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 .
Election/Restrictions
Applicant’s election without traverse of Group I: Claims 1-18 in the reply filed on December 11, 2025 is acknowledged.
Claims 19 and 20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claim Status
Claims 1-20 are pending in the present application. Claims 19 and 20 are withdrawn. Claims 1-18 are under examination.
Priority/Effective Filing Date
The present application, filed on August 3, 2023, claims benefit of U.S. Provisional Patent Application 63/395,276, filed on August 4, 2022. No other priority claims presently exist in the application. Therefore, the effective filing date is determined to be August 4, 2022.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. See “Drw.supp dated august 3, 2022”. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
Presently, the abstract reads: “Disclosed herein, inter alia, are methods for increasing monoclonal nucleic acid amplification products on a solid support.”
The disclosure is objected to because of the following informalities: page 46 contains extraneous text and/or code “ “\*MERGEFORMAT\* MERGEFORMAT ”.
Appropriate correction is required.
The use of the terms AMPure, CF, Biotium, Alexa Fluor, Thermo Fisher, DyLight, Cy, GE Healthcare, IRDyes, Li-Cor, HyLyte, Bst 2.0, Illumina, Singular Genomics, NucleoMag, SPRI, Axygen, Bst 3.0, SMRT, which are each a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the 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.
Claim Objections
Claim 18 is objected to because of the following informalities: The phrase “a complement of second the template sequence” at lines 20-21 appears to comprise an erroneous typographical transposition of the words “second” and “the”. It appears that the claim is intended to read, “a complement of the second template sequence”, and has been interpreted as such below. Appropriate correction is required.
Claim Interpretation
Special definitions of the terms “platform primer” and “about” have been provided by the applicant in the specification at paragraphs [0031] and [0020], respectively.
At paragraph 0020, the specification reads, “As used herein, the term “about” means a range of values including the specified value, which a person of ordinary skill in the art would consider reasonably similar to the specified value.” This definition is referenced in the 112(b) rejections which follow.
At paragraph 0031, the specification reads, “As used herein, a “platform primer” is a primer oligonucleotide immobilized or otherwise bound to a solid support (i.e. an immobilized oligonucleotide).”
In light of this definition, The examiner has interpreted the claim term “a/the… platform primer” as exclusive of primer oligonucleotides that are not bound to a solid support.
For example, Claim 14, step a recites “hybridizing a second platform primer binding sequence of a first immobilized polynucleotide to a second platform primer…”. In light of the definition in the specification, this claim language has been interpreted as excluding possible embodiments wherein the first immobilized polynucleotide hybridizes to a primer that is identical to the “second platform primer” but is not bound to the solid support (i.e. “free” primers).
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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.
Claims 6-13 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 6-11, which each depend from claim 1, recite the limitations “the blocking element” and "the second blocking elements". Claim 1 recites “a plurality of blocking elements…a blocking element bound to one of [the] third platform primer binding sequences of [the] second polynucleotide; or … a blocking element bound to [the] third platform primers”. It is unclear whether “the blocking element” and “the second blocking elements” are intended to reference different subsets of the plurality of blocking elements that bind to the third platform primers or a complement thereof, or are intended to refer to something else, such as [a] blocking element[s] that bind to a different platform primer or platform primer binding sequence (e.g. the second platform primer/binding sequence). Therefore, there is insufficient antecedent basis for this limitation in the claim.
