A method for analyzing detergent-liberated nuclei and/or chromatin debris for nuclei-associated epitopes, the method comprising: providing a single reagent solution comprising one or more cell lysis reagents, a fluorescent nucleic acid dye, and two or more fluorescent nuclei-associated epitope-specific antibodies or ligands (NAESA/L) that specifically bind to two or more nuclei-associated epitopes of interest, wherein the NAD and the two or more NAESA/L have distinct fluorescent emission spectra, and wherein the two or more NAESA/L comprise a NAESA/L that detects a marker associated with double-strand DNA breaks and a NAESA/L that detects a marker associated with aneugenic activity, and wherein the single reagent solution further comprises a reagent responsive to cytotoxicity; contacting a sample containing eukaryotic cells with the single reagent solution, said contacting being effective to digest eukaryotic cell cytoplasmic membranes but not nuclear membranes, aggregate metaphase chromosomes of a single cell into a single bundle of chromosomes, label chromatin with the NAD, and label the two or more nuclei-associated epitopes with the two or more NAESA/L; evaluating the contacted sample by: exciting the NAD and the two or more NAESA/L with light of an appropriate excitation wavelength; and detecting fluorescent emission and light scatter produced by the nuclei and/or chromatin debris and counting one or more of the following events: the number of nuclei, the number of nuclei positively labeled by the two or more NAESA/L, the number of chromatin debris, the number of chromatin debris positively labeled by the two or more NAESA/L, the number of nuclei in G1, S, and G2/M phases of the cell cycle, and the number of polyploid nuclei; and determining one or more of the following measurements: the frequency of nuclei positively labeled by the two or more NAESA/L relative to total nuclei, the frequency of chromatin debris positively labeled by the two or more NAESA/L relative to total chromatin debris and/or total nuclei, the proportion of nuclei in G1, S, and G2/M phases of the cell cycle, the proportion of polyploid nuclei, and mean and/or median fluorescence by the two or more NAESA/L; wherein said evaluating is carried out without further processing of the contacted sample prior to said exciting. providing a single reagent solution comprising one or more cell lysis reagents, a fluorescent nucleic acid dye, and two or more fluorescent nuclei-associated epitope-specific antibodies or ligands (NAESA/L) that specifically bind to two or more nuclei-associated epitopes of interest, wherein the NAD and the two or more NAESA/L have distinct fluorescent emission spectra, and wherein the two or more NAESA/L comprise a NAESA/L that detects a marker associated with double-strand DNA breaks and a NAESA/L that detects a marker associated with aneugenic activity, and wherein the single reagent solution further comprises a reagent responsive to cytotoxicity; contacting a sample containing eukaryotic cells with the single reagent solution, said contacting being effective to digest eukaryotic cell cytoplasmic membranes but not nuclear membranes, aggregate metaphase chromosomes of a single cell into a single bundle of chromosomes, label chromatin with the NAD, and label the two or more nuclei-associated epitopes with the two or more NAESA/L; evaluating the contacted sample by: exciting the NAD and the two or more NAESA/L with light of an appropriate excitation wavelength; and detecting fluorescent emission and light scatter produced by the nuclei and/or chromatin debris and counting one or more of the following events: the number of nuclei, the number of nuclei positively labeled by the two or more NAESA/L, the number of chromatin debris, the number of chromatin debris positively labeled by the two or more NAESA/L, the number of nuclei in G1, S, and G2/M phases of the cell cycle, and the number of polyploid nuclei; and exciting the NAD and the two or more NAESA/L with light of an appropriate excitation wavelength; and detecting fluorescent emission and light scatter produced by the nuclei and/or chromatin debris and counting one or more of the following events: the number of nuclei, the number of nuclei positively labeled by the two or more NAESA/L, the number of chromatin debris, the number of chromatin debris positively labeled by the two or more NAESA/L, the number of nuclei in G1, S, and G2/M phases of the cell cycle, and the number of polyploid nuclei; and determining one or more of the following measurements: the frequency of nuclei positively labeled by the two or more NAESA/L relative to total nuclei, the frequency of chromatin debris positively labeled by the two or more NAESA/L relative to total chromatin debris and/or total nuclei, the proportion of nuclei in G1, S, and G2/M phases of the cell cycle, the proportion of polyploid nuclei, and mean and/or median fluorescence by the two or more NAESA/L; wherein said evaluating is carried out without further processing of the contacted sample prior to said exciting.