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 claims 1-4, 19, 29-30, 32, 35-36, 52-54, and 61-66 and of 5-methylcytosine as the species of modified cytosine in the reply filed on 31 March 2026 is acknowledged.
Claims 67 and 70 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 31 March 2026.
Information Disclosure Statement
The information disclosure statement (IDS) filed 7 January 2025 is considered, initialed, and attached hereto.
Claim Status
Claims 1-4, 19, 29-30, 32, 35-36, 52-54, 61-67, and 70 are pending.
Claims 5-18, 20-28, 31, 33-34, 37-51, 54-60, 68-69, and 71-73 are canceled.
Claims 67 and 70 are withdrawn.
Claims 1-4, 19, 29-30, 32, 35-36, 52-54, and 61-66 are under examination.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). These sequences are on the end of page 91 and beginning of page 92 of the specification filed 30 May 2024.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. These sequences are in Figure 26(A)-(F).
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.831(a) and 1.831(b). However, this application fails to comply with the requirements of 37 CFR 1.831-1.834. The examiner has noted that all of the sequences described above as lacking a sequence identifier are missing from the "Sequence Listing XML". Applicant must provide:
• A replacement “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2., as well as
• A statement that identifies the location of all additions, deletions, or replacements of sequence information in the “Sequence Listing XML” as required by 1.835(b)(3);
• A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.835(b)(4);
• A statement that the “Sequence Listing XML” includes no new matter in accordance with 1.835(b)(5); and
• A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(b)(2), consisting of:
o A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
o A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
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. 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). No petition for acceptance of color drawings has been received.
The drawings filed 30 May 2024 are objected to because views in pages 5-6 of the drawings are numbered “Figure 6 (cont.)”, the view in page 7 of the drawings is numbered “Figure 9 (cont.)”, a view in page 9 of the drawings is numbered “Figure 10 (cont.)”, and views in pages 22-26 of the drawings are numbered “Figure 26 (cont.)”. The numbering of views must comply with 37 C.F.R. 1.84(u):
(u) Numbering of views.
(1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The use of terms such as Milli-Q, NEBNext, USER, and MyOne, 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 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 61 is objected to because of the following informalities:
Claim 61 recites “the at least one second polynucleotide sequence comprising the at least one second polynucleotide sequence” in lines 10-11, which is tautological. Based on the recitation “the at least one first polynucleotide sequence comprising the first portion” in lines 8-9, Examiner believes that the recitation in lines 10-11 was intended to read “the at least one second polynucleotide sequence comprising the second portion”.
Appropriate correction is required.
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.
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 1-4, 19, 29-30, 32, 35-36, 52-54, and 61-66 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.
Claim 1 recites “the template is generated from a target polynucleotide to be sequenced via complementary base pairing” in lines 11-12. It is unclear whether “via complementary base pairing” limits the method of generating the template from a polynucleotide or the method of sequencing the target polynucleotide. Therefore, the metes and bounds of claim 1 are unclear. For the purpose of examination, prior art teaching either interpretation will read on the limitation. Claims 2-4, 19, 29-30, 32, 35-36, 52-54, and 61-66 are also rejected based on their dependency on claim 1.
Claim 32 recites the limitation “a step of preparing the first portion and the second portion for concurrent sequencing” in lines 2-3. However, neither the claims nor the specification provide any clear definition on the limitations involved in preparing for concurrent sequencing. On page 55 the instant specification recites “a step of preparing the first portion and the second portion for concurrent sequencing” and provides examples on page 56, but these examples are not limiting. On page 62 of the instant specification, Figures 21 to 23 are recited as various ways in which portions can be prepared for concurrent sequencing, but are not limiting. Therefore, the metes and bounds of claim 32 are unclear. For the purpose of examination, this limitation is interpreted as broadly encompassing any further step that does not prevent concurrent sequencing.
Claim 52 recites the limitations "the first signal" in line 1 and “the second signal” in lines 1-2. There is insufficient antecedent basis for these limitations in the claim. For the purpose of examination, claim 52 is interpreted as being dependent on claim 35 or claim 36, as these are the only previous claims that recite a first second and a second signal.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 53 recites the broad recitation "a solid support", and the claim also recites "preferably wherein the solid support is a flow cell" which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 65 recites the limitation "using a method according to any one of claims 35 to 52" in lines 2-3. As claims 37-51 have been cancelled, there is insufficient antecedent basis for this limitation in the claim. Examiner also notes that if claim 52 becomes amended to be multiply dependent upon claim 35 or 36, consistent with the interpretation given in the 35 U.S.C. 112(b) rejection of claim 52 above, then claim 65 will be in improper multiple dependent form due to depending upon claim 52, a multiple dependent claim. For the purpose of examination and compact prosecution, this recitation in claim 65 is interpreted as if it read “using a method according to any one of claims 35 and 36”, which are the only claims in 35-52 that are not canceled and would not lead to improper multiple dependent form.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-4, 19, 29-30, and 32 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Kohli et al. (US 2025/0283170, effectively filed 12 July 2021), herein Kohli.
