Methods of differentiating metastatic and non-metastatic tumors

Abstract

Methods of screening for a tumor or tumor progression to the metastatic state are disclosed. The screening methods are based on the characterization of DNA by principal components analysis of spectral data yielded by Fourier transform-infrared spectroscopy of DNA samples. The methods are applicable to a wide variety of DNA samples and cancer types. A model developed using multivariate normal distribution equations and discriminant analysis is particularly well suited for distinguishing primary cancerous tissue from metastatic cancerous tissue.

1 . A method for defining the state of tissue comprising the steps: 
 (a) subjecting DNA from a first plurality of tissue samples to Fourier transform-infrared (FT-IR) spectroscopy to produce FT-IR spectral data;    (b) analyzing the FT-IR spectral data of step (a) by principal components analysis (PCA) to provide a principal component (PC) scores;    (c) applying cluster analysis to the PC scores of step (b) to distinguish outlier and non-outlier tissue samples; and    (d) generating an equation, called a first equation, that defines a multivariate version of a normal bell-shaped curve which best fits the PC values from the non-outlier tissue samples, where the first equation defines the state of the first plurality of tissue samples.    
     
     
         2 . A method according to  claim 1 , further comprising repeating steps (a) through (d) with a second plurality of tissue samples, to provide a second equation, where the second equation defines the state of the second plurality of tissue samples.  
     
     
         3 . A method according to  claim 2 , further comprising applying multivariate discrimination analysis to the first and second equations, to provide first and second probability equations, respectively.  
     
     
         4 . A method according to  claim 3 , further comprising the steps: 
 (e) subjecting a DNA sample from a tissue having a state of interest to FT-IR spectroscopy to produce FT-IR spectral data;    (f) analyzing the FT-IR spectral data of step (e) by PCA to provide a set of PC scores; and    (g) combining the PC scores of step (f) with each of the first and second probability equations to provide first and second probability scores, respectively.    
     
     
         5 . A method according to any of claims  1  wherein the tissue is breast, urogenital, liver, renal, pancreatic, lung, blood, brain or colorectal tissue.  
     
     
         6 . A method according to  claim 1  wherein the tissue is cancerous tissue.  
     
     
         7 . A method according to  claim 6  wherein the tissue is cancerous breast, prostate, ovarian or endometrial tissue.  
     
     
         8 . A method for assessing the genotoxicity of an environment comprising the steps of: 
 (a) subjecting DNA from a plurality of first organism in a first environment to Fourier transform-infrared (FT-IR) spectroscopy to produce FT-IR spectral data;    (b) analyzing the FT-IR spectral data of step (a) by principal components analysis (PCA) to provide a principal component (PC) scores;    (c) applying cluster analysis to the PC scores of step (b) to distinguish outlier and non-outlier organisms; and    (d) generating an equation, called a first equation, that defines a multivariate version of a normal bell-shaped curve which best fits the PC values from the non-outlier organisms, where the first equation defines the first organisms in the first environment.    
     
     
         9 . A method according to  claim 8 , further comprising repeating steps (a) through (d) with second organisms from a second environment, to provide a second equation, where the second equation defines the state of the second organisms in the second environment.  
     
     
         10 . A method according to  claim 9 , further comprising applying multivariate discrimination analysis to the first and second equations, to provide first and second probability equations, respectively.  
     
     
         11 . A method according to  claim 10 , further comprising the steps: 
 (e) subjecting a DNA sample of an organism of interest from an environment of interest to FT-IR spectroscopy to produce FT-IR spectral data;    (f) analyzing the FT-IR spectral data of step (e) by PCA to provide a set of PC scores; and    (g) combining the PC scores of step (f) with each of the first and second probability equations to provide first and second probability scores, respectively.    
     
     
         12 . A method according to  claim 9  wherein at least one of the first and second environments is a polluted environment.  
     
     
         13 . A method according to  claim 9  wherein the first and second organisms are non-identical, however the first and second environments are identical.  
     
     
         14 . A method according to  claim 9  wherein the first and second organisms are identical, however the first and second environments are non-identical.