Methods for assessing genetic and phenotypic markers by simultaneous multicolor visualization of chromogenic dyes using brightfield microscopy and spectral imaging

Abstract

The present invention is directed to an improved method for detecting a genetic marker in a biological sample comprising contacting the biological sample with a nucleic acid probe linked to a detectable moiety, whereby the detectable moiety can be detected by the presence of a chromogenic dye associated with the detectable moiety, obtaining a spectral image of the biological sample using brightfield microscopy, and detecting the presence of the chromogenic dye, thereby detecting the genetic marker in the biological sample. The present invention also provides an improved method for detecting a phenotypic marker in a biological sample comprising contacting the biological sample with a compound comprising a detectable moiety, whereby the compound associates with the phenotypic marker and whereby the detectable moiety can be detected by the presence of a chromogenic dye associated with the detectable moiety, obtaining a spectral image of the biological sample using brightfield microscopy, and detecting the presence of the chromogenic dye, thereby detecting the phenotypic marker in the biological sample.

What is claimed is:  
     
         1 . An improved method for detecting a genetic marker in a biological sample comprising: 
 a) contacting the biological sample with a nucleic acid probe linked to a detectable moiety, whereby the detectable moiety can be detected by the presence of a chromogenic dye associated with the detectable moiety;    b) obtaining a spectral image of the biological sample using brightfield microscopy; and    c) detecting the presence of the chromogenic dye, thereby detecting the genetic marker in the biological sample.    
     
     
         2 . The method of    claim 1   , wherein the biological sample is contacted with more than one nucleic acid probe.  
     
     
         3 . The method of    claim 1   , wherein the biological sample is attached to a substrate.  
     
     
         4 . The method of    claim 1   , wherein step (a) further comprises contacting the biological sample with a cytological stain.  
     
     
         5 . The method of    claim 1   , wherein step (c) further comprises distinguishing the cytological stain from the detectable moiety.  
     
     
         6 . The method of    claim 1   , wherein the genetic marker is selected from the group consisting of a centromere, a telomere, a general genetic loci, a specific genetic loci, a chromosome band, a chromosome-specific loci, a chromosome fragment, and a whole chromosome.  
     
     
         7 . The method of    claim 1   , wherein the detectable moiety comprises a hapten.  
     
     
         8 . An improved method for detecting a phenotypic marker in a biological sample comprising: 
 a) contacting the biological sample with a compound comprising a detectable moiety, whereby the compound associates with the phenotypic marker and whereby the detectable moiety can be detected by the presence of a chromogenic dye associated with the detectable moiety;    b) obtaining a spectral image of the biological sample using brightfield microscopy; and    c) detecting the presence of the chromogenic dye, thereby detecting the phenotypic marker in the biological sample.    
     
     
         9 . The method of    claim 8   , wherein the biological sample is contacted with more than one compound.  
     
     
         10 . The method of    claim 8   , wherein the biological sample is attached to a substrate.  
     
     
         11 . The method of    claim 8   , wherein step (a) further comprises contacting the biological sample with a cytological stain.  
     
     
         12 . The method of    claim 8   , wherein step (c) further comprises distinguishing the cytological stain from the detectable moiety.  
     
     
         13 . The method of    claim 8   , wherein the phenotypic marker is selected from the group consisting of an RNA, a protein, and an antibody.  
     
     
         14 . The method of    claim 8   , wherein the detectable moiety comprises a hapten.