Regarding claim 1¸Kohli teaches a method of preparing polynucleotide sequences for detection of modified cytosines (“As the original target strand and deamination-resistant copy strand are linked, sequencing both halves of the molecule generates the genetic and epigenetic information together (FIG. 5C Bottom). A schematic is provided with one method for achieving this goal (FIG. 5D)” [0124], end of 5D recites sequencing including 5mC and 5hmC epigenetic info), comprising: synthesizing at least one first polynucleotide sequence comprising a first portion and at least one second polynucleotide sequence comprising a second portion, wherein the at least one first polynucleotide sequence comprising a first portion and the at least one second polynucleotide sequence comprising a second portion each comprise portions of a double-stranded nucleic acid template, and the first portion comprises a forward strand of the template, and the second portion comprises a reverse complement strand of the template; or wherein the first portion comprises a reverse strand of the template, and the second portion comprises a forward complement strand of the template; wherein the template is generated from a target polynucleotide to be sequenced via complementary base pairing (“Following indexing, the libraries can then be sequenced in paired-end mode to have both genetic and epigenetic information read out (FIG. 5D)” [0124] and “Index + paired-end sequencing” FIG. 5D, by indexing a polynucleotide is synthesized that includes the index, the first polynucleotide sequence comprising a first portion labeled as ‘read 1: epigenetic info’ and the second polynucleotide sequence comprising a second portion labeled as ‘read 2: genetic sequence; alternatively, amplification of the indexed template in FIG. 5D for sequencing generates a complementary polynucleotide templated off the indexed template such that the indexed template is considered the first polynucleotide and the complementary polynucleotide is considered the second polynucleotide, for which any portion where the polynucleotides are complementary can be considered the first and second portions of the respective polynucleotide; evidence that the indexing and sequencing of Kohli includes amplification: “The sample is then treated with at least one deaminase and PCR amplified followed by sequencing of PCR amplicons and generation of methylation profiles” [0018], “The bisulfite-treated DNA is amplified and sequenced thereby creating a first library” [0023]; “DM-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix” [0107]; “Purified BS-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix” [0107]; “PCR amplification and sequencing” [0120]), and wherein the target polynucleotide has been pre-treated using a conversion reagent, wherein the conversion reagent is configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil, and/or wherein the conversion reagent is configured to convert an unmodified cytosine to uracil or a nucleobase which is read as thymine/uracil (“These molecules can have native 5hmC's protected by βGT and then be deaminated by A3A” [0124]; “from cytosine to uracil by DNA deaminases” [0036]; “APOBEC3A (A3A), the most active of AID/APOBEC deaminases” [0053]; “unmodified C and 5mC can be efficiently deaminated by A3A” [0054]).
Regarding claim 2, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the target polynucleotide has been pre-treated using a conversion reagent configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil (“unmodified C and 5mC can be efficiently deaminated by A3A” [0054], 5mC is a modified cytosine).
Regarding claim 3, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the target polynucleotide has been pre-treated using a conversion reagent configured to convert an unmodified cytosine to thymine or a nucleobase which is read as thymine/uracil (“unmodified C and 5mC can be efficiently deaminated by A3A” [0054]).
Regarding claim 4, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the conversion agent comprises a chemical agent and/or an enzyme (“APOBEC3A (A3A), the most active of AID/APOBEC deaminases” [0053]; “unmodified C and 5mC can be efficiently deaminated by A3A” [0054]).
Regarding claim 19, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the target polynucleotide is treated with a further agent prior to treatment with the conversion reagent (“These molecules can have native 5hmC's protected by βGT and then be deaminated by A3A” [0124], βGT is the further agent; FIG. 5D).
Regarding claim 29, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the modified cytosine is 5-methylcytosine, the elected species of modified cytosine (“unmodified C and 5mC can be efficiently deaminated by A3A” [0054], 5mC is 5-methylcytosine).
