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 .
DETAILED ACTION
1. Upon reconsideration the finality of the previous office action has been withdrawn and the claims are considered for examination.
Status of the Application
2. Claims 1, 4 and 21 are pending under examination. Claims 2-3, 5-20 and 22 are canceled. The Applicant’s arguments and the amendment have been considered and found persuasive for the following reasons.
Response to Arguments:
3. The objection to the sequence listing has been withdrawn in view of the replacement sequence listing submitted.
4. The rejection of claims 1, 4 and 21 under 35 USC 112(b) has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 112
5. 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 and 21 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 ‘primer polynucleotide comprising at least 2 tandem repeats of unit sequence that is 1 to 60 nucleotides long. The limitation is unclear and indefinite because it is not clear if the limitation ‘1 to 60 nucleotides long’ is refering to the primer length or a repeat unit length. The specification on page 5 defines unit sequence is a microsatellite sequence having 2-9 nucleotides long or 10 to 60 nucleotides long. It is unclear how at least two single nucleotide repeats would represent a primer having at least two tandem repeat units of minimum 1 nucleotide long.
Claim Rejections - 35 USC § 103
6. 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.
Claims 1, 4 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Whitfield et al. (Angewandlte. Chem. Int. Ed., Vol. 54, p.8971-8974, (2015)) in view of Livak et al. (US 6,309,829).
Whitfield et al. teach a thermocycling method of claim 1 for increasing the number of tandem repeats of a unit sequence that is 1 to 60 nucleotides long in a linear polynucleotide, the method comprising:
i) providing a double stranded oligonucleotide comprising at least two tandem repeats of a unit sequence that is 1 to 60 nucleotides long, denaturing the double stranded linear oligonucleotide primer to provide single stranded linear primer (page 8971, paragraph 1 on right-hand side column, Scheme 1, page 8972, line 1-35, paragraph 1, table 1, page 8973, paragraphs 1-4, Figure 3-4);
ii) contacting the primer polynucleotide with a single stranded template polynucleotide comprising at least two tandem repeats that are complementary to the unit sequence of the primer polynucleotide under conditions that permit mismatched duplex formation between a unit sequence and its complement such that a 5’ overhang of the template polynucleotides generated, wherein the 5’ overhang comprises at least one tandem repeat that is complementary to the unit sequence of the primer polynucleotide ((page 8971, paragraph 1 on right- hand side column, Scheme 1, page 8973, paragraphs 1-4); and
iii) contacting the mismatched duplexes with a thermostable 5’ to 3’ polymerase and nucleotides under extension conditions that permit polynucleotide extension in a 5’ to 3’ direction ((page 8971, paragraph 1 on right-hand side column, Scheme 1, page 8972, line 1-35, paragraph 1, table 1, page 8973, paragraphs 1-4, Figure 3-4);
iv) denaturing the duplexes of ii) under denaturing conditions to generate single stranded immobilized polynucleotide; and v) repeating the steps ii) to iii) at least once to increase the number of tandem repeats in the polynucleotide (page 8971, paragraph 1 on right-hand side column, Fig. 1, Scheme 1, page 8972, line 1-35, paragraph 1, table 1).
With reference to claim 4, Whitfield et al. teach that the primer polynucleotide comprises at least tandem repeats of the unit sequence ((page 8971, paragraph 1 on right-hand side column, Scheme 1, page 8973, paragraphs 1-4, Figure 3).
With reference to claims 21, Whitfield et al. teach that the thermostable polymerase lacks or substantially lack 3’ to 5’ proof-reading activity (page 8972, paragraph 1 on left hand side column).
However, Whitfield et al. did not specifically teach immobilizing the primer on a solid substrate.
Livak et al. teach a method for determining the number of repeat units in a repeat region of a target nucleic acid, wherein the method comprises a immobilizing oligonucleotide primers on a solid support, hybridizing a target nucleic acid comprising variable length repeat region that generates a 5’overhang of the target nucleic acid and extending primer in discrete increments such that in each increment of primer extension the primer is extended by an amount corresponding to the repeat unit, counting the number of repeats in repeated primer extension products (col. 3, line 7 to line 61 on col. 4, col. 6, line 15-16, col. 11, line 59 to line 39 on col. 12).
It would have been prima facie obvious to one of the ordinary person skilled in the art before the effective filling date of the invention to combine the method of Whitfield et al. with the immobilization of the primer on a solid support as taught by Livak et al. to improve the method for analyzing tandem repeats. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would improve the sensitivity of the method because Livak et al. explicitly taught immobilizing primers on a solid support that allows repeated primer extension to determine the number of repeats in a repeat region of a target nucleic acid (col. 4, line 6-61) and such a modification of the method is considered obvious over the cited prior art.
Conclusion
No claims are allowable.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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