Automated method for detecting cancers and high grade hyperplasias

Abstract

Automated methods for detecting cancer and related hyperplasias in biological samples.

1 . An automated method of screening for the presence and/or extent of a pathology in a subject, the pathology characterized by an abnormal chromosomal component in a cell of the subject, comprising the steps of
 a) contacting a biological sample comprising cell nuclei from said subject with one or more distinguishable labeled probes directed to at least one chromosomal sequence that characterizes the abnormality under conditions that promote hybridization of the one or more probes to the at least one sequence;   b) automatically obtaining a representation of the one or more distinguishable labels hybridized to the chromosomal sequences;   c) automatically analyzing the distribution and intensity of binding of the one or more labels in the representation to determine the presence and/or extent of an abnormal chromosomal component; and   d) automatically reporting results of the analysis of step c);   wherein steps b)-d) are carried out without intervention by a human.   
     
     
         2 . The method described in  claim 1  wherein an automated microscope system carries out steps b)-d). 
     
     
         3 . The method described in  claim 1  wherein a probe targets at least one of a single nucleotide polymorphism (SNP), a mutated sequence, a duplicated or amplified gene or portion thereof, a centromere of chromosome 3, a centromere of chromosome 7, and a sequence comprising the TERC gene or a portion thereof. 
     
     
         4 . The method described in  claim 1  further comprising contacting the sample under the hybridizing conditions with a tagged reference probe directed to a chromosomal locus known not to be abnormal, or contacting the sample with a reference stain, and referencing the representing and analysis steps to the reference probe or stain. 
     
     
         5 . An automated method of screening for an abnormality related to a cancer, a high grade hyperplasia or a high grade dysplasia in a subject, comprising the steps of:
 a) obtaining a biological sample comprising nuclei from the subject;   b) contacting the nuclei in the sample with a first probe bearing a first detectable label directed to a chromosomal sequence related to the abnormality under conditions that promote hybridization of the probes to targeted chromosomal loci;   c) contacting the sample under the hybridizing conditions with at least one of a detectably labeled reference probe directed to a chromosomal locus known not to be abnormal and a reference stain;   d) automatically imaging the labels bound to the chromosomal sequences, and imaging the stain if used;   e) automatically analyzing an image for the distribution and intensity of hybridized labels and stain if used; and   f) automatically reporting results of the analysis of step e);   wherein steps d)-f) are performed without intervention by a human;   thereby providing an assessment of the abnormality in the subject.   
     
     
         6 . The method described in  claim 5  wherein an automated microscope performs steps d)-f). 
     
     
         7 . The method described in  claim 5  wherein prior to the contacting step the nuclei are isolated from the sample and are deposited to form a layer. 
     
     
         8 . The method described in  claim 5  wherein the sample comprises one or more of a biopsy, surgical resection specimen, blood, lymph, urine, an effusion fluid, a biological fluid, an epithelial scraping, a lavage fluid, aspiration fluid, sputum, and a tissue. 
     
     
         9 . The method described in  claim 5  wherein a label is a fluorescent label. 
     
     
         10 . The method described in  claim 5  wherein a probe targets at least one of a single nucleotide polymorphism (SNP), a mutated sequence, a duplicated or amplified gene or portion thereof a centromere of chromosome 3, a centromere of chromosome 7, and a sequence comprising the TERC gene or a portion thereof. 
     
     
         11 . An automated method for monitoring the efficacy over time of a course of therapy in the treatment of a cancer or high grade hyperplasia in a patient, said method comprising the steps of
 (a) obtaining from the patient a fluid biological sample in which cells associated with the cancer or high grade hyperplasia are found;   (b) treating said fluid biological sample or a portion thereof with one or more detectably labeled chromosomal probes having a high degree of sequence similarity to one or more chromosomal loci associated with, or whose amplification is associated with, said cancer or high grade hyperplasia, under conditions sufficient to enable hybridization of said probes to chromosomes in the sample;   (c) automatically scanning said treated fluid biological sample and detecting said one or more labels bound to any chromosomes in said sample;   (d) automatically detecting the number of cells associated with said chromosomes hybridized to said chromosomal probes; and   (e) automatically comparing the hybridization patterns of a label and cell number results provided in steps (c) and (d) at differing times in the therapeutic treatment course, thereby evaluating the efficacy of the therapy in the treatment of the cancer or high grade hyperplasia.   
     
     
         12 . The method of  claim 11  wherein monitoring is performed at intervals of 1 day or greater. 
     
     
         13 . The method described in  claim 11  wherein the fluid biological sample comprises one or more of blood, lymph, urine, an effusion fluid, an epithelial scraping, a lavage fluid, aspiration fluid, and sputum. 
     
     
         14 . The method described in  claim 11  wherein an automated microscope system performs steps (c)-(e) without intervention by a human. 
     
     
         15 . The method described in  claim 14  wherein the automated microscope system automatically optimizes the field scanning the sample. 
     
     
         16 . The method described in  claim 14  wherein the automated microscope scans two or more planes in a field of the sample. 
     
     
         17 . The method described in  claim 11  wherein a probe targets at least one of a single nucleotide polymorphism (SNP), a mutated sequence, a duplicated or amplified gene or portion thereof, a centromere of chromosome 3, a centromere of chromosome 7, and a sequence comprising the TERC gene or a portion thereof. 
     
     
         18 . The method described in  claim 11  wherein a patient obtains samples without assistance from another human. 
     
     
         19 . A method for the automated high throughput characterization of a chromosomal abnormality comprising the steps of
 a) providing at least one microscope slide comprising a biological sample thereon, wherein the sample is suspected of harboring the chromosomal abnormality and wherein the sample has been hybridized to at least one detectably labeled probe specific for detection of the abnormality;   b) installing the at least one sample-bearing slide in a means for automated, reversible, placement of the slide on the stage of an automated microscope;   c) causing the placement means automatically and reversibly to place a sample-bearing slide to be reversibly placed on the microscope stage;   d) causing the microscope automatically to obtain at least one image of the specimen wherein the image comprises a representation of a labeled probe hybridized to a chromosome,   e) causing the microscope automatically to analyze the image in order to characterize the abnormality;   f) automatically reporting the results of the analysis of step (e); and   g) automatically repeating steps (c)-(f).   
     
     
         20 . The method described in  claim 19  wherein the automated microscope operates without intervention by a human. 
     
     
         21 . The method described in  claim 19  wherein obtaining the image automatically optimizes the field in which the image occurs. 
     
     
         22 . The method described in  claim 19  wherein the automated microscope obtains images from two or more planes in a field of nuclei. 
     
     
         23 . The method described in  claim 19  wherein the sample comprises one or more of a biopsy, surgical resection specimen, blood, lymph, urine, an effusion fluid, a biological fluid, an epithelial scraping, a lavage fluid, aspiration fluid, sputum, and a tissue. 
     
     
         24 . The method described in  claim 19  wherein a probe targets at least one of a single nucleotide polymorphism (SNP), a mutated sequence, a duplicated or amplified gene or portion thereof, a centromere of chromosome 3, a centromere of chromosome 7, and a sequence comprising the TERC gene or a portion thereof.