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 . Applicant’s amendment filed 3/4/2026 is acknowledged. Claims 1-22 have been canceled. Claim 41 has been amended. Claims 23-42 are pending. Claims 31-33 and 42 are withdrawn from consideration as being drawn to a non-elected invention.
All of the amendments and arguments have been thoroughly reviewed and considered. Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims.
This action is made 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.
The substitute specification filed 3/4/2026 is acknowledged and has been entered.
Previous Rejection
The objection of the specification is withdrawn in view of Applicant’s amendment and submission of a substitute specification. The rejection under 35 USC 112 second paragraph is withdrawn in view of Applicant’s amendment of the claim. The prior art rejections under 35 USC 103 are maintained and discussed below. The double patenting rejection is maintained and discussed below.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim(s) 23-25, 28-30 and 34-41 is/are finally rejected under 35 U.S.C. 103 as being unpatentable over Banerjee et al {Banerjee, used interchangeably herein} (US 20100111768, May 2010) in view of Tsien et al (WO 9106678) and further in view of Rothberg et al (WO 0120039).
Regarding claims 23-25, 28-30, 34-41, Banerjee teaches a method of sequencing of nucleic acid comprising the use of a substrate that comprise a flowcell. Flowcells may have one or more fluidic channels in which the polynucleotide is displayed (e.g., wherein the polynucleotides are directly attached to the flowcell or wherein the polynucleotides are attached to one or more beads arrayed upon the flowcell. The flowcells may comprise of glass, silicon, plastic, or various combinations thereof (para. [0009]). The flowcells may be placed into flowcell holders such that chemistry operations can be performed in parallel order (see e.g., [0048]). Banerjee al teach that the nucleic acid to be sequence can be immobilized upon a substrate (e.g., a substrate within a flowcell or one or more beads upon a substrate such as a flowcell, (etc. [0061]). Banerjee et al teach wherein the nucleic acid may be non-covalently attached to the substrate and that any suitable sequencing technique may be used with the methodology [0063], such as sequencing-by-synthesis (SBS). Banerjee teaches a temperature control system that regulates the temperature of the support/substrate and/or of the reagents [0007]. The reference teaches that in some instances, the substrate (support) can move away from a detector in order to interact with the temperature control system for both heating and/or cooling (where ([0008], [0068], [0085], [0094]-[0095]).
Banerjee teaches at para. [0064] in SBS, four fluorescently labeled modified nucleotides are used to sequence dense clusters of amplified DNA (possibly millions of clusters) present on the surface of a substrate (e.g., a flowcell).
At para. [0065] - [0066], Banerjee et al teach:
[0065] In particular uses of the systems/devices herein the flowcells containing the nucleic acid samples for sequencing are placed within the appropriate flowcell holder of the present invention. The samples for sequencing can take the form of single molecules, amplified single molecules in the form of clusters, or beads comprising molecules of nucleic acid. The nucleic acids are prepared such that they comprise an oligonucleotide primer adjacent to an unknown target sequence. To initiate the first SBS sequencing cycle, one or more differently labeled nucleotides, and DNA polymerase, etc., are flowed into/through the flowcell by the fluid flow subsystem. Either a single nucleotide can be added at a time, or the nucleotides used in the sequencing procedure can be specially designed to possess a reversible termination property, thus allowing each cycle of the sequencing reaction to occur simultaneously in the presence of all four labeled nucleotides (A, C, T, G). Where the four nucleotides are mixed together, the polymerase is able to select the correct base to incorporate and each sequence is extended by a single base. In such methods of using the systems of the invention, the natural competition between all four alternatives leads to higher accuracy than wherein only one nucleotide is present in the reaction mixture (where most of the sequences are therefore not exposed to the correct nucleotide). Sequences where a particular base is repeated one after another (e.g., homopolymers) are addressed like any other sequence and with high accuracy.
Banerjee teaches at para. [0066], the fluid flow subsystem also flows the appropriate reagents to remove the blocked 3' terminus (if appropriate) and the fluorophore from each incorporated base. The substrate can be exposed either to a second round of the four blocked nucleotides, or optionally to a second round with a different individual nucleotide. Such cycles are then repeated and the sequence of each cluster is read over the multiple chemistry cycles.
Banerjee et al teach that placement and movement of the flowcell (and thus the nucleic acids to be sequenced) is controlled and secured by e.g., a movable stage upon which the flowcell and flowcell holders (or other substrate) are located [0106].
