Diagnosis and prognosis of various types of cancers

Abstract

The present invention provides nucleic acid sequences that are used for identification, classification and diagnosis of specific types of cancers. The nucleic acid sequences can also be used for prognosis evaluation of a subject based on the expression pattern of a biological sample.

1 . A method for distinguishing between high grade bladder carcinoma and low grade bladder carcinoma, the method comprising: obtaining a biological sample from a subject; determining in said sample an expression level of nucleic acid sequences selected from the group consisting of SEQ ID NOS: 11-21 and 31-39, a fragment thereof or a sequence having at least about 80% identity thereto; whereby the differential higher expression of any of said nucleic acid sequences allows the classification of high grade bladder carcinoma. 
     
     
         2 . The method of  claim 1 , wherein said sample is a bladder sample. 
     
     
         3 . A method for distinguishing between small intestine carcinoid tumor and small intestine stromal tumor, the method comprising: obtaining a biological sample from a subject; determining in said sample an expression level of nucleic acid sequences selected from the group consisting of SEQ ID NOS: 1-10 and 22-30, a fragment thereof or a sequence having at least about 80% identity thereto; whereby the differential higher expression of any of said nucleic acid sequences allows the classification of small intestine carcinoid tumor. 
     
     
         4 . The method of  claim 3 , wherein said sample is a small intestine sample. 
     
     
         5 . A method for distinguishing between hepatocellular carcimoma (HCC) and liver metastasis, the method comprising: obtaining a biological sample from a subject; determining in said sample an expression level of nucleic acid sequences selected from the group consisting of SEQ ID NOS: 40-62, a fragment thereof or a sequence having at least about 80% identity thereto; whereby the differential expression of any of said nucleic acid sequences allows the classification of HCC versus liver metastasis. 
     
     
         6 . The method of  claim 5 , wherein said sample is liver sample. 
     
     
         7 . The method of  claim 1 , wherein said biological sample is selected from the group consisting of bodily fluid, a cell line and a tissue sample. 
     
     
         8 . The method of  claim 7 , wherein said sample is a fresh, frozen, fixed, wax-embedded or formalin fixed paraffin-embedded (FFPE) tissue. 
     
     
         9 . The method of  claim 1 , wherein the method comprises determining the expression levels of at least two nucleic acid sequences. 
     
     
         10 . The method of  claim 9 , wherein the method further comprises combining one or more expression ratios of said nucleic acid sequences. 
     
     
         11 . The method of  claim 7 , wherein the expression levels are determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. 
     
     
         12 . The method of  claim 11 , wherein the nucleic acid hybridization is performed using a solid-phase nucleic acid biochip array or in situ hybridization. 
     
     
         13 . The method of  claim 11 , wherein the nucleic acid amplification method is real-time PCR. 
     
     
         14 . A kit for determining the grade of bladder carcinoma, said kit comprising a probe comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 11-21 and 31-39, a fragment thereof and a sequence having at least about 80% identity thereto. 
     
     
         15 . A kit for diagnosing a subject with a small intestine tumor, said kit comprising a probe comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: 1-10 and 22-30, a fragment thereof and a sequence having at least about 80% identity thereto. 
     
     
         16 . The kit of  claim 15 , wherein said small intestine tumor is small intestine carcinoid tumor or small intestine stromal tumor. 
     
     
         17 . A kit for diagnosing a subject with hepatocellular carcimoma (HCC) or with liver metastasis, said kit comprising a probe comprising a nucleic acid sequence selected from the group consisting of SEQ ID NOS: SEQ ID NOS: 40-62, a fragment thereof and a sequence having at least about 80% identity thereto. 
     
     
         18 . The method of  claim 3 , wherein said biological sample is selected from the group consisting of bodily fluid, a cell line and a tissue sample. 
     
     
         19 . The method of  claim 5 , wherein said biological sample is selected from the group consisting of bodily fluid, a cell line and a tissue sample. 
     
     
         20 . The method of  claim 3 , wherein the method comprises determining the expression levels of at least two nucleic acid sequences. 
     
     
         21 . The method of  claim 5 , wherein the method comprises determining the expression levels of at least two nucleic acid sequences.