Regarding claim 30, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the forward strand of the template is not identical to the reverse complement strand of the template (see in 35 U.S.C. 102 rejection of claim 1 above the consideration that, in FIG. 5D, ‘read 1: epigenetic info’ is the first polynucleotide sequence and ‘read 2: genetic sequence’ is the second polynucleotide sequence, these sequences are not identical due to C and 5mC in the original template being read as U/T in the first polynucleotide and as C in the second polynucleotide).
Regarding claim 32, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the method further comprises a step of preparing the first portion and the second portion for concurrent sequencing, which is interpreted as broadly encompassing any further step that does not prevent concurrent sequencing as discussed in the 35 U.S.C. 112(b) rejection of claim 32 (“These molecules can have native 5hmC's protected by βGT and then be deaminated by A3A” [0124]; the protection by βGT is a further step and would not prevent concurrent sequencing because it only affect what modifications are present on nucleotides of the target polynucleotide).
Therefore, claims 1-4, 19, 29-30, and 32 are anticipated by Kohli.
Claims 1-4, 19, 29-30, 32, 35, 53, and 61 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Witters et al. (US 2025/0154555, effectively filed 11 February 2022), herein Witters.
Regarding claim 1, Witters teaches a method of preparing polynucleotide sequences for detection of modified cytosines (“Example 2. Linked Duplex Sequencing: Cytosine Conversion with Methylation Retention” [0341-0342]; “Linked Duplex Sequencing: Clustering and Use in Sequencing” [0373-0374]), comprising: synthesizing at least one first polynucleotide sequence comprising a first portion and at least one second polynucleotide sequence comprising a second portion, wherein the at least one first polynucleotide sequence comprising a first portion and the at least one second polynucleotide sequence comprising a second portion each comprise portions of a double-stranded nucleic acid template, and the first portion comprises a forward strand of the template, and the second portion comprises a reverse complement strand of the template; or wherein the first portion comprises a reverse strand of the template, and the second portion comprises a forward complement strand of the template, wherein the template is generated from a target polynucleotide to be sequenced via complementary base pairing (“FIG. 5C shows an immobilized P1 primer annealed to the immobilized template polynucleotide. In the presence of a polymerase, an extension is performed” [0364], interpretation 1: the extended product of P1 in the frame of FIG. 5C labeled ‘Extension’ is the first polynucleotide sequence; “The process is then repeated to continue amplification of the template polynucleotide” [0364], the extended product of the left copy of P2 in the frame of FIG. 5C labeled ‘Continue solid-phase amplification’, templated on the first polynucleotide sequence, is the second polynucleotide sequence; alternatively, interpretation 2: the extended product of P1 in the frame of FIG. 5C labeled ‘Extension’ is considered to be a polynucleotide comprising both the first polynucleotide sequence comprising a first portion and a second polynucleotide sequence comprising a second portion wherein the first and second portions are complements as shown in the frame of FIG. 5C labeled ‘Denature, wash, rehyb.’ since the extended product of P1 has a first polynucleotide sequence that self-hybridizes with a second polynucleotide sequence), and wherein the target polynucleotide has been pre-treated using a conversion reagent, wherein the conversion reagent is configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil, and/or wherein the conversion reagent is configured to convert an unmodified cytosine to uracil or a nucleobase which is read as thymine/uracil (“A conversion technique may be applied as known in the art and described herein. For example, the enzymatic and chemical conversion method depicted in FIG. 4A may be applied, which converts the unmodified cytosine nucleobases to uracil analogs (depicted as squares)” [0364], note that the polynucleotide immobilized at P2 in the frame of FIG. 5C labeled Extension is the target polynucleotide; [0010]).
Regarding claim 2, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the target polynucleotide has been pre-treated using a conversion reagent configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil (“A conversion technique may be applied as known in the art and described herein” [0364]; FIG. 4B; [0010]).
Regarding claim 3, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the target polynucleotide has been pre-treated using a conversion reagent configured to convert an unmodified cytosine to thymine or a nucleobase which is read as thymine/uracil (“A conversion technique may be applied as known in the art and described herein” [0364]; FIG. 4A, C; [0010]).
Regarding claim 4, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the conversion agent comprises a chemical agent and/or an enzyme (“A conversion technique may be applied as known in the art and described herein” [0364]; FIG. 4A-C; [0010]).
Regarding claim 19, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the target polynucleotide is treated with a further agent prior to treatment with the conversion reagent (“A conversion technique may be applied as known in the art and described herein” [0364]; FIG. 4C, the 2nd enzymatic conversion is the conversion reagent that converts a C to a U/T, the 1st enzymatic conversion is the further agent; [0010]).
