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 1-3, 7, 9, 11, 15-19, 22, 24, 28-29, 31-32 and 36-38 are pending, and are being examined on the merits.
Election/Restrictions
Applicant’s election without traverse of the species for Groups A, B and C in the reply filed on November 13, 2025 is acknowledged. However, since art was found on both the elected species and the non-elected species, all of the species and all of the claims are considered in this Office Action. The election of species requirement is withdrawn.
Information Disclosure Statement
The Information Disclosure Statements submitted December 8, 2022, January 11, 2023, February 23, 2023, April 10, 2023, July 17, 2024, September 12, 2024, December 20, 2024 and April 11, 2025 have each been considered.
Specification
The disclosure is objected to because of the following informalities: Para. 1 should be updated to indicate that the instant application is a national stage filing under 35 USC § 371 of PCT/US2021/033191.
Appropriate correction is required.
The use of the terms for various reporter and quencher molecules, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following each term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Specifically, the following trademarks appear in the specification, at least, at paras. 188-190, 211-213, 251, 359: Cy[X], ATTO[X], TWEEN[X], TRITON[X], Texas Red [X], BODIPY [X], Cascade Blue [X], Lucifer Yellow [X], Alexa Fluor [X], DyLight, CAL Fluor, JOE, Oregon Green, WellRED, IRDyes.
Claim Objections
Claims 1, 22 and 37 are objected to because of the following informalities:
In claim 1, the limitation “said nucleic acid sequence or to produce …” in l. 1 of step (b)
should be “said nucleic acid sequence to produce …”. Further, the limitation “is performed in absence” in l. 3 of step (d) should be “is performed in the absence in the absence”.
In claim 22, the limitation “to determine identity” in l. I of step (ii) should be “to determine the identity”.
In claim 37, the word “sequence” in l. 2 should be “sequences”.
Appropriate correction is required.
Claim Interpretation
Claims 22, 24 and 28 each recite, in part, a “polymer-nucleotide conjugate”. The term “polymer-nucleotide conjugate” does not have a fixed meaning in the art, however, the instant specification describes it as “a polymer core and a detectable label coupled thereto” (para. 5), and as “a polymer core and a plurality of nucleotide moieties attached thereto” (para. 8). An embodiment of polymer-nucleotide conjugate is shown in Fig. 28 (para. 50). Thus, the broadest reasonable interpretation of the term “polymer-nucleotide complex”, when read in light of the specification, is a construct comprising a polymer core with nucleotides moieties and a detectable label attached thereto.
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 9, 17-19 and 36 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Indefiniteness rejections
Claim 9 recites that the plurality of colonies comprising the primed nucleic acid sequence is present at a surface density of greater than or equal to about 300K/mm2. Claim 9 additionally recites an optional limitation indicating that the colony density is additionally less than or equal to about 500K/mm2. It is not clear how both of these limitations can be met at the same time, at least in some embodiments. That is, in embodiments where the colony density in the optional limitation is below 300K/mm2, both limitations cannot be met at the same time. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claim 18, which incorporates claim 1 steps (a) through (d), additionally recites the limitations “(e) performing a primer extension reaction on said primed nucleic acid sequence”, and “(f) repeating (a) to (e) for each successive nucleotide to identify a sequence of said primers nucleic acid sequence”. The meaning of these additional limitations is unclear. Specifically, step (e) is presented following step (d), however, it is not clear if the method steps are intended to be practiced in that order. That is, step (c) recites contacting the circular nucleic acid sequence with a primer to produce a primed nucleic acid sequence, while step (d) recites performing a nucleotide binding reaction with the primed nucleic acid sequence to identify a nucleotide of said primed nucleic acid sequence. It is not clear if it is intended that step (e) is then requiring an additional primer extension step that is performed after the (d) nucleotide identification step, or if it is intended that step (e) is supposed to occur after step (c), i.e., by extending the primer sequence, and prior to the (d) nucleotide identification step. Further, repeating steps (a) through (d) “for each successive nucleotide” would require repeating the nucleic acid coupling step, the enzymatically circularizing step and the primer contacting step for each successive nucleotide in the original nucleic acid sequence. It is also not clear if that is the intended order of the method steps. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Claim 19 depends from claim 18, and consequently incorporates the limitations of claim 18.