The term “about” in claims 10 and 13 is a relative term which renders the claim indefinite. The term “about” is not defined by the claim, and at paragraph 0020, the specification reads, “As used herein, the term “about” means a range of values including the specified value, which a person of ordinary skill in the art would consider reasonably similar to the specified value.” The reference to “a range… which a person of ordinary skill in the art would consider reasonably similar to the specified value” does not provide concrete guidance as to the metes and bounds of the claimed range. Accordingly, the recitation of “about 5 to about 35 nucleotides”, recited by claim 10, appears to cover any value for which an oligonucleotide blocking element would be expected to accomplish the function of a “blocking element” (i.e. impedes hybridization/amplification of one of the plurality of polynucleotides comprising the template sequence(s)). Similarly, the recitation “about 5 minutes to about 4 hours” appears to cover any value the ordinary artisan would expect to be required to perform “the amplifying”. Furthermore, the use of the subjective and relative term “reasonably similar” does not inform concrete metes and bounds of the claimed range of values. Therefore, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claims 10, 12, and 13 recite limitations “comprising about 5 to 35 nucleotides”, “comprises 1 to 100 bridge-PCR amplification cycles”, and “comprises about 5 minutes to about 4 hours”, respectively. The open claim language “comprising/comprises” recited before these ranges renders the range indefinite with respect to the maximum value included within the claimed range. AT paragraph 0021, the instant specification provides “the words “comprise”, “comprises”, and “comprising” will be understood to imply the inclusion of a stated step or element or group of steps or elements but not the exclusion of any other step or element or group of steps or elements.” Therefore, a recitation of “comprising” a minimum value to a maximum value necessarily includes all possible values greater than the minimum value. As such, the recited maximum value of the claimed range appears not to impose any meaningful limitation on the scope of the claims. Claims 10, 12, and 13 have accordingly been given their broadest reasonable interpretation encompassing “about 5 [or more] nucleotides” and “1 [or more] bridge-PCR amplification cycles”, and “at least about 5 minutes” respectively.
Claim 18 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The structure of the polynucleotides and/or the “hybridizing” and “extending” steps recited by claim 18 is/are unclear. Claim 18 defines “the first polynucleotide comprises the first platform primer binding sequence, a first template sequence, and a second platform primer sequence”; “the second polynucleotide comprises the first platform primer binding sequence, a second template sequence, and a third platform primer sequence” : diagrammed below:
1ST POLY: 3’---[1st platform binding]—[template 1]---[2nd platform]---5’
2ND POLY: 3’ ---[1st platform binding]—[template 2]---[3rd platform]—5’
The claim recites “hybridizing a first platform primer binding sequence of the second polynucleotide to one of said second platform primers”.
It is unclear how a first platform primer binding sequence is intended to hybridize to a second platform primer.
The claim further requires the steps:
(a) “extending the first platform primer with a polymerase to form the first immobilized polynucleotide comprising the first platform primer sequence, a complement of the first template sequence, and a second platform primer binding sequence” diagrammed below:
Surface-5’---[1st platform]---[template 1 complement]---[2nd platform binding]—3’
AND
(b) “extending the second platform primer with a polymerase to form the second immobilized polynucleotide comprising the first platform primer sequences, a complement of second the template sequence, and a third platform primer binding sequence”.
Both polynucleotides recited in claim 18 comprise a first platform primer binding sequence, and as such would both be extended at step (a) above, forming the first and second immobilized polynucleotides.
Only the first polynucleotide (after the first extending step) comprises a second platform primer binding sequence. Therefore, the immobilized first polynucleotide would be amplified by the extension of the second platform primer recited in step (b) above (assuming an omitted intervening bridge hybridization step). Step (b) recites that the extending the second platform primer step forms the second immobilized polynucleotide comprising the first platform primer sequence, a complement of the second template sequence, and a third platform primer binding sequence. It is unclear how an extension of the second platform primer can produce the second immobilized polynucleotide as presently claimed because the second polynucleotide does not comprise a second platform primer binding sequence.
It is unclear whether applicant intended to recite that the second polynucleotide comprises a second platform primer binding sequence rather than the presently recited first platform primer binding sequence, diagrammed below:
Hypothetical 2nd Poly: 3’—[2nd platform binding]—[template 2]—[3rd platform]—5’
Which, upon hybridization to a second platform primer and subsequent extension of said second platform primer would produce the following hypothetical immobilized second polynucleotide:
Surface—5’—[2nd platform]—[template 2 complement]—[3rd platform binding]—3’
OR
Some other combination of structural elements comprised by the recited polynucleotides or combination of active steps.
