Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
For reissue applications filed on or after September 16, 2012, all references to 35 U.S.C. 251 and 37 CFR 1.172, 1.175, and 3.73 are to the current provisions.
Status of Application and Claims
US Patent 9,593,365 issued on 3/14/17 with claims 1-43. Reissue application 16/353,937 was filed on 3/14/19 and broadened the claims of the ’365 patent; the ’937 application issued as US Patent RE50,065 on 7/20/24. This application was filed on 6/18/24 as a continuation of the ’937 application. Patent claims 1, 2, 6, and 31 have been amended, and new claims 44-61 have been added. Claims 1-61 are pending and under examination.
This reissue application is a continuation of the ’937 application, but no certificate of correction has been submitted in US Patent RE50,065 to inform the public about the presence of this reissue application. See MPEP 1451(II) (“If the parent reissue application issues without any cross reference to the continuation reissue application, amendment of the parent reissue patent to include a cross-reference to the continuation reissue application must be effected at the time of allowance of the continuation reissue application by certificate of correction.”). Applicant should submit the required certificate of correction in the RE’065 patent.
Claim Objections
Claim 26 is objected to for omitting the word “the” after “to” at line 4. Claim 26 might also be amended to refer to “ends” (plural) rather than “end” (singular).
Nucleotide and/or Amino Acid Sequence Disclosures
This application is governed by ST.26 rules. Sequence listings submitted in either non-provisional applications filed under 35 U.S.C. 111(a) or provisional applications filed under 111(b) that have a filing date on or after 7/1/22, including reissue applications, must be in XML format and comply with WIPO Standard ST.26 and 37 CFR 1.831 through 1.835. See MPEP 1410, 2415.01.
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:
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 the sequence listing provided on 6/18/24 was filed in accordance with WIPO ST.25, not ST.26 as is required. See “Sequence Listing Report for Application No: 18746841” dated 2/9/26.
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
• An amendment to the specification inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(b)(2) and as governed by 37 CFR 1.173(b) and (d); and a statement that the specification amendment contains no new matter.
Reissue Declaration
The reissue oath/declaration filed with this application is defective because it fails to identify at least one error which is relied upon to support the reissue application. The reissue declaration submitted with this application provides exactly the same error statement as that set forth in parent reissue application 16/353,937. This is improper because the ’937 application has already corrected the identified error by issuance of US Patent RE50,065. If the same error corrected in the parent is also being corrected in the continuation reissue application, but the error is being corrected in a different way, a statement is needed to explain compliance with 37 CFR 1.175(f)(2). See MPEP 1414(II)(D).
Claim Rejections – 35 U.S.C. 251
Claims 1-61 are rejected as being based upon a defective reissue declaration under 35 U.S.C. 251 as set forth above. See 37 CFR 1.175.
The nature of the defect in the declaration is set forth in the discussion above in this Office action.
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 1-61 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 is a method for localized or spatial detection and/or analysis of RNA, but the conclusion of claim 1 at line 16 only refers to “spatially detecting” RNA. It is unclear whether the claim refers to both localized and spatial relationships and also whether it is limited to detection or also includes “analysis” of the RNA. If the latter is the case, the difference between the “detecting” and the “analysis” is unclear. Clarification is required.
Claim 1 is also a method for detection and/or analysis of RNA in a tissue sample or a portion thereof, but the method refers at lines 7 and 14-16 to “the tissue sample.” It is not clear whether the steps of claim 1 apply only to the embodiment in which the subject of the detection/analysis steps is a tissue sample per se or also to embodiments in which the subject is a portion of a tissue sample. Clarification is required.
Claims 2-43 depend from claim 1 and do not rectify the indefiniteness, so they must also be rejected under 35 U.S.C. 112, second paragraph.
In addition, claims 2, 4, 6, 9, 13, 18, 31, and 35-39 depend directly or indirectly from claim 1 and refer to “the tissue sample” or “a tissue sample,” but as discussed above, claim 1’s preamble refers to a tissue sample or a portion thereof. It is unclear whether these claims intend to limit the method to embodiments in which the subject of the detection/analysis steps are a tissue sample per se. (Compare to claim 3, e.g., which refers to both.) See MPEP 2173.05(e). Clarification is required.
Claim 26 refers at line 2 to “a surface probe,” i.e., a singular probe. It then goes on to refer to “surface probes that are immobilized on the object substrate,” i.e., a plurality of probes. It is unclear whether one surface probe or more than one surface probe is hybridized and immobilized. Claims 27-29 likewise refer to “surface probes,” i.e., a plurality, and are likewise indefinite. See MPEP 2173.05(e) (“two levers” example).
Claim 44 refers at line 7 to “a captured nucleic acid molecule” and at line 8 to a “nucleic acid molecule” generated from that captured nucleic acid molecule, but it then refers at lines 9-10 to simply “the nucleic acid molecule.” It is unclear whether the molecule at lines 9-10 refers to the captured nucleic acid molecule or to the nucleic acid molecule generated in step (c). See MPEP 2173.05(e) (“two levers” example). Clarification is required. Claims 45-52 depend from claim 44 and do not rectify the indefiniteness, so they must also be rejected under 35 U.S.C. 112, second paragraph.
In addition, claims 45 and 46 refer to “the nucleic acid,” but it is unclear which nucleic acid in claim 44 they are referencing. Clarification is required. See MPEP 2173.05(e) (“two levers” example).