Regarding claim 29, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the modified cytosine is 5-methylcytosine, the elected species of modified cytosine (“A conversion technique may be applied as known in the art and described herein” [0364]; FIG. 4B, the nucleotide that starts as 5mC, 5-methylcytosine, is converted to a T; [0010]).
Regarding claim 30, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the forward strand of the template is not identical to the reverse complement strand of the template (the forward and reverse complements would only be identical if the first and second polynucleotide are a reverse palindrome sequence and Wittwers has no requirement that the template be a reverse palindrome sequence, so the vast majority of the range of sequences for the template will read on this limitation and would be immediately clear to one of ordinary skill in the art reading the disclosure of Witters; in the case that Applicant intended for claim 30 to require that the forward strand and reverse complement strand do not have perfect complementarity, in interpretation 2 in the 35 U.S.C. 102 rejection of claim 1 over Witters the forward strand and reverse complement strand are not identical and do not have perfect complementarity as seen in the alignment of A with C in the frame of FIG. 5C labeled ‘Denature, wash, rehyb.’).
Regarding claim 32, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the method further comprises a step of preparing the first portion and the second portion for concurrent sequencing, which is interpreted as broadly encompassing any further step that does not prevent concurrent sequencing as discussed in the 35 U.S.C. 112(b) rejection of claim 32 (the 1st enzymatic conversion step in FIG. 4C is a further step and would not prevent concurrent sequencing because it only affect what modifications are present on nucleotides of the target polynucleotide).
Regarding claim 35, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein a proportion of first portions is capable of generating a first signal and a proportion of second portions is capable of generating a second signal, wherein an intensity of the first signal is substantially the same as an intensity of the second signal (“In embodiments, the method provides sequencing both strands of a double stranded nucleic acid” [0205-0206]; “Examples of sequencing include, but are not limited to, sequencing by synthesis (SBS) processes in which reversibly terminated nucleotides carrying fluorescent dyes are incorporated into a growing strand, complementary to the target strand being sequenced. In embodiments, the nucleotides are labeled with up to four unique fluorescent dyes” [0253], as both strands are sequenced, as long as the first portion and second portion have a single type of nucleotide (A, T, C, G) in common, then sequencing by synthesis will lead to both generating the same signal with the same intensity when comparing the detection of the same type of nucleotide).
Regarding claim 53, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the at least one first polynucleotide sequence comprising the first portion and the at least one second polynucleotide sequence comprising the second portion are attached to a solid support (“immobilized P1 primer” [0364]; FIG. 5C, note that all extension products are attached to the horizontal line representing a surface that they are immobilized to; “The products of solid-phase amplification reactions described herein wherein both P1 and P2 primers are covalently immobilized on the solid surface and may be referred to as “bridged structures” formed by annealing of pairs of immobilized polynucleotide strands and immobilized complementary strands, both strands being attached to the solid support at the 5′ end” [0382]).
Regarding claim 61, Witters teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Witters above), wherein the step of synthesizing at least one first polynucleotide sequence comprising a first portion and at least one second polynucleotide sequence comprising a second portion comprises: synthesizing a loop-ligated precursor polynucleotide by connecting a 3’-end of the forward strand of the target polynucleotide and a 5’-end of the reverse strand of the target polynucleotide with a loop, or connecting a 5’-end of the forward strand of the target polynucleotide and a 3’-end of the reverse strand of the target polynucleotide with a loop, synthesizing the at least one first polynucleotide sequence comprising the first portion by forming a complement of the loop-ligated precursor polynucleotide, synthesizing the at least one second polynucleotide comprising the at least one second polynucleotide sequence by forming a complement of the at least one first polynucleotide sequence (“FIG. 5B shows subsequent denaturation and washing away of the original template strand, allowing rehybridization of the immobilized, methyltransferase-treated strand into a Y-template-hairpin construct [0364], the hairpin connects the forward and reverse strands of the precursor/target polynucleotide by ligating them together with a loop structure; the first polynucleotide is synthesized based on the precursor/target polynucleotide and the second polynucleotide is synthesized based on the first polynucleotide as discussed regarding interpretation 1 in the 35 U.S.C. 102 rejection of claim 1 over Witters above).