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 1-5, 12, and 14-18 are rejected under 35 U.S.C. 103 as being unpatentable over Trepagnier et al., US 2018/0312917 A1 (published November 1, 2018) in view of Fisher et al., WO 2022/055729 A1 (published March 17, 2022).
Regarding claims 1, 14, and 18, Trepagnier et al. teach methods for differentially amplifying subpopulations of polynucleotides having different orthogonal primer binding sites on a solid support comprising primers with orthogonal blocking groups (Trepagnier et al., paragraph 0014-0016) (i.e. hybridizing pluralities of template polynucleotides having different platform primer binding sequences to blocked platform primers). Trepagnier et al. teach deblocking one of the set of orthogonal primer sets and selectively incorporating nucleotides only to the deblocked subpopulation of primers (Trepagnier et al., paragraph 0014). The incorporated nucleotides may additionally comprise the corresponding blocking group of the orthogonal primer set (i.e. a blocking element) (Trepagnier et al., paragraph 0014). Furthermore, Trepagnier et al. teach orthogonality of primer sets and blocking groups can be increased using greater than two orthogonal primer/blocking group sets (i.e. a first, second, and third, etc. blocked platform primer sequence). Trepagnier further teaches amplifying the plurality of polynucleotides on the solid support by bridge amplification (Trepagnier et al., paragraph 0025).
Trepagnier et al. generally teach iterative cycles of selectively deblocking one of the plurality of orthogonally blocked immobilized primers (i.e. platform primers) and adding a labeled and blocked nucleotide to one subset of the captured template polynucleotides hybridized to the (now deblocked) platform primer during the sequence-determining amplification step rather than the bridge amplification step.
However, Fisher et al. teach methods of preferentially amplifying particular subsets of polynucleotides on a solid support during the bridge amplification step (Fisher et al., paragraph 0060). Fisher et al. teach biased bridge amplification is useful in sequencing applications to enhance cluster monoclonality (i.e. the homogeneity of polynucleotide template sequences in a particular region on the surface) (Fisher et al., paragraph 0060).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods of Trepagnier et al. comprising selective incorporation (i.e. differential amplification) of a subset of immobilized polynucleotides within a plurality of immobilized polynucleotides comprising orthogonal primer/blocking group sets during the sequencing step to differentially amplify the orthogonally primed and blocked subsets of polynucleotides during the bridge amplification step, as taught by Fisher et al. The ordinary artisan would have been motivated to modify the method of Trepagnier et al. with the teachings of Fisher et al. because Fisher et al. teach that biased (i.e. selective) amplification during cluster generation (i.e. bridge amplification) predictably and beneficially enhances the monoclonality of resulting sequencing clusters (Fisher et al., paragraph 0060).
Regarding claim 2, Fisher et al. and Trepagnier et al. teach performing bridge amplification (i.e. cycles comprising hybridization of the free 3’ end of an immobilized polynucleotide to a platform primer, extension of the platform primer with a polymerase, and denaturing the amplification product (see Fisher et al., Figure 3).
Regarding claim 3, Trepagnier et al. teach contacting the solid support with blocking elements during each amplification cycle (Trepagnier et al., paragraph 0018).
Regarding claims 4, 5, and 17 Trepagnier et al. teach iteratively removing each one of the plurality of orthogonal blocking elements, amplifying each one of the plurality of orthogonally-blocked template polynucleotides, and blocking the amplified polynucleotides. (i.e. removing the first blocking group and amplifying the second plurality…) (Trepagnier et al., paragraph 0014).
Regarding claim 12, Trepagnier et al. teach the amplification can proceed for one or more cycles comprising 1 to [more than 100] cycles (Trepagnier et al., paragraph 0070).
