise measurements and gather data) (abstract lines 1-16; pg. 1108 column 1 1st full paragraph lines 1-21; pg. 1108 column 2 1st full paragraph lines 1-14; pg. 1109 paragraph bridging column 1 & 2 lines 1-4; pg. 1109 column 2 1st full paragraph lines 1-17; pg. 1110 column 2 1st full paragraph lines 1-18; pg. 1111 paragraph bridging column 1 & 2 lines 20-34; Figure 1). Second, as discussed above, Green is recited for teaching specific sequencing of a processed nucleic acid molecule to identify a processed nucleic acid molecule sequence and not for performing steps (d) and (e) on the same instrument. Further, even though Green is not relied upon for teaching performing steps (d) and (e) on the same instrument, given the broadest reasonable interpretation of the same instrument, as discussed further above, Green teaches steps of analyzing biologically active polypeptides and sequencing coding nucleic acid sequences (sequencing processed nucleic acid molecule) on instruments that take precise measurements and gather data (same instrument). Third, as discussed above, the instant specification does not define “performed on the same instrument” and discusses an example in which the beads displaying DNA with fluorescently incorporated base (sequencing by synthesis) and polypeptide bound to fluorescently-labeled antibody (assay of polypeptide binding function) are then put on the sequencing instrument, here a flow cytometer, in order to read the sequence and the binding of each bead on the same instrument (paragraph [0143] of the instant specification). Therefore, interpreting in light of the specification, Gan also fits this interpretation of wherein (d) and (e) are performed on the same instrument.
The response also asserts that independent claim 82, in addition to claims 83, 84, 86, 88, 90, 92, 93, & 95-101 dependent therefrom, are not obvious over Gan in view of Green. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
The response also asserts that Khatawani fails to cure the abovementioned deficiencies of Gan Green and claim 85, which is dependent from independent claim 82, and includes all elements of claim 82, is therefore non-obvious over the asserted references at least for the same reasons. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
The response also asserts that Hulme fails to cure the abovementioned deficiencies of Gan Green and claims 87 & 91, which is dependent from independent claim 82, and includes all elements of claim 82, is therefore non-obvious over the asserted references at least for the same reasons. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
The response also asserts that Elshal fails to cure the abovementioned deficiencies of Gan Green and claim 89, which is dependent from independent claim 82, and includes all elements of claim 82, is therefore non-obvious over the asserted references at least for the same reasons. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 82-93 & 95-98 are rejected.
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 BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