Therefore, claims 1-4, 19, 29-30, 32, 35, 53, and 61 are anticipated by Witters.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 36, 52, and 62-66 are rejected under 35 U.S.C. 103 as being unpatentable over Kohli et al. (US 2025/0283170, effectively filed 12 July 2021), herein Kohli as applied to claims 1-4, 19, 29-30, 32, 35, 53, and 61 above, and further in view of Boutell (US 2017/0298430, published 19 October 2017, effectively filed 5 November 2014).
Regarding claim 36, Kohli teaches the method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Kohli above). However, Kohli does not teach that the method further comprises a step of selectively processing. This deficiency is made up for in the teachings of Boutell.
Regarding claim 36, Boutell teaches a method of sequencing that has the advantage of increasing the rate of sequencing and density of sequencing data (“a sequencing method which allows for increased rates of sequencing and an increase in the density of sequencing data” [0003]), wherein the method comprises a step of selectively processing polynucleotide sequences comprising a first portion and a second portion, such that a proportion of first portions are capable of generating a first signal and a proportion of second portions are capable of generating a second signal, wherein the selective processing causes an intensity of the first signal to be greater than an intensity of the second signal ([0037-0043]; “Once intensity readings and imaging has been obtained, base calls can be made for each location with multiple calls being made at each position for each cycle of sequencing. Each call at each position will then need to be allocated to the correct extension read. This can be done chemically, for example by making one of the reads brighter than the other by using a mixture of blocked and unblocked primer” [0122], the use of a mixture of blocked and unblocked primers to make one read brighter than the other is considered a step of selectively processing; [0124]).
Regarding claim 52, the combination of Kohli and Boutell teach a method of sequencing (see 35 U.S.C. 103 rejection of claim 36 above), and Boutell further teaches that the first signal and the second signal are spatially unresolved (“at least two primers able to hybridise to the same strand of said nucleic acid at different positions” [0039], because the signals are generated from the same strand they are co-localized and spatially unresolvable).
Regarding claim 62, the combination of Kohli and Boutell teach a method of sequencing (see 35 U.S.C. 103 rejection of claim 36 above), and Boutell further teaches concurrently sequencing nucleobases in the first portion and the second portion (“Preferably the plurality of extension reads comprise simultaneous extension reads” [0044]).
Regarding claim 63, the combination of Kohli and Boutell teach a method of sequencing polynucleotide sequences to detect modified cytosines, comprising: preparing polynucleotide sequences for detection of modified cytosines using a method according to claim 1 (see 35 U.S.C. 102 rejection of claim 1 over Kohli above); concurrently sequencing nucleobases in the first portion and the second portion (Boutell’s method of sequencing in [0037-0043]; “Preferably the plurality of extension reads comprise simultaneous extension reads” [0044]); and identifying modified cytosines by detecting differences when comparing a sequence output from the first portion with a sequence output from the second portion (“method provides an unmodified polynucleotide strand in the linked complementary strand of the template nucleic acid following the cytosine conversion protocol, providing an internal reference for modifications present on each template nucleic acid molecule that can subsequently be sequenced, simultaneously increasing sequencing depth and accurate detection of nucleobase modifications” [0372]).
Regarding claim 64, the combination of Kohli and Boutell teach the method according to claim 63 (see 35 U.S.C. 103 rejection of claim 63 above), and Boutell further teaches that the step of concurrently sequencing nucleobases comprises performing sequencing-by-synthesis or sequencing-by-ligation (“In certain embodiments, the method comprises sequencing by synthesis” [0045]; “In certain embodiments, the method comprises sequencing by ligation” [0047]).
Regarding claim 65, the combination of Kohli and Boutell teach the method according to claim 63 (see 35 U.S.C. 103 rejection of claim 63 above) wherein the step of preparing the polynucleotide sequences comprises using a method according to claim 36 (see 35 U.S.C. 103 rejection of claim 36 above); and wherein the step of concurrently sequencing nucleobases in the first portion and the second portion is based on the intensity of the first signal and the intensity of the second signal (“Once intensity readings and imaging has been obtained, base calls can be made for each location with multiple calls being made at each position for each cycle of sequencing. Each call at each position will then need to be allocated to the correct extension read. This can be done chemically, for example by making one of the reads brighter than the other by using a mixture of blocked and unblocked primer” Boutell [0122]).
Regarding claim 66, the combination of Kohli and Boutell teach the method according to claim 63 (see 35 U.S.C. 103 rejection of claim 63 above), and Kohli further teaches that the method further comprises a step of conducting paired-end reads (“Following indexing, the libraries can then be sequenced in paired-end mode to have both genetic and epigenetic information read out (FIG. 5D)” [0124]; “paired-end sequencing” FIG. 5D).
