Methods of analyzing chromosomal translocations using fluorescence in situ hybridization (fish)

A method for determining the presence or absence of a reciprocal chromosomal translocation