Banerjee summarizes another embodiment of SBS at paragraphs 0201-0204: [0201] As an overview, in particular examples of sequencing by SBS, genomic DNA is randomly fragmented, end capped with known sequences, and covalently attached to a substrate (such as the channel in a flowcell), e.g., by hybridization to a covalent primer. From such attached DNA, an array of nucleic acid clusters is created. SBS analysis can generate a series of images of the clusters, which can then be processed to read the sequence of the nucleic acids in each cluster which can then be aligned against a reference sequence to determine sequence differences, a larger overall sequence, or the like. [0203] After the incorporation step wherein a fluorescently labeled nucleotide is bound to the nucleic acid of the members of the clusters through a cleavable linker, the channels of the flowcell are washed out by the fluid flow subsystem in order to remove any unincorporated nucleosides and enzyme. [0204].
With regards to the limitation, “wherein the solid supports are unencapsulated”, Banerjee teaches that the substrates may comprises of one or more beads arrayed upon the flowcell and can be comprised of glass, silicon, plastic or various combinations and further wherein the polynucleotides are directly attached to the flowcell or attached to the beads ([0009]). The reference teaches that the polynucleotides can be directly covalently attached an intermediate material and the intermediate material non-covalently attached to the substrate or matrix, e.g., glass substrate [0062]). The instant specification supports this interpretation at page 7.
Banerjee teaches blocking solutions comprising 50 mM potassium acetate, 20 mM Tris-acetate, 10 mM magnesium acetate, 1 mM dithiothreitol (pH 7.9) and washing solution comprising Tween ([0237] –[0261]).
Banerjee does not expressly recite wherein the method comprises the use of a regeneration solution in another container.
However, with regards to the regeneration solution, the specification states that the regeneration and/or washing solution may comprise of a reagent that can simultaneously remove a label from the labeled sequencing probe or a reagent that can remove the labeled sequencing probe from the nucleic acid molecule (page 11). The specification teaches that the labeled nucleotide and the reagent for removing the label from the labeled nucleotide suitable for use in the sequencing-by-synthesis is well known in the art, (page 12).
Tsien et al teaches a DNA sequencing method wherein said method can be carried out in a single reaction zone with multiple differentiable reporters or in multiple reaction zones with a single reported in each zone. It can be carried out by detecting the incremental signal change after addition of reporter or by noting each added reporter separately (page 7). The various reporters can be measured in the reaction zones while attached to the growing molecule or they can be separated from the molecule and them measured (page 7). Tsien et al teach in the Figure 3 wherein the method may employ four reaction zones in which in each of the four zones, a different one of the four nucleotides is associated with a reporter so that the identity of the nucleotide incorporated at each state can be determined (page 8). Tsien et al teach the utilization of 3’ blocking agents (page 10 and 12), washing solutions and deblocking or regeneration solution which is carried out in a reaction zone followed by a wash (page 13). Tsien et al teach that the process is repeated as need and is easily automated. Tsien discusses exemplary disclosures of blocking reagents (pages 15-17 and 20-23) and deblocking (regeneration) solutions (see e.g., pages 15-17 and 24, 25, 28. See also example 5 which discuss a deblocking solution). Tsien et al teach that a blocking solution is employed to prevent inadvertent extra addition during the synthesis reaction and must meet the criteria of having the ability to accurately and efficiently incorporate the nucleotide carrying the 3’-blocking groups into the cDNA chain and the availability of mild conditions for rapid and quantitative regeneration (pages 20 and 21). Tsien et al teaches that the deblocking solutions are used to remove blocking groups to allow chain synthesis to continue to occur (page 23). See also Example 5 which discuss both the use of deblocking and wash solution to a reaction chamber. Tsien et al teaches that the method is advantageous because it allows the sequencing method steps to be perform in stages and repeated as needed to grow out in portions the complementary DNA chain (page 8).
Further with regards to the separate reaction containers, Rothberg, like Banerjee and Tsien, teach a method of sequencing which encompasses a plurality of solid supports having nucleic acid molecules immobilized herein wherein the method further comprises a sequencing apparatus which comprises of a plurality of tubes which allows for entry of sequencing reagents which each of the tubes are in communication with a plurality of sequencing dispensing reagent vessels (page 30). Rothberg teach that the sequencing apparatus is designed to allow linear flow solution over the surface of the substrate surface to allow for fast exchange of reagents (page 32, lines 1-2).
It would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to combine the teachings of Banerjee with the teachings of Tsien and Rothberg because all of the cited prior art are directed to improved methodologies of performing sequencing assays of nucleic acids using similar techniques. The ordinary artisan would have been motivated to utilize multiple containers (reaction zones) and a regeneration solution as taught by Tsien et al and Rothberg into the sequencing method of Banerjee for the advantages taught by Tsien et al that the method allowances the sequencing method to be performed in stages and repeated as needed which increases cost and efficiency as taught by Tsien et al and advantages by Rothberg that the use of multiple reagent tubes (containers) in the sequencing reaction allows for fast exchange of reagents which further increases efficiency of the sequencing analysis.
