Methods to determine carcinogenesis, identify markers for early cancer diagnosis and identify targets of therapy

Abstract

Methods and techniques to identify carcinogenesis pathways and markers for early cancer diagnosis. Cell sampling is performed on a single tumor with multiple samples being taken from the tumor and outward toward the periphery and beyond. Large scale analysis is performed, such as whole genomic sequencing, to identify the differences between the cells of the various samples. The differences are evaluated to determine which differences represent a change along the carcinogenesis pathway.

What is claimed is: 
     
         1 . A method of analyzing carcinogenesis of a tumor, comprising:
 taking at least one cell sample at a location within the tumor;   taking at least one cell sample at a location within a periphery of the tumor;   performing large scale analysis on all of the cell samples; and   identifying differences between cells of the cell samples.   
     
     
         2 . The method of  claim 1 , wherein the cell samples are from a solid tumor. 
     
     
         3 . The method of  claim 1 , wherein the cell samples are taken by microdissection. 
     
     
         4 . The method of  claim 2 , wherein the large scale analysis comprises at least one of transcriptome sequencing, microRNA profiling, whole genomic sequencing, and bisulfate sequencing. 
     
     
         5 . The method of  claim 1 , wherein the cell samples are taken from a single patient. 
     
     
         6 . The method of  claim 5 , wherein the differences between the cells of the cell samples are compared to differences between cells of cell samples taken from at least one other individual. 
     
     
         7 . The method of  claim 1 , further comprising:
 taking at least one cell sample from normal tissue.   
     
     
         8 . The method of  claim 7 , wherein differences between normal tissue cells and precancerous cells are identified. 
     
     
         9 . The method of  claim 8 , further comprising:
 determining which of the differences between normal tissue cells and precancerous cells are present in cells within the tumor.   
     
     
         10 . The method of  claim 1 , further comprising:
 determining which differences between the cells of the cell samples contribute to the carcinogenesis.   
     
     
         11 . A method of identifying carcinogenesis mutations, comprising:
 sampling cells within a tumor;   sampling cells at a periphery of the tumor;   performing large scale analysis of the samplings of cells; and   identifying differences between cells of the cell samples.   
     
     
         12 . A method of identifying diagnostic markers of cancer, comprising:
 sampling cells at at least one location within a tumor;   sampling cells at a periphery of the tumor;   performing large scale analysis of the samplings of cells; and   identifying differences between cells of the cell samples.   
     
     
         13 . A method of identifying therapeutic targets of cancer, comprising:
 sampling cells at at least one location within a tumor;   sampling cells at a periphery of the tumor;   performing large scale analysis of the samplings of cells; and   identifying differences between cells of the cell samples.