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 .
Priority
This application is a CON of 16/117,248 filed 08/30/2018, now U.S. Patent No. 11,680,284, which is a CON of 14/989,073 filed 01/06/2016, now U.S. Patent No. 10, 066,259 which claims benefit of 62/100,254 filed on 01/06/2015.
Status of the claims
Claims 1-20 are pending and currently under examination.
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 1-15 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 limitation “connecting together two of the MIPs via arms that have hybridized to the same molecule to create an inter-probe product”, which is found to lack clarity as it omits one or more essential elements, such omission(s) amounting to a gap between the elements. See MPEP § 2172.01.
The omitted elements relate to the generation of the claimed “inter-probe product” and to “identifying a structural variant of the genome in the nucleic acid”.
As recited, there is no structural cooperative relationship between generation of the claimed inter-probe product and identifying a structural variant of the genome in the nucleic acid and it is not clear whether or not, OR even how generation of an inter-probe product assists in/accomplishes the preamble’s goal of identifying/detecting structural variant(s) in a nucleic acid genome.
The following critical elements have been omitted in claim 1:
Claim 1 omits limitations that clarify that connecting together the targeting arms of each MIP that have hybridized to the same molecule generates a circularized MIP, wherein the circularized MIP is generated using a polymerase that fills in the gap between the two targeting arms of each MIP along the strand of nucleic acid, and a DNA ligase that covalently closes the two arms of each MIP that have hybridized to the same molecule.
Claim 1 also omits limitations that clarify that connecting together two of the MIPs that each hybridize to the same nucleic acid by only one of its two targeting arms generates an inter-probe product by action of a polymerase that fills in the gap between the targeting arms of each of the two MIPs and a DNA ligase to ligate the two MIPs probes.
Claim 1 omits limitations fails to recite how the inter-probe product reports the structural variant or that a structural variant is reported only when the inter-probe product is formed in and hybridized to a nucleic acid region comprising one or more breakpoints, substitution(s) or mutations in the nucleic acid.
Claims 2-10 and 12-15 are further rejected as they depend from claim 1 and lack clarity based on the omissions in claim 1 stated above.
Claims 13-14 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 13 depend from claim 12 and while claim 12 is directed to sequencing an inter-probe product to produce sequence reads and comparing the sequence reads to the genome to report the structural variant, claim 13 fails to recite any association between the identified structural variant and identification that a person is a carrier of a hereditary disorder.
Claim 6 is 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 6 recites the limitation “at least moiety” which lacks clarity and clarity of scope. It is unclear whether the limitation simply intends for each MIP in the plurality of MIPS to comprise at least one exonuclease resistant moiety and/or how many exonuclease resistant moieties the claim requires per each MIP.
Claim 11 is 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 11 recites the limitation “describing one or more breakpoints in the nucleic acid based on the two MIPs that each hybridizes to the nucleic acid by only one of its two targeting arms”, which lacks clarity as claim 11 depends from claim 1 and claim 1 only requires/recites “each MIP comprising two targeting arms designed to hybridize upstream and downstream of a target in a genome” and recites “connecting together two of the MIPs via arms that have hybridized to the same molecule to create an inter-probe product”.
Claim 11 fails to relate the inter-probe product as a distinct product generated only from one target arm of two adjacent MIPs that are hybridize upstream and downstream of a same target gene in a genome, each of MIP having two targeting arms; as compared to claim 1’s limitation which connects two of the MIPs via arms.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10,066,259.
Although the claims at issue are not identical, they are not patentably distinct from each other because both the method of the instant claims and the claims of the ‘259 patent are directed to a method of identifying a structural variant, the method comprising:
exposing a nucleic acid to a plurality of molecular inversion probes (MIPs),
each MIP comprising two targeting arms designed to hybridize upstream and downstream of a target in a genome;
connecting together two of the MIPs via arms that have hybridized to the same molecule to create an inter-probe product;
detecting the inter-probe product; and
identifying a structural variant of the genome in the nucleic acid.
The claims of U.S. Patent No. 10,066,259 recites a more specific version of the methods of the instant claims 1-20.
The limitations of the instant claim 27 is recited in claim 1 of the ‘132 patent.
The limitations of the instant claim 28 is recited in claim 2 of the ‘132 patent.
The limitations of the instant claim 1 is recited in claim 1 of the ‘259 patent.
The limitations of the instant claim 2 is recited in claim 2 of the ‘259 patent.
The limitations of the instant claim 3 is recited in claim 3 of the ‘259 patent.
The limitations of the instant claim 4 is recited in claim 4 of the ‘259 patent.
The limitations of the instant claim 5 is recited in claim 5 of the ‘259 patent.
The limitations of the instant claim 6 is recited in claim 6 of the ‘259 patent.
The limitations of the instant claim 7 is recited in claim 7 of the ‘259 patent.
The limitations of the instant claim 8 is recited in claim 8 of the ‘259 patent.
The limitations of the instant claim 9 is recited in claim 9 of the ‘259 patent.
The limitations of the instant claim 10 is recited in claim 10 of the ‘259 patent.
The limitations of the instant claim 11 is recited in claim 1 of the ‘259 patent.
The limitations of the instant claim 12 is recited in claim 11 of the ‘259 patent.
The limitations of the instant claim 13 is recited in claim 12 of the ‘259 patent.
The limitations of the instant claim 14 is recited in claim 13 of the ‘259 patent.
The limitations of the instant claim 15 is recited in claim 14 of the ‘259 patent.
The limitations of the instant claim 16 is recited in claim 15 of the ‘259 patent.
The limitations of the instant claim 17 is recited in claim 16 of the ‘259 patent.
The limitations of the instant claim 18 is recited in claim 17 of the ‘259 patent.
The limitations of the instant claim 19 is recited in claim 18 of the ‘259 patent.
The limitations of the instant claim 20 is recited in claim 19 of the ‘259 patent.
The claims of ‘259 patent are found to anticipate the instant claims.
Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims of U.S. Patent No. 11,680,284.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are directed to methods of identifying a structural variant, the method comprising:
exposing a nucleic acid to a plurality of molecular inversion probes (MIPs),
each MIP comprising two targeting arms designed to hybridize upstream and downstream of a target in a genome;
connecting together two of the MIPs via arms that have hybridized to the same molecule to create an inter-probe product;
detecting the inter-probe product; and
identifying a structural variant of the genome in the nucleic acid;
while
the claims of U.S. Patent No. 11,680,284 are drawn nucleic acid product(s) comprising:
a first molecular inversion probe comprising a linked pair of targeting arms designed to hybridize upstream and downstream of a first target in a reference genome;
a second molecular inversion probe comprising a linked pair of targeting arms designed to hybridize upstream and downstream of a second target in a reference genome,
wherein the first and second targets are noncontiguous; and an inter-probe region connecting one of the targeting arms of the first molecular inversion probe with one of the targeting arms of the second molecular inversion probe,
wherein the second molecular inversion probe and the inter-probe region have been ligated to the first molecular inversion probe to form an inter-probe product;
wherein at least one of the first and second molecular inversion probes comprises a phosphorothioate base.
The instant claims 1-20 are directed to methods for making and using of the inter-probe products as claimed by claims 1-20 of U.S. Patent No. 11,680,284.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
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