Response to Response
Applicant’s traversal
6. Applicant traverses the rejection on the following grounds:
(a) Applicant summarizes the claimed invention and states that none of the cited references disclose or suggest (i) adopting a contact reaction protocol (“contacting solid support with reaction solutions”) in a non-flow design; or (ii) that the solid supports are in an unencapsulated state, and reaction control is not achieved relying on closed chambers such as flowcells, closed reaction zones, or perfusion chambers.
(b) Applicant states that Banerjee adopts a flowcell structure and reaction solution continuously flow through the flow cell channel via a fluid direction system belonging to a continuous flow reaction system. Applicant states that Banerjee has a different type of solid support than what is claimed. Specifically, the solid supports in Banerjee are encapsulated within the flowcells channels and reagent flow and reaction control are achieved relying on the closed structure of the flow cell. Applicant states that Tsien has different structures of reaction zones than what is claimed. Applicant states that Tsien is a closed reaction zone structure and the carriers are encapsulated within the closed reaction zone which is distinct from what is claimed. Applicant states that Rothberg teaches solid supports fixed within the perfusion chamber or optical fiber array belonging to an encapsulated design, unable to react independently outside the chamber; the unencapsulated supports in the claim 23 can be operated flexibly without being restricted by the chamber structure. Applicant states that all of the cited references are silent about using unencapsulated supports. Applicant states that the prior art does not recognize the disadvantages such as complex instruments, channel blockage and adaptability problems.
Examiner’s Response
7. All of the amendment and arguments have been thoroughly reviewed and considered: The examiner acknowledges Applicant’s arguments at (a) through (c) above but respectfully disagree. In response to Applicant’s arguments concerning the lack of a teaching of unencapsulated solid support, firstly, neither the specification nor the claims provide a limiting definition for the term “unencapsulated” as it relates to “solid supports”. Secondly, given the broadest reasonable interpretation in light of a lack of limiting definition in the specification, “unecapsulated solid supports”, may be interpreted “sequencing reagents flowed over the surface of a solid support matrix (i.e., anchor pads), wherein delivery of various sequencing reagents is performed by immersion of cavities of the support” such as taught by Rothberg et al (page 45). With regards to Applicant’s arguments concerning the art not recognizing the disadvantages such as complex instruments, channel blockage and adaptability problems caused by encapsulated supports + flow reaction, this argument is not commensurate in scope with the claims as currently filed because neither the claims nor specification provide a limiting definition of the term “unencapsulated solid supports”. In fact, no recitation of the term “unencapsulated” is even recited in the specification. Thus, given the broadest reasonable interpretation, the examiner maintains that the cited prior art meets the limitation of the claims. Applicant is reminded that KSR forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See the Board decision Ex parte Smith, --USPQ2d--, slip op. at 20, (Bd. Pat. App. & Interf. June 2007) (citing KSR, 82 USPQ2d at 1396). Applicant’s arguments are not found persuasive to obviate the claimed rejection.
Double Patenting
8. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
9. Claims 23, 26-30 and 34-41 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6 and 10-19 of U.S. Patent No. 11/692,221 (US Patent ‘221 used interchangeably herein).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the claim 23 of the instant invention and the claim 1 of US Patent ‘221 are directed to a method for sequencing a nucleic acid using a contact reaction protocol which the instant specification defines throughout as an immersion reaction protocol, comprising the steps of a) providing a first batch of solid supports having nucleic acid molecules immobilized thereon, b) contacting the nucleic acid molecules immobilized on the solid supports with one or more reaction solutions to generate a signal representing one or more nucleotides that bind to the nucleic acid molecules on the solid supports, wherein each of the one or more reaction solutions is placed in a separate reaction container, wherein, after removing the contact between the solid supports and the reaction solutions, contacting the solid supports with one or more washing solutions to remove the reaction solutions remaining on the solid supports, c) detecting the signal on the solid supports, and f) optionally, repeating the steps b) to c), wherein the first batch of solid supports consists of one or more solid supports.
The claim 23 of the instant invention only varies slightly in wording from the claim 1 of US Patent ‘221 and clearly comprise of a species/genus relationship.
The limitations of the claim 24 of the instant invention are embodied in the claim 1 of US Patent ‘221.
The limitations of the claim 26 of the instant invention are embodied in the claim 2 of US Patent ‘221.
The limitations of the claims 27 of the instant invention are embodied in the claim 3 of US Patent ‘221.
The limitations of the claim 28 of the instant invention are embodied in the claim 4 of US Patent ‘221.
The limitations of the claim 29 of the instant invention are embodied in the claim 5 of US Patent ‘221.
The limitations of the claim 30 of the instant invention are embodied in the claim 6 of US Patent ‘221.
The limitations of the claim 34 of the instant invention are embodied in the claim 10 of US Patent ‘221.
The limitations of the claim 35 of the instant invention are embodied in the claim 11 of US Patent ‘221.
The limitations of the claim 36 of the instant invention are embodied in the claim 12 of US Patent ‘221.
The limitations of the claim 37 of the instant invention are embodied in claim 13 of US Patent ‘221.
The limitations of the claim 38 of the instant invention are embodied in the claims 14, 15 and 17 of Patent ‘221.
The limitations of the claim 39 of the instant invention are embodied in the claim 16 of Patent ‘221.
The limitation of the claim 40 of the instant invention are embodied in the claim 18 of US Patent ‘221.
The limitation of the claim 41 of the instant invention are embodied in the claim 19 of US Patent ‘221.
The claims 23, 26-30 and 34-41 of the instant invention falls entirely within the scope of the claims 1-6 and 10-19 of US patent 11/692,221. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), “a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
10. Claims 23-30, 34-39 and 41 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 23-32 and 36-41 of copending Application No. 18/144124 {copending ‘124 used interchangeably herein}.
Although the claims at issue are not identical, they are not patentably distinct from each other because both the claim 23 of the instant invention and the claim 23 of copending application ‘124 are directed to a method for sequencing a nucleic acid using a contact reaction protocol, comprising the steps of a) providing a first batch of solid supports having nucleic acid molecules immobilized thereon, b) contacting the nucleic acid molecules immobilized on the solid supports with one or more reaction solutions to generate a signal representing one or more nucleotides that bind to the nucleic acid molecules on the solid supports, removing the contact between the solid supports and the reaction solutions and contacting the solid supports with first washing reagents, c) detecting the signal on the solid supports, and f) optionally, repeating the steps b) to c), wherein the reaction solutions and the first washing reagents are reused (repeated) at least once, wherein the first batch of solid supports consists of one or more solid supports. The claim 23 of the instant invention only varies slightly in wording from the claim 23 of US Patent ‘124 and clearly comprise of a species/genus relationship.
The limitations of the claim 24 of the instant invention are embodied in the claim 31 of copending application ‘124.
The limitations of the claim 25 of the instant invention are embodied in the claim 24 of copending application ‘124.
The limitations of the claims 26 of the instant invention are embodied in the claim 23 of copending application ‘124.
The limitations of the claim 27 of the instant invention are embodied in the claim 25 of copending application ‘124.
The limitations of the claim 28 of the instant invention are embodied in the claim 31 of copending application ‘124.
The limitations of the claim 29 of the instant invention are embodied in the claim 39 of copending application ‘124.
The limitations of the claim 30 of the instant invention are embodied in the claim 32 of copending application ‘124.
The limitations of the claim 34 of the instant invention are embodied in the claim 36 of copending application ‘124.
The limitations of the claim 35 of the instant invention are embodied in the claim 37 of copending application ‘124.
The limitations of the claim 36 of the instant invention are embodied in the claim 38 of copending application ‘124.
The limitations of the claim 37 of the instant invention are embodied in claim 39 of copending application ‘124.
The limitations of the claim 38 of the instant invention are embodied in the claim 40 of copending application ‘124.
The limitations of the claim 39 of the instant invention are embodied in the claim 37 of copending application ‘124.
The limitation of the claim 41 of the instant invention are embodied in the claim 41 of copending application ‘124.
The claims 23-30, 34-39 and 41 of the instant invention falls entirely within the scope of the claims 23-32 and 36-41 of US patent 18/144124. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), “a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
11. Applicant traverses the rejection on the grounds that the claims of the present invention are distinct from the 11/692221 and 18144124 in view of the foregoing response to the obvious rejection and as such there is no obviousness type double patenting. Applicant state that a terminal disclaimer will be filed at a later date, if necessary, when patentable subject matter is identified.
12. All of the amendment and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons that follows. The examiner acknowledges Applicant’s arguments but respectfully disagree because the inventions of 11/692224 and 18/1444121 comprise of overlapping scope and clearly have a species genus/relationship. Since double patenting rejections are not “as to form”, the USPTO does not hold such rejections in abeyance. A proper terminal disclaimer in compliance with 37 CFR 1.321(c) or (d) is required to overcome the double patenting rejection.
Conclusion
14. No claims are allowed. 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 CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681
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