Abstract: The present invention provides methods for preparing cells with highly condensed chromosomes, such as sperm, and methods for detecting and quantifying specific cellular target molecules in intact cells. Specifically, methods are provided for detecting chromosomes and chromosomal abnormalities, including aneuploidy, in intact cells using fluorescence in situ hybridization of cells in suspension, such as sperm cells.

Abstract: The present invention provides methods of detecting and/or quantifying specific cellular target molecules in intact cells. The present invention further provides methods of processing an intact cell to facilitate in situ hybridization for use in flow cytometry.

Abstract: Combinatorially-synthesized deoxyribonucleic acid (DNA) oligonucleotides attached to encoded beads that are hybridized to amplified and labeled genomic DNA or ribonucleic acid (RNA) are analyzed using a flow imaging system. Oligonucleotides and corresponding reporters are bound to the surfaces of a plurality of small beads such that different beads bear different oligo sequences. Each bead bears a unique optical signature comprising a predefined number of unique reporters, where each reporter comprises a predefined combination of different fluorochromes. The composite spectral signature in turn identifies the unique nucleotide sequence of its attached oligo chains. This optical signature is rapidly decoded using an imaging system to discriminate the different reporters attached to each bead in a flow in regard to color and spatial position on the bead.