Gene fusion

Abstract

The disclosure provides gene fusion variants and novel associations with disease states, as well as kits, probes, and methods of using the same.

1 - 8 . (canceled) 
     
     
         9 . A method of detecting lung squamous cell carcinoma or thyroid carcinoma in a human tissue or blood sample, the method comprising:
 amplifying a CCDC6/RET gene fusion or fusion gene product using a set of probes that specifically recognize at least one nucleic acid in the CCDC6/RET gene or fusion gene product of Table 4; and   detecting the presence of the CCDC6/RET gene fusion or fusion gene product in the sample;   wherein detecting the presence of the CCDC6/RET fusion or fusion gene product, indicates lung squamous cell carcinoma or thyroid carcinoma is present in the sample.   
     
     
         10 . A method of detecting breast carcinoma in a human tissue or blood sample, the method comprising:
 amplifying a ERC1/RET gene fusion using a set of probes that specifically recognize at least one nucleic acid in the ERC1/RET fusion gene or a fusion gene product of Table 4; and   detecting the presence of the ERC1/RET gene fusion or fusion gene product in the sample;   wherein detecting the presence of the ERC1/RET fusion gene or fusion gene product, indicates breast carcinoma is present in the sample.   
     
     
         11 - 12 . (canceled) 
     
     
         13 . The method of  claim 9 , wherein the sample is a patient tumor sample. 
     
     
         14 . The method of  claim 13 , further comprising diagnosing the patient as having bladder carcinoma, head and neck squamous cell carcinoma, or lung squamous cell carcinoma when a nucleic acid comprising a sequence selected from SEQ ID NOs: 1-12 is present in the patient sample. 
     
     
         15 . The method of  claim 13 , further comprising diagnosing the patient as having breast carcinoma when the ERC1/RET fusion gene or fusion gene product is present in the sample. 
     
     
         16 . The method of  claim 13 , further comprising diagnosing the patient as having thyroid carcinoma when the CCDC6/RET fusion gene or fusion gene product is present in the sample. 
     
     
         17 . The method of  claim 10 , wherein the sample is a patient tumor sample. 
     
     
         18 . The method of  claim 10 , wherein the detecting is by sequencing of the amplified nucleic acid. 
     
     
         19 . A method of detecting a TMPRSS2/ERG gene fusion comprising a breakpoint of Table 3 in a human tissue or blood sample from a patient having prostate cancer, the method comprising:
 generating a reaction mixture comprising a plurality of primers that specifically hybridize to a target nucleic acid comprising one of the TMPRSS2/ERG breakpoints of Table 3 and nucleic acid from the human tissue or blood sample wherein the sample comprises one or more target nucleic acid(s);   amplifying the target nucleic acid(s) using the plurality of primers, thereby producing amplicons;   sequencing the amplicons; and   detecting the presence of a TMPRSS2/ERG gene fusion comprising a breakpoint of Table 3.   
     
     
         20 . The method of  claim 19 , wherein the sample is a patient tumor sample. 
     
     
         21 . The method of  claim 19 , wherein the sequencing is by next generation sequencing technology.