Office Action 2: Notice of Allowance (2025-02-03)

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:
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

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