Lack of antecedent basis rejections
Claim 17 recites in ll. 1-2 that, prior to step (c) (of claim 1), "said circular nucleic acid sequence or derivative thereof" is amplified. There is insufficient antecedent basis for this limitation in the claim. That is, a derivative of said circular nucleic acid appears in step (c) of claim 1, but not prior to it, thus there is no derivative prior to step (c) that can be amplified. Similarly, claim 36 recites two instances of “said nucleic acid … derivative” in reference to the enzymatically circularizing step, which is also prior to step (c). These instances in claim 36 are rejected with the same reasoning.
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 9, 11, 15-19, 29, 31-32 and 36-38 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac (US Patent App. Pub. No. 2017/0175184 A1).
Regarding independent claim 1, Drmanac teaches …
A method of nucleic acid sequencing, said method comprising: (a) bringing a nucleic acid sequence into contact with a surface under conditions sufficient to couple said nucleic acid sequence to said surface (Fig. 1A; paras. 39, 136; Method 1: paras. 126-129: “the adapter can be prepared with an internal biotin … to allow for … direct amplification on the surface);
(b) enzymatically circularizing said nucleic acid sequence to produce a circular nucleic acid sequence (Fig. 1A; paras. 47, 136);
(c) contacting said circular nucleic acid sequence or a derivative thereof with a primer sequence complementary thereto, thereby producing a primed nucleic acid sequence (Figs. 1A, 1E; paras. 39, 136);
and (d) performing a nucleotide binding reaction with said primed nucleic acid sequence to identify a nucleotide of said primed nucleic acid sequence, which nucleotide binding reaction is performed in absence of incorporation of a nucleotide into said primed nucleic acid sequence (paras. 89, 136: sequencing by hybridization (“SBH”)).
Although Drmanac teaches all of the limitations of claim 1, it does not do so in a single embodiment. Specifically, the step (a) limitation “under conditions sufficient to couple said nucleic acid sequence to said surface” is taught in a separate embodiment from the remainder of the claim 1 steps. However, it would have been obvious to modify the cited Drmanac embodiment to incorporate a step where the nucleic acid sequence is coupled to the surface, or is capable of being coupled to the surface.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the cited Drmanac method with the step of coupling (or of making capable of being coupled) the nucleic acid sequence to the surface. The ordinary artisan would have been motivated to do so to achieve the expected advantage of allowing easy removal of unwanted reaction components (through washing) while retaining the target nucleic acid sequence on the surface. The ordinary artisan would have had an expectation of success as Drmanac specifically teaches that such nucleic acid sequences can be directly attached to the surface.
Regarding dependent claim 2, Drmanac additionally teaches that the enzymatically circularizing the nucleic acid sequence comprises performing splint ligation (Fig. 2A; paras. 48, 158-159).
Regarding dependent claim 9, Drmanac additionally teaches that the plurality of colonies is present at a surface density of greater than 300K/mm2 (para. 29: more than 10,000, 100,000 or 1 million spots/mm2).
Regarding dependent claim 11, Drmanac additionally teaches that the primed nucleic acid sequence comprises one or more adaptors comprising an index site having a sequence complementary to at least a portion of a capture nucleic acid molecule coupled to the surface (paras. 34, 46: DNA circles comprising an adapter sequence with an index site are formed – the DNA circles then have a primer hybridized to them and the primer is extended in RCA, thus generating a population of concatemers comprising the complement of the adapter oligonucleotide and the DNA fragment – the complement of the adapter is also considered an adapter sequence).
