Methods for determining a nucleotide sequence contiguous to a known target nucleotide sequence

1. A method of determining the nucleotide sequence contiguous to a known target nucleotide sequence, the method comprising:

(a) ligating a target nucleic acid comprising the known target nucleotide sequence with a universal oligonucleotide tail-adaptor, wherein the universal oligonucleotide tail-adaptor comprises a blocking strand and an amplification strand;

(b) amplifying a portion of the target nucleic acid and the amplification strand of the universal oligonucleotide tail-adaptor with a first adaptor primer and a first target-specific primer;

(c) amplifying a portion of the amplicon resulting from step (b) with a second adaptor primer and a second target-specific primer; and

(d) sequencing the amplified portion from step (c) using a first and second sequencing primer;

wherein the universal oligonucleotide tail-adaptor comprises a first ligatable duplex end and a second unpaired end;

wherein the blocking strand comprises a 5′ duplex portion;

wherein the amplification strand comprises an unpaired 5′ portion, a 3′ duplex portion, and a 3′ T overhang;

wherein the amplification strand comprises nucleic acid sequences identical to the first and second sequencing primers;

wherein the duplex portions of the blocking strand and the amplification strand are substantially complementary and form the first ligatable duplex end comprising a 3′ T overhang;

wherein the duplex portion is of sufficient length to remain in duplex form at the ligation temperature;

wherein the first target-specific primer comprises a nucleic acid sequence that can specifically anneal to the known target nucleotide sequence of the target nucleic acid at the annealing temperature;

wherein the second target-specific primer comprises a 3′ portion comprising a nucleic acid sequence that can specifically anneal to a portion of the known target nucleotide sequence comprised by the amplicon resulting from step (b), and a 5′ portion comprising a nucleic acid sequence that is identical to the second sequencing primer and the second target-specific primer is nested with respect to the first target-specific primer;

wherein the first adaptor primer comprises a nucleic acid sequence identical to a 5′ portion of the first sequencing primer; and

wherein the second adaptor primer comprises a nucleic acid sequence identical to a portion of the first sequencing primer and is nested with respect to the first adaptor primer.

2. The method of claim 1 , wherein the blocking strand of the universal oligonucleotide tail-adaptor further comprises a 3′ unpaired portion which is not substantially complementary to the 5′ unpaired portion of the amplification strand; and

wherein the 3′ unpaired portion of the blocking strand is not substantially complementary to or substantially identical to any of the primers.

3. The method of claim 1 , wherein the second adaptor primer is nested with respect to the first adaptor primer by at least 3 nucleotides.

4. The method of claim 1 , wherein the portion of the amplification strand that comprises a nucleic acid sequence identical to the first and second sequencing primers is comprised, at least in part, by the 5′ unpaired portion of the amplification strand.

5. The method of claim 1 , wherein the first target-specific primer further comprises a 5′ tag sequence portion comprising a nucleic acid sequence of high GC content which is not substantially complementary to or substantially identical to any other portion of any of the primers.

6. The method of claim 1 , wherein the second adaptor primer is identical to the full length of the first sequencing primer.

7. The method of claim 1 , wherein the method further comprises prior to step (a), the steps of:

mechanically shearing a nucleic acid sample to produce the target nucleic acid;

subjecting the target nucleic acid to end-repair;

subjecting the target nucleic acid to phosphorylation;

and subjecting the target nucleic acid to adenylation.

8. The method of claim 1 , wherein the target nucleic acid is prepared from a sample comprising RNA, and the method further comprises a first step of subjecting the sample to a reverse transcriptase regimen.

9. The method of claim 1 , wherein the known target sequence is comprised by a gene rearrangement.

10. The method of claim 9 , wherein the gene rearrangement comprises a fusion oncogene.

11. The method of claim 1 , wherein the amplified portion from step (c) is sequenced by a next-generation sequencing method.

12. The method of claim 1 , wherein the method comprises contacting the target nucleic acid, or separate portions of the target nucleic acid, with a plurality of sets of first and second target-specific primers.

13. The method of claim 1 , wherein the universal oligonucleotide tail-adaptor further comprises a barcode portion.

14. The method of claim 13 , wherein multiple samples are each contacted with a universal oligonucleotide tail-adaptor with a unique barcode portion and wherein the samples are pooled after step (a).

15. The method of claim 1 , wherein the target nucleic acid is obtained from a subject in need of treatment for a disease associated with a genetic alteration.

16. The method of claim 1 , wherein the known target sequence comprises a sequence from a gene selected from the group of:

anaplastic lymphoma kinase (ALK); c-ros oncogene 1 (ROS1); and rearranged during transfection (RET).

17. A method of treating cancer, the method comprising:

detecting, in a tumor sample obtained from a subject in need of treatment for cancer, the presence of one or more oncogene rearrangements using the method of claim 1 ; and

administering a cancer treatment which is effective against tumors having any of the detected oncogene rearrangements.

18. The method of claim 17 , wherein the cancer treatment is selected from the group consisting of:

an ALK inhibitor; crizotinib (PF-02341066); AP26113; LDK378; 3-39; AF802; IPI-504; ASP3026; X-396; GSK-1838705A; CH5424802; and NVP-TAE684.

19. The method of claim 17 , wherein the cancer treatment is selected from the group consisting of:

a ROS1 inhibitor; an ALK inhibitor; crizotinib (PF-02341066); AP26113; LDK378;

3-39; AF802; IPI-504; ASP3026; X-396; GSK-1838705A; CH5424802;

and NVP-TAE684.

20. The method of claim 17 , wherein the cancer treatment is selected from the group consisting of:

a RET inhibitor; DP-2490; DP-3636; SU5416; BAY 43-9006; BAY 73-4506 (regorafenib); ZD6474; NVP-AST487; sorafenib; RPI-1; XL184; vandetanib; sunitinib; imatinib; pazopanib; axitinib; motesanib; gefitinib; and withaferin A.