Office Action 1: Non-Final Rejection (2024-08-29)
Rejection types: Double Patenting

CLAIMS:
AMENDMENTS TO THE CLAIMS

This listing of claims will replace all prior versions, and listings, of claims in the application:

Listing of Claims:

1-32. (Cancelled) 231

33\. (New) A composition for analyzing a target polynucleotide in a sample, the composition comprising:
a first probe configured to hybridize to a first target sequence of the target polynucleotide, the first probe including (i) an interrogation site bar code that is non-complementary to the first target sequence,
(ii) a first complementary sequence portion 5' of the interrogation site barcode, the first complementary sequence portion being complementary to the first target sequence,
(iii) a second complementary sequence portion 3' of the interrogation site barcode, the second complementary sequence portion being complementary to the first target sequence, and
(iv) a universal sequence that is non-complementary to the first target sequence, the universal sequence being 5' of the first complementary sequence portion; and
a second probe configured to hybridize to a second target sequence of the target polynucleotide, the second probe including (i) a complementary sequence portion that is complementary to the second target sequence, and
(ii) a non-complementary sequence that is non-complementary to the second target sequence.

34\. (New) The composition of claim 34, wherein the non-complementary sequence of the second probe and the complementary sequence of the second probe are immediately adjacent one another.

35\. (New) The composition of claim 34, wherein the non-complementary sequence of the second probe is 3' of the complementary sequence of the second probe.

36\. (New) The composition of claim 33, wherein the non-complementary sequence of the second probe comprises a universal sequence.

37\. (New) The composition of claim 36, wherein the universal sequence of the second probe and the universal sequence of the first probe are the same.

38\. (New) The composition of claim 33, wherein the 3' end of the first probe is complementary to one form of a single nucleotide polymorphism (SNP) or other genetic variation.

39\. (New) The composition of claim 33, wherein the first and second probes are configured to be adjacent one another when hybridized to the target polynucleotide.

40\. (New) The composition of claim 33, wherein the first and second probes are configured to be spaced by 1 to 500 nucleotides when hybridized to the target polynucleotide.

41\. (New) The composition of claim 33, wherein the interrogation site bar code is 10-16 nucleotides in length.

42\. (New) A composition for analyzing a target polynucleotide in a sample, the composition comprising:
a first probe configured to hybridize to a first target sequence of the target polynucleotide, the first probe including (v) an interrogation site bar code that is non-complementary to the first target sequence,
(vi) a first complementary sequence portion 5' of the interrogation site barcode, the first complementary sequence portion being complementary to the first target sequence, (vii) a second complementary sequence portion 3' of the interrogation site barcode, the second complementary sequence portion being complementary to the first target sequence, and
(viii) a universal sequence that is non-complementary to the first target sequence; and
a second probe configured to hybridize to a second target sequence of the target polynucleotide, the second probe including (iii) a complementary sequence portion that is complementary to the second target sequence, and
(iv) a non-complementary sequence that is non-complementary to the second target sequence, wherein the first probe is configured to hybridize to the target polynucleotide 5' of the second probe.

43\. (New) The composition of claim 42, wherein the non-complementary sequence of the second probe and the complementary sequence of the second probe are immediately adjacent one another.

44\. (New) The composition of claim 43, wherein the non-complementary sequence of the second probe is 3' of the complementary sequence of the second probe.

45\. (New) The composition of claim 42, wherein the non-complementary sequence of the second probe comprises a universal sequence.

46\. (New) The composition of claim 45, wherein the universal sequence of the second probe and the universal sequence of the first probe are the same.

47\. (New) The composition of claim 42, wherein the 3' end of the first probe is complementary to one form of a single nucleotide polymorphism (SNP) or other genetic variation.

48\. (New) The composition of claim 42, wherein the first and second probes are configured to be adjacent one another when hybridized to the target polynucleotide.

49\. (New) The composition of claim 42, wherein the first and second probes are configured to be spaced by 1 to 500 nucleotides when hybridized to the target polynucleotide.

50\. (New) The composition of claim 42, wherein the interrogation site bar code is 10-16 nucleotides in length.

51\. (New) A kit for analyzing a target polynucleotide in a sample, the kit comprising:
the composition of claim
33; and
a set of primers, at least one of which is a universal primer complementary to the universal sequence of the first probe.

52\. (New) The kit of claim 51, further comprising an additional sequence that includes one or more of: a sample index; an adaptor for next generation sequencing; or a capture probe or sequence, wherein the set of primers is configured to add the additional sequence.
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OFFICE ACTION:
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 .
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 33-52 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11,118,216. Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘216 claims, while directed to methods of using the instantly claimed probes, nevertheless disclose the structure of the instantly claimed probes.
Conclusion

APPLICANT REBUTTAL: REMARKS
Claims 33-52 were rejected on the ground of nonstatutory double patenting as being
unpatentable over claims 1-19 of U.S. Patent No. 11,118,216. Enclosed herewith is a Terminal Disclaimer over U.S. Patent No. 11,118,216. Withdrawal of the rejection and allowance of the application is respectfully requested.
The Director is hereby authorized to charge any fees that may be due, and to credit any overpayment to Deposit Account No. 02-4800.
Respectfully submitted, BUCHANAN INGERSOLL & ROONEY PC