Regarding claim 15, Trepagnier et al. teach removing a blocking element of the plurality of orthogonal blocking elements from the plurality of orthogonal platform primers and amplifying the corresponding template polynucleotide by extending the deblocked primer with a polymerase (Trepagnier et al., paragraph 0014).
Regarding claim 16, Trepagnier et al. teach the solid support comprises a population of orthogonal platform primers, each having orthogonal blocking groups and each being immobilized to the solid support (Trepagnier et al., paragraph 0014-0017).
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Trepagnier et al., US 2018/0312917 A1 (published November 1, 2018) in view of Fisher et al., WO 2022/055729 A1 (published March 17, 2022) as applied to claims 1-5, 12, and 14-18 above, and further in view of Adams et al., US 5,641,658 (issued June 24, 1997).
Regarding claim 13, Trepagnier et al. teach the amplification can be rolling circle amplification, cluster amplification, bridge amplification, among others (Trepagnier et al., paragraph 0051-0052) comprising 1 to [more than 100] cycles (Trepagnier et al., paragraph 0070). Trepagnier et al. do not teach the amount of time required to perform their amplification steps.
However, Trepagnier et al. cites Adams et al. as describing useful bridge amplification methods.
Adams et al. teach formation of an approximately 1 kb amplification product by bridge amplification (one cycle) comprises: denaturing the DNA at 94°C for 1 minute, hybridizing at 55°C for one minute, and amplifying DNA at 75°C for 5 minutes (i.e. about 7 minutes per cycle) (Adams et al., column 13, paragraph 5-7). Therefore, embodiments comprising 1 to more than 100 cycles (as taught by Adams et al.) require about 7 to more than about 700 minutes (i.e. 7 minutes-about 11.6 hours) (i.e. amplification comprises about 5 minutes to about 4 hours of bridge amplification).
Therefore, it would have been prima facie obvious prior the effective filing date of the claimed invention for one of ordinary skill in the art to have selected a particular amplification program (i.e. temperatures, step duration, and cycle number) required for bridge amplification of a particular target sequence by the methods of Trepagnier et al. in view of Fisher et al. as informed by the guidance of Adams et al. for bridge amplification of nucleic acids. The ordinary artisan would have been motivated to consult Adams et al. for guidance for bridge amplification because Trepagnier et al. specifically cite Adams et al. as teaching bridge amplification methods.
Claims 6-11 are rejected under 35 U.S.C. 103 as being unpatentable over Trepagnier et al., US 2018/0312917 A1 (published November 1, 2018) in view of Fisher et al., WO 2022/055729 A1 (published March 17, 2022) as applied to claims 1-5, and 12-18 above, and further in view of Geipel et al., WO 2018/137826 A1 (published August 2, 2018).
Regarding claim 1, Trepagnier et al. in view of Fisher et al. teach methods for differentially amplifying subpopulations of polynucleotides having different orthogonal primer binding sites on a solid support comprising primers with orthogonal blocking groups (Trepagnier et al., paragraph 0014-0016) (i.e. hybridizing pluralities of template polynucleotides having different platform primer binding sequences to blocked platform primers). Trepagnier et al. teach deblocking one of the set of orthogonal primer sets and selectively incorporating nucleotides only to the deblocked subpopulation of primers (Trepagnier et al., paragraph 0014). The incorporated nucleotides may additionally comprise the corresponding blocking group of the orthogonal primer set (i.e. a blocking element) (Trepagnier et al., paragraph 0014). Furthermore, Trepagnier et al. teach orthogonality of primer sets and blocking groups can be increased using greater than two orthogonal primer/blocking group sets (i.e. a first, second, and third, etc. blocked platform primer sequence). Trepagnier further teaches amplifying the plurality of polynucleotides on the solid support by bridge amplification (Trepagnier et al., paragraph 0025).