Claim 53 refers in its preamble to spatial detection in a tissue section or a portion thereof, but lines 7 and 16-17 refer to “the tissue section.” It is not clear whether the steps of claim 53 apply only to the embodiment in which the subject of the detection step is a tissue sample per se or also to embodiments in which the subject is a portion of a tissue sample. Clarification is required. Claims 54-61 depend from claim 53 and do not rectify the indefiniteness, so they must also be rejected under 35 U.S.C. 112, second paragraph.
In addition, claims 54 and 55 refer to “the nucleic acid,” but it is unclear which nucleic acid in claim 53 they are referencing. Clarification is required. See MPEP 2173.05(e) (“two levers” example).
Double Patenting
Terminal Disclaimer Filed in Parent Applications
A terminal disclaimer was filed in application 14/434,274 over application 14/111,182, which is now US Patent 10,030,261. A terminal disclaimer was also filed in application 16/353,937 (now RE50,065) over the ’261 patent. Where a terminal disclaimer was filed and approved in an original application, a copy of that terminal disclaimer is not required to be filed by applicant in the reissue application. MPEP 1490(VI)(B).
Rejection
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 1-61 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-57 of U.S. Patent No. RE50,065. Although the claims at issue are not identical, they are not patentably distinct from each other.
The ’065 patent claims a method for spatial detection of RNA in a tissue section (claim 1), which is an embodiment of the preamble to examined independent claims 1, 44, and 53.
The ’065 patent claims a first step of providing an object substrate on which at least one species of capture probe comprising a capture domain is directly immobilized on the object substrate such that the capture probe is oriented to have a free 3’ end such that it functions as a primer for reverse transcriptase (RT). (Claim 1, step (a).) This step is an embodiment of step (a) of examined claim 1 with respect to the nature of the immobilization and the type of enzyme that employs the primer. It is also an embodiment of steps (a) and a portion of (b) of examined claim 44 and of step (a) of examined claim 53 for the same reasons.
The ’065 patent then claims a step of contacting the object substrate with a tissue section such that RNA within the section directly hybridizes to the capture probe under a first set of conditions. (Claim 1, step (b).) This step is an embodiment of examined claim 1, step (b), with respect to the nature of the hybridization. It is also an embodiment of the second portion of step (b) of examined claim 44 and of step (b) of examined claim 53 for the same reasons.
The ’065 patent then claims a step of generating first-strand cDNA molecules from the hybridized RNA using the capture probes as RT primers and a fluorescently labeled oligonucleotide, thereby incorporating that labeled oligonucleotide into the cDNA, wherein the incorporation and generation steps are contemporaneous. (Claim 1, step (c).) This step is an embodiment of steps (c) and (d) of examined claim 1 with respect to the nature of the enzyme employing the primers and the order of the steps. It is also an embodiment of step (c) of examined claim 44 with respect to the enzyme and an embodiment of step (c) of examined claim 53 with respect to the enzyme, the sort of labeled nucleic-acid molecule, the type of label, and the order of steps.
The ’065 patent then claims a step of detecting a signal from the fluorescently labeled cDNA on the object substrate, thereby spatially detecting RNA within the tissue section. (Claim 1, step (d).) This step is an embodiment of step (e) of examined claim 1 with respect to the nature of the detection. It is also an embodiment of step (d) of examined claim 44 with respect to the detected nucleic-acid molecule and an embodiment of step (e) of examined claim 53 with respect to the detected nucleic-acid molecule.
The ’065 patent contains an optional step of imaging the tissue section and combining the signal from the fluorescently labeled cDNA molecules with that image, thereby spatially detecting the RNA in the tissue section. (Claim 1, step (e).) This step is an embodiment of step (f) of examined claim 1 with respect to the nature of the correlation. It is also an unrecited but permitted step within examined claim 44 and an embodiment of step (e) of examined claim 53 with respect to the nature of the correlation.
Claim 1 of the ’065 patent therefore anticipates each of examined claims 1, 44, and 53 because it represents embodiments lying within the scope of these claims.
Claims 2-43 of the ’065 patent correspond to examined claims 2-43, respectively. Claims 45-52 correspond to examined claims 45-52, respectively, and to examined claims 54-61, respectively.
Maintenance Fees
Applicant is reminded of the requirement to pay all applicable maintenance fees on the original patent. See MPEP 1415.01.
Duty to Disclose
Applicant is reminded of the continuing obligation under 37 CFR 1.178(b), to timely apprise the Office of any prior or concurrent proceeding in which Patent No. 9,593,365 is or was involved. These proceedings would include any trial before the Patent Trial and Appeal Board, interferences, reissues, reexaminations, supplemental examinations, and litigation.
Applicant is further reminded of the continuing obligation under 37 CFR 1.56, to timely apprise the Office of any information which is material to patentability of the claims under consideration in this reissue application.
These obligations rest with each individual associated with the filing and prosecution of this application for reissue. See also MPEP §§ 1404, 1442.01 and 1442.04.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lora E Barnhart Driscoll, whose telephone number is (571)272-1928. The examiner can normally be reached M-F 7:00-4:00 p.m. ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Patricia Engle, can be reached at 571-272-6660. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Lora E Barnhart Driscoll/Patent Reexamination Specialist, Art Unit 3991
Conferees:
/KSO/Patent Reexamination Specialist, Art Unit 3991
/Patricia L Engle/SPRS, Art Unit 3991
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