Methods of detecting gene fusions

1. A method of detecting presence of a gene fusion in a sample from a subject comprising:

contacting the sample with one or more first probes complementary to a first nucleic acid from a first gene, wherein the one or more first probes are linear nucleic acids and complementary to the first nucleic acid 5′ to a fusion point between the first nucleic acid and a second nucleic acid from a second gene, under conditions sufficient for the one or more first probes to specifically hybridize to the first nucleic acid, wherein the sample comprises cell lysate or isolated nucleic acids, and wherein the first nucleic acid and the second nucleic acid are mRNA;

contacting the sample with one or more second probes complementary to the first nucleic acid, wherein the one or more second probes are linear nucleic acids and complementary to the first nucleic acid 3′ to the fusion point between the first nucleic acid and the second nucleic acid, under conditions sufficient for the one or more second probes to specifically hybridize to the first nucleic acid;

wherein the one or more first probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 187, 189, 191, or 192 or the complement thereof, the one or more second probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 197-200 or the complement thereof, or a combination of two or more thereof;

contacting the sample with a nuclease specific for single-stranded nucleic acids;

detecting an amount of the one or more first probes and an amount of the one or more second probes in the sample;

determining a ratio consisting of the amount of the one or more first probes to the amount of the one or more second probes in the sample; and

detecting the presence of the gene fusion if the ratio of the one or more first probes to the one or more second probes is significantly different from a control by at least two standard deviations.

2. The method of claim 1 , further comprising determining that the gene fusion does not comprise a 3′ portion of the first nucleic acid if the ratio of the one or more first probes to the one or more second probes is greater than a control by at least two standard deviations or determining that the gene fusion does not comprise a 5′ portion of the first nucleic acid if the ratio of the one or more first probes to the one or more second probes is less than a control by at least two standard deviations.

3. The method of claim 1 , wherein the one or more first probes and the one or more second probes are each 50-200 nucleotides in length.

4. The method of claim 1 , wherein detecting the one or more first probes and the one or more second probes comprises contacting the sample with one or more first detection probes which are capable of hybridizing with the one or more first probes and one or more second detection probes which are capable of hybridizing with the one or more second probes.

5. The method of claim 1 , further comprising:

contacting the sample with a fusion probe comprising a 5′ portion complementary to the first nucleic acid and a 3′ portion complementary to the second nucleic acid under conditions sufficient for the probe to specifically hybridize to the gene fusion, wherein the fusion probe spans a fusion point of the first nucleic acid and the second nucleic acid, prior to contacting the sample with the nuclease;

detecting an amount of the fusion probe;

determining a ratio consisting of the amount of the fusion probe to the amount of the one or more first probes in the sample, thereby determining a percentage of the gene fusion in the sample relative to the first nucleic acid or determining a ratio consisting of the amount of the fusion probe to the amount of the one or more second probes in the sample, thereby determining a percentage of the gene fusion in the sample relative to the second nucleic acid.

6. The method of claim 5 , wherein the fusion probe is about 10 to 200 nucleotides in length.

7. The method of claim 1 , wherein the one or more first probes and the one or more second probes each further comprise a detectable label.

8. The method of claim 7 , wherein the one or more first probes and the one or more second probes each comprise a different detectable label or wherein the one or more first probes and the one or more second probes each comprise the same detectable label.

9. The method of claim 1 , wherein the cell lysate or isolated nucleic acid sample is obtained from tissue, a tumor biopsy, blood, or a bodily fluid.

10. The method of claim 1 , wherein:

contacting the sample with one or more first probes comprises contacting the sample with two or more first probes complementary to the first nucleic acid 5′ to a fusion point between the first nucleic acid and the second nucleic acid; and

contacting the sample with one or more second probes comprises contacting the sample with two or more second probes complementary to the first nucleic acid 3′ to the fusion point between the first nucleic acid and the second nucleic acid.

11. The method of claim 10 , further comprising:

contacting the sample with one or more third probes complementary to a third nucleic acid from a third gene, wherein the one or more third probes are complementary to the third nucleic acid 5′ to a fusion point between the third nucleic acid and a fourth nucleic acid from a fourth gene, under conditions sufficient for the one or more third probes to specifically hybridize to the third nucleic acid; and

contacting the sample with one or more fourth probes complementary to the third nucleic acid, wherein the one or more fourth probes are complementary to the third nucleic acid 3′ to the fusion point between the third nucleic acid and the fourth nucleic acid, under conditions sufficient for the one or more fourth probes to specifically hybridize to the third nucleic acid;

detecting an amount of the one or more third probes and an amount of the one or more fourth probes in the sample;

determining a ratio consisting of the amount of the one or more third probes to the amount of the one or more fourth probes in the sample; and

detecting the presence of a gene fusion between the third and fourth genes if the ratio of the one or more third probes to the one or more fourth probes is significantly different from a control by at least two standard deviations.

12. The method of claim 11 , wherein:

contacting the sample with one or more third probes comprises contacting the sample with two or more third probes complementary to the third nucleic acid 5′ to a fusion point between the third nucleic acid and the fourth nucleic acid; and

contacting the sample with one or more fourth probes contacting the sample with two or more fourth probes complementary to the third nucleic acid 3′ to the fusion point between the third nucleic acid and the fourth nucleic acid.