Trepagnier et al. generally teach iterative cycles of selectively deblocking one of the plurality of orthogonally blocked immobilized primers (i.e. platform primers) and adding a labeled and blocked nucleotide to one subset of the captured template polynucleotides hybridized to the (now deblocked) platform primer during the sequence-determining amplification step rather than the bridge amplification step.
However, Fisher et al. teach methods of preferentially amplifying particular subsets of polynucleotides on a solid support during the bridge amplification step (Fisher et al., paragraph 0060). Fisher et al. teach biased bridge amplification is useful in sequencing applications to enhance cluster monoclonality (i.e. the homogeneity of polynucleotide template sequences in a particular region on the surface) (Fisher et al., paragraph 0060).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods of Trepagnier et al. comprising selective incorporation (i.e. differential amplification) of a subset of immobilized polynucleotides within a plurality of immobilized polynucleotides comprising orthogonal primer/blocking group sets during the sequencing step to differentially amplify the orthogonally primed and blocked subsets of polynucleotides during the bridge amplification step, as taught by Fisher et al. The ordinary artisan would have been motivated to modify the method of Trepagnier et al. with the teachings of Fisher et al. because Fisher et al. teach that biased (i.e. selective) amplification during cluster generation (i.e. bridge amplification) predictably and beneficially enhances the monoclonality of resulting sequencing clusters (Fisher et al., paragraph 0060).
Regarding claims 6-7, Trepagnier et al. in view of Fisher et al. do not teach that the blocking elements are oligonucleotides that comprise a complementary sequence to the platform primer(s) or a complement thereof.
However, Geipel et al. teach methods for enriching template nucleic acids comprising selective hybridization of primer sequences to platform primers wherein a protecting oligonucleotide complementary to the primer occludes hybridization between the platform primer and the complementary primer sequence on the polynucleotide comprising template sequence (Geipel et al., page 38-39). Geipel et al. further teach that the protecting oligonucleotides may comprise blocking groups (Geipel et al., page 15, paragraph 2).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have modified the methods taught by Trepagnier et al. in view of Fisher et al. comprising selective bridge amplification using orthogonal 3’ blocked platform primers corresponding to a primer binding sequence in a subpopulation of a plurality of immobilized polynucleotides comprising a template sequence with the methods taught by Geipel et al. comprising preventing non-specific hybridization between platform primers and template polynucleotides comprising platform primer binding sequences using blocked “protecting” oligonucleotides that hybridize to primer sequences to be suppressed in a particular amplification step (i.e. a platform primer or platform primer-binding sequence other than that desired to be amplified).
The ordinary artisan would have been motivated to substitute the 3’ blocked platform primers taught by Trepagnier et al. in view of Fisher et al. with the 3’ blocked “protecting oligonucleotides” that hybridize to the platform primers or complementary primer sequences on the template oligonucleotides taught by Geipel et al. because the ordinary artisan would have recognized that the non-extendible primers (taught by Trepagnier et al. in view of Fisher et al.) and non-extendible oligonucleotides that are complementary to primers or primer-complementary sequences (taught by Geipel et al.) are interchangeable equivalent components for preventing hybridization and extension of a particular primer sequence to a template sequence.
Regarding claims 8 and 9, Geipel et al. teach that the “blocking” or “protecting” oligonucleotides can comprise PNAs (peptide nucleic acids), RNA:DNA chimeras and 3’ blocking groups (Geipel et al., page 13, paragraph 5-page 14, paragraph 1 ).
Regarding claim 10, Geipel et al. teach the length of the protecting oligonucleotides may be within the range 4-100 nucleotides and in preferred embodiments, within 10-50 nucleotides or 20-40 nucleotides (i.e. comprising about 5 to about 35 nucleotides).
Regarding claim 11, Geipel et al. teach the blocking elements are non-extendable oligonucleotides (Geipel et al., page 13, paragraph 5-page 14, paragraph 1).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZACHARY MARK TURPIN whose telephone number is (703)756-5917. The examiner can normally be reached Monday-Friday 8:00 am - 5:00 pm.
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/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682