Methods of detecting gene fusions

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.

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.