Disclosed are compositions, methods, and kits useful for detection of the presence and/or quantity of one or more chromosomes from single cells, groups of cells, or subcellular compartments. Provided is a lysis buffer for the preparation of substantially accessible nucleic acid molecules from a single cell. Also provided are moderately-repeated highly-conserved nucleic acid sequences, and oligonucleotide primer and probe molecules which hybridize specifically thereto. Methods for the detection of the presence or quantity of one or more chromosomes from a single cell are included, as are methods for the assessment of the reliability of the results of the methods of the invention. Kits for the convenient practice of the invention are also included.