NEXT OFFICE ACTION: EXAMINER'S AMENDMENT
An examiner’s amendment to the record appears below. Should the changes and/or additions be unacceptable to applicant, an amendment may be filed as provided by 37 CFR 1.312. To ensure consideration of such an amendment, it MUST be submitted no later than the payment of the issue fee.
Authorization for this examiner’s amendment was given in an interview with Mythili Markowski on 01/23/2025.
The application has been amended as follows:
Amend claim 34 to depend from claim 33.
Conclusion

CITED REFERENCE SUMMARIES: Ref US11118216: Claims:
1. A method for analyzing one or more target polynucleotides in one or more samples, the method comprising the steps of:
(a) providing one or more samples, each sample comprising one or more target polynucleotides, each target polynucleotide comprising a first target sequence and a second target sequence;
(b) providing a plurality of first and second complementary probes comprising a first and second complementary probe for each target polynucleotide,
(i) each first complementary probe having two sequence portions that are complementary to a first target sequence of the target polynucleotide, and two sequence portions that are non-complementary to the first target sequence, wherein the non-complementary portions include an interrogation site bar code sequence and a universal sequence, and wherein a first complementary sequence portion is at 5′ of the interrogation site bar code and a second complementary sequence portion is at 3′ of the interrogation site bar code, wherein the universal sequence is 5′ to the first complementary sequence portion; and
(ii) each second complementary probe having a sequence portion that is complementary to a second target sequence of the target polynucleotide and an immediately adjacent sequence portion that is non-complementary to said second target sequence;

(c) incubating said plurality of first and second complementary probes with each sample under hybridization conditions such that first and second complementary probes hybridize to their complementary target polynucleotide in a sample to form a hybridization complex;
(d) joining first and second complementary probes that are hybridized to first and second target sequences of a target polynucleotide in a sample to form a product polynucleotide; and
(e) determining the presence, absence, amount or copy number of each target polynucleotide in said one or more samples by analyzing product polynucleotides or the complements thereof.
2. The method according to claim 1, wherein the immediately adjacent sequence portion of said second complementary probe comprises a universal sequence.
3. The method according to claim 2, wherein the universal sequence of said second complementary probe comprises a universal primer sequence that is complementary to a primer sequence which can be used to add one or more of (i) a sample index, (ii) an additional sequence, (iii) an additional sequence for sequence data generation or another form of detection, and (iv) another moiety.
4. The method according to claim 3 wherein the universal primer sequence includes a PCR primer sequence and/or a primer sequence to add an additional sequence for sequence data generation or another form of detection.
5. The method according to claim 3, wherein the additional sequence for sequence data generation or another form of detection is an adapter for next generation sequencing.
6. The method according to claim 3, wherein the additional sequence for sequence data generation or another form of detection is a capture sequence, optionally wherein the capture sequence is for capture on a solid support.
7. The method according to claim 1, wherein the universal sequence of said first complementary probe comprises a universal primer sequence that is complementary to a priming sequence which can be used to add one or more of (i) a sample index, (ii) an additional sequence, (iii) an additional sequence for sequence data generation or another form of detection, and (iv) another moiety.
8. The method according to claim 7 wherein the universal primer sequence includes a PCR primer sequence and/or a primer sequence to add an additional sequence for sequence data generation or another form of detection.
9. The method according to claim 7, wherein the additional sequence for sequence data generation or another form of detection is an adapter for next generation sequencing.
10. The method according to claim 7, wherein the additional sequence for sequence data generation or another form of detection is a capture sequence, optionally wherein the capture sequence is for capture on a solid support.
11. The method according to claim 1, wherein the method is solution-based.
12. The method according to claim 1, wherein the 3′ end of the first complementary probe is complementary to one form of a single nucleotide polymorphism (SNP) or other genetic variation.
13. The method according to claim 1, wherein the method is for use in genotyping, wherein the method comprises providing one or more variants of the first complementary probe, wherein the variants differ in the identity of the nucleotide or nucleotides at the 3′ end of the first complementary probe, and wherein said determining comprises quantifying the relative frequencies of product polynucleotides or complements thereof comprising the sequences of the one or more variants of the first complementary probe compared to the sequences of the other variants of said first complementary probe and correlating said frequencies with a genotype.
14. The method according to claim 1, wherein the method is for use in determining the copy number variation of a target polynucleotide, and wherein said determining comprises comparing the amount of signal produced for a product polynucleotide or the complement thereof to a known reference or to the amount of signal produced by another product polynucleotide or the complement thereof.
15. The method according to claim 1, wherein the method is for use in expression analysis in determining presence of a target polynucleotide, wherein the target polynucleotide is an RNA transcript, and wherein said determining comprises comparing the amount of signal produced for a product polynucleotide or the complement thereof to a known reference or to the amount of signal produced by another product polynucleotide or the complement thereof.
16. The method according to claim 1 further comprising pooling product polynucleotides formed from the samples.
17. The method according to claim 16, further comprising enriching said product polynucleotides prior to the pooling step.
18. The method according to claim 17, wherein said enriching comprises, (a) providing a set of PCR priming sequences comprising a first primer that is associated with a priming sequence on the first complementary probe, and a second primer that is complementary to a PCR priming sequence on the second complementary probe, and (b) amplifying the product polynucleotide.
19. The method according to claim 1, wherein in (a) two or more samples are provided.