In view of the advantages of rate of sequencing and density of sequencing data taught by Boutell, one of ordinary skill in the art would be motivated to combine the method of preparing polynucleotide sequences for detection of modified cytosines by sequencing taught by Kohli with the advantageous sequencing method taught by Boutell (MPEP § 2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because Kohli teaches their method of preparation as being compatible with next-gen sequencing technologies (“few representative adapters compatible with next-generation sequencing” [0029]) and the method of Boutell does not teach their method as requiring specific input templates that would prevent the polynucleotides prepared in the method of Kohli from being able to be used. Therefore, the invention as a whole of claims 36, 52, and 62-66 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Double Patenting
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.
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Claims 1-4, 19, 29-30, 32, 35-36, 53, and 62-63 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 19, 29-30, 32, 34-35, 44, and 62-63 of copending Application No. 18/413,996 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding instant claim 1, reference application claim 1 recites a method with identical or equivalent language to instant claim 1 with the exception of “synthesising at least one polynucleotide sequence comprising a first portion and a second portion” instead of “synthesising at least one first polynucleotide sequence comprising a first portion and at least one second polynucleotide sequence comprising a second portion”. As the first and second polynucleotide sequences of instant claim 1 can be on the same polynucleotide molecule, the instant claim 1 includes in its scope the situation where a single polynucleotide sequence comprises the first and second polynucleotide sequences and their respective portions. The single polynucleotide sequence is equivalent to the at least one polynucleotide sequence of reference application claim 1. However, reference application claim 1 is narrower than instant claim 1, since instant claim 1 includes species where the first and second polynucleotide sequences are on separate strands as well, which is not encompassed by reference application claim 1. Similarly, reference application claim 1’s recitation in the preamble of “preparing at least one polynucleotide sequence for detection” is equal to or narrower in scope in comparison to instant claim 1’s recitation in the preamble of “preparing polynucleotide sequences for detection”. Therefore, reference application claim 1 anticipates instant claim 1 and the claims are not patentably distinct.
Regarding instant claims 2-4, 19, 29-30, 32, 35, and 62-63, reference application claims 2-4, 19, 29-30, 32, 34, and 62-63 recite identical or equivalent language to the respective instant claim (instant claim 35 is respective to reference application claim 34), with the exception of the differences in claim 1 on which all of the above claims depend upon, which is discussed above. Therefore, reference application claims 2-4, 19, 29-30, 32, 34, and 62-63 anticipate, respectively, instant claims 2-4, 19, 29-30, 32, 35 and 62-63 and the claims are not patentably distinct.
Regarding instant claim 36, reference application claim 35 recites nearly identical language, with the exceptions of the differences in claim 1 on which the claim depends (see discussion regarding differences in claim 1 above) and the recitation of “selectively processing the at least one polynucleotide sequence comprising the first portion and the second portion” instead of “selectively processing the at least one first polynucleotide sequence comprising a first portion and the at least one second polynucleotide sequence comprising a second portion”. As discussed regarding claim 1 above, the first and second polynucleotide sequences may be part of a single polynucleotide sequence, which is equivalent to the at least one polynucleotide sequence of reference application claim 35. Therefore, reference application claim 35 anticipates instant claim 36 and the claims are not patentably distinct.
Regarding instant claim 53, reference application claim 44 recites nearly identical language, with the exceptions of the differences in claim 1 on which the claim depends (see discussion regarding differences in claim 1 above) and the recitation of “the at least one polynucleotide sequence comprising the first portion and the second portion is/are attached to a solid support, wherein the solid support is a flow cell” instead of “wherein the at least one first polynucleotide sequence comprising the first portion and the at least one second polynucleotide sequence comprising the second portion are attached to a solid support, preferably wherein the solid support is a flow cell”. As discussed regarding claim 1 above, the first and second polynucleotide sequences may be part of a single polynucleotide sequence, which is equivalent to the at least one polynucleotide sequence of reference application claim 44. The lack of the word ‘preferably’ in reference application claim 44 does not make it patentably distinct, as it merely leads to a further limit on the scope of the claim. Therefore, reference application claim 44 anticipates instant claim 53 and the claims are not patentably distinct.
Conclusion
Claims 1-4, 19, 29-30, 32, 35-36, 52-54, and 61-66 are rejected. Claims 5-18, 20-28, 31, 33-34, 37-51, 54-60, 68-69, and 71-73 are canceled. Claims 67 and 70 are withdrawn.
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/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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