13. The method of claim 1 , further comprising:

contacting the sample with one or more third probes complementary to a third nucleic acid from a third gene, wherein the one or more third probes are complementary to the third nucleic acid 5′ to a fusion point between the third nucleic acid and a fourth nucleic acid from a fourth gene, under conditions sufficient for the one or more third probes to specifically hybridize to the third nucleic acid;

contacting the sample with one or more fourth probes complementary to the third nucleic acid, wherein the one or more fourth probes are complementary to the third nucleic acid 3′ to the fusion point between the third nucleic acid and the fourth nucleic acid, under conditions sufficient for the one or more fourth probes to specifically hybridize to the third nucleic acid;

detecting an amount of the one or more third probes and an amount of the one or more fourth probes in the sample;

determining a ratio consisting of the amount of the one or more third probes to the amount of the one or more fourth probes in the sample; and

detecting the presence of a gene fusion between the third and fourth genes if the ratio of the one or more third probes to the one or more fourth probes is significantly different from a control by at least two standard deviations.

14. The method of claim 13 , wherein:

contacting the sample with one or more third probes comprises contacting the sample with two or more third probes complementary to the third nucleic acid 5′ to a fusion point between the third nucleic acid and the fourth nucleic acid; and

contacting the sample with one or more fourth probes comprises contacting the sample with two or more fourth probes complementary to the third nucleic acid 3′ to the fusion point between the third nucleic acid and the fourth nucleic acid.

15. The method of claim 1 , wherein the one or more first probes and the one or more second probes are DNA.

16. A method of detecting presence of a gene fusion in a sample from a subject, comprising:

contacting the sample with one or more first probes complementary to a first nucleic acid from a first gene, wherein the one or more first probes are linear nucleic acids 50-200 nucleotides in length and complementary to the first nucleic acid 5′ to a fusion point between the first nucleic acid and a second nucleic acid from a second gene, under conditions sufficient for the one or more first probes to specifically hybridize to the first nucleic acid, wherein the sample comprises cell lysate or isolated nucleic acids, and wherein the first nucleic acid and the second nucleic acid are mRNA;

contacting the sample with one or more second probes complementary to the first nucleic acid, wherein the one or more second probes are linear nucleic acids 50-200 nucleotides in length and complementary to the first nucleic acid 3′ to the fusion point between the first nucleic acid and the second nucleic acid, under conditions sufficient for the one or more second probes to specifically hybridize to the first nucleic acid;

wherein the one or more first probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 187, 189, 191, or 192 or the complement thereof, the one or more second probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 197-200 or the complement thereof, or a combination of two or more thereof;

contacting the sample with a nuclease specific for single-stranded nucleic acids;

detecting an amount of the one or more first probes and an amount of the one or more second probes in the sample;

determining a ratio consisting of the amount of the one or more first probes to the amount of the one or more second probes in the sample; and

detecting the presence of the gene fusion if the ratio of the one or more first probes to the one or more second probes is significantly different from a control by at least two standard deviations.

17. A high-throughput method of detecting presence of gene fusions in multiple samples from one or more subjects, comprising:

contacting two or more samples contemporaneously with one or more first probes complementary to a first nucleic acid from a first gene, wherein the one or more first probes are linear nucleic acids 50-200 nucleotides in length and complementary to the first nucleic acid 5′ to a fusion point between the first nucleic acid and a second nucleic acid from a second gene, under conditions sufficient for the one or more first probes to specifically hybridize to the first nucleic acid, wherein the two or more samples comprise cell lysate or isolated nucleic acids, and wherein the first nucleic acid and the second nucleic acid are mRNA;

contacting the two or more samples contemporaneously with one or more second probes complementary to the first nucleic acid, wherein the one or more second probes are linear nucleic acids 50-200 nucleotides in length and complementary to the first nucleic acid 3′ to the fusion point between the first nucleic acid and the second nucleic acid, under conditions sufficient for the one or more second probes to specifically hybridize to the first nucleic acid; wherein the one or more first probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 187, 189, 191, or 192 or the complement thereof, the one or more second probes comprise the nucleic acid sequence of any one of SEQ ID NOs: 197-200 or the complement thereof, or a combination of two or more thereof;

contacting the two or more samples contemporaneously with a nuclease specific for single-stranded nucleic acids;

detecting an amount of the one or more first probes and an amount of the one or more second probes in the two or more samples contemporaneously;

determining a ratio consisting of the amount of the one or more first probes to the amount of the one or more second probes in the two or more samples contemporaneously; and

detecting the presence of the gene fusion if the ratio of the one or more first probes to the one or more second probes is significantly different from a control by at least two standard deviations.

18. The method of claim 17 , further comprising:

contacting the two or more samples contemporaneously with one or more third probes complementary to a third nucleic acid from a third gene, wherein the one or more third probes are linear nucleic acids 10 to 200 nucleotides in length and complementary to the third nucleic acid 5′ to a fusion point between the third nucleic acid and a fourth nucleic acid from a fourth gene, under conditions sufficient for the one or more third probes to specifically hybridize to the third nucleic acid;

contacting the two or more samples contemporaneously with one or more fourth probes complementary to the third nucleic acid, wherein the one or more fourth probes are linear nucleic acids 10 to 200 nucleotides in length and complementary to the third nucleic acid 3′ to the fusion point between the third nucleic acid and the fourth nucleic acid, under conditions sufficient for the one or more fourth probes to specifically hybridize to the third nucleic acid;

detecting an amount of the one or more third probes and an amount of the one or more fourth probes in the two or more samples contemporaneously;

determining a ratio consisting of the amount of the one or more third probes to the amount of the one or more fourth probes in the two or more samples contemporaneously; and

detecting the presence of a gene fusion between the third and fourth genes if the ratio of the one or more third probes to the one or more fourth probes is significantly different from a control by at least two standard deviations.

19. The method of claim 17 , wherein at least 10 different gene fusions are detected.