Regarding dependent claim 15, Drmanac additionally teaches that the surface comprises a hydrophilic polymer layer coupled thereto (para. 53: polyacrylamide-coated glass).
Regarding dependent claim 16, Drmanac additionally teaches that the primed nucleic acid sequence comprises a concatemer of two or more repeats of an identical sequence (Fig. 1A; paras. 10, 31, 87).
Regarding dependent claim 17, Drmanac additionally suggests amplifying the circular nucleic acid sequences using RCA prior to step (c). Specifically, Drmanac teaches modifying amplification steps depending on the target nucleic acid (e.g., paras. 29, 34, 45, 126, 129).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to arrive at the amplification steps of claim 17. The ordinary artisan would have been motivated to do so customize the assay as needed through routine optimization, and would have had an expectation of success as the design and modification of nucleic acid amplification assays is well-known in the art.
Regarding dependent claims 18-19, as noted above in conjunction with the 35 USC §112(b) rejections, the (e) and (f) limitations in claim 18 are unclear. However, Drmanac teaches performing a primer extension reaction on the primed nucleic acid sequence, and repeating the steps for each successive nucleotide to identify a sequence of said primed nucleic acid sequence (Fig. 1A; paras. 15, 33, 89, 136). Drmanac also teaches various times associated with the steps (e.g., para. 108).
Regarding dependent claim 29, Drmanac additionally teaches or suggests that enzymatically circularizing comprises (i) hybridizing a 5’ end of a single-stranded nucleic acid molecule to a 3' end of said nucleic acid sequence and hybridizing a 3' end of said single-stranded nucleic acid molecule to a 5' end of said nucleic acid sequence, or (ii) hybridizing a 3' end of a single-stranded nucleic acid molecule to a 5' end of said nucleic acid sequence and hybridizing a 5' end of said single-stranded nucleic acid molecule to a 3' end of said nucleic acid sequence (Fig. 2A; paras. 48, 128-129, 158-159). Specifically, Drmanac teaches, in part, circularizing the (target) nucleic acid sequence by hybridizing it to the (splint) single-stranded nucleic acid molecule. It does not explicitly teach which end of the splint hybridizes to the target first, but the ordinary artisan understands that there are only a limited number options (perhaps, the 2 recited options) that can occur in this step.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to arrive at the claim limitations of claim 29. The ordinary artisan would have been motivated to do so customize the assay as needed through routine optimization, and would have had an expectation of success as there are only two options to select from.
Regarding dependent claim 31, Drmanac additionally teaches or suggests that the nucleic acid sequence comprises one or more UMIs at a 5’ end or a 3’ end (Fig. 8; paras. 34, 46, 128-129). Specifically, Drmanac teaches attaching UMIs to the nucleic acid sequence via an adapter, and teaches that adapters can be attached at either the 5’ end or the 3’ end of the nucleic acid sequence.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to arrive at the claim limitations of claim 31. The ordinary artisan would have been motivated to do so customize the assay as needed through routine optimization, and would have had an expectation of success as there are only two options of positions to attach the UMI to the nucleic acid sequence.
Regarding dependent claim 32, Drmanac additionally teaches adding one or more adaptors to a 5’ end or a 3’ end of said nucleic acid sequence comprising an index site having a nucleic acid sequence coupled to the surface (Method 1: paras. 126-129: “the adapter can be prepared with an internal biotin … to allow for … direct amplification on the surface), and suggests that the nucleic sequence has at least a portion corresponding to at least a portion of a capture nucleic acid molecule. Specifically, Drmanac teaches attaching a nucleic acid to the surface through the use of a corresponding portion of a capture nucleic acid molecule in another embodiment (para. 46).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to attach the nucleic acid sequence to the surface through hybridization with at least a portion of a capture nucleic acid molecule. The ordinary artisan would have been motivated to do so customize the assay as needed through routine optimization, and would have had an expectation of success as Drmanac teaches that nucleic acid sequences can be coupled to surfaces in such a manner.
Regarding dependent claim 36, Drmanac additionally teaches that the enzymatically circularizing the nucleic acid sequence comprises ligating a 5’ end and a 3’ end of the nucleic acid sequence together under conditions sufficient to produce the circular nucleic acid sequence (Fig. 1A; paras. 47, 136).
Regarding dependent claim 37, Drmanac additionally teaches performing steps (a) through (d) for a plurality of nucleic acid sequences (Fig. 1A; paras. 89, 136).
Regarding dependent claim 38, Drmanac additionally teaches incorporating a nucleotide into the primed nucleic acid sequence (Fig. 1A; para. 33: rolling circle replication).
Claims 22, 24 and 28 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac (US Patent App. Pub. No. 2017/0175184 A1 as applied to claim 1 above, and further in view of O’Malley (US Patent App. Pub. No. 2004/0023248 A1).
Regarding dependent claim 22, Drmanac additionally teaches that the nucleotide binding reaction in (d) comprises: (i) bringing the primed nucleic acid sequence into contact with one or more polymer-nucleotide conjugates under conditions sufficient to form a stable multivalent binding complex between a nucleotide moiety of said one or more polymer-nucleotide conjugates and a nucleotide of said primed nucleic acid sequence. Specifically, Drmanac teaches the use of linear and branched polymers to which target polynucleotides are attached (e.g., para. 40), but does not teach using the conjugate as described in claim 22 (ii).
However, O’Mally teaches (ii) detecting the stable multivalent binding complex to determine the identity of said nucleotide of said primed nucleic acid sequence or derivative thereof. Specifically, O’Malley teaches contacting the target nucleic acid sequence with a polymer-conjugate with a detectable label (e.g., Fig. 1; paras. 5, 7, 10).
Regarding dependent claims 24 and 28, O’Malley teaches (paras. 5, 10, 16) that the polymer-nucleotide conjugates two or more types of conjugates, as recited in claim 24, and that the plurality of types each comprise a distinct detectable label, as recited in claim 28.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to use the polymer-nucleotide conjugate to determine the identity of the primed nucleic acid sequence, as taught by O’Malley. Drmanac teaches the need for improved detection schemes for high density arrays. O’Malley teaches that the polymer-nucleotide conjugates are particularly useful to detect target nucleic acids on microarrays and are highly sensitive compared to other detection methods used with microarrays. Thus, the ordinary artisan would have been motivated to further modify the modified Drmanac method to achieve the expected advantage of a microarray with an improved detection sensitivity. The ordinary artisan would have had an expectation of success as the substitution of detection schemes is well-known in the art, and because O’Malley teaches that the detection system is highly useful for microarrays.
Claims 3 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac (US Patent App. Pub. No. 2017/0175184 A1) as applied to claim 1 above, and further in view of Ammar (A comparative analysis of DNA barcode microarray feature size, BMC Genomics, 10:471, 1-7, 2009).
Regarding dependent claim 7, Ammar teaches that the surface density of about 4,000
oligonucleotides per µm2 (p. 2, left col., para. 2).
Regarding dependent claim 3, as noted above, Drmanac teaches the colony density (para. 29), while Ammar teaches the density of the nucleic acids in each colony (p. 2, left col., para. 2), but neither explicitly teaches the concentration of the fluid comprising the nucleic acid sequence when it is placed into contact with the surface. However, it would be obvious to arrive at this concentration.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Drmanac method, discussed above, to arrive at the recited surface density and solution concentration limitations. The ordinary artisan would have been motivated to do so customize the assay as needed through routine optimization, and would have had an expectation of success as Drmanac and Amman teach principles of array design and modification.
Conclusion
Claims 1-3, 7, 9, 11, 15-19, 22, 24, 28-29, 31-32 and 36-38 are being examined and are rejected. Claims 1, 22 and 37 are objected to. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Examiner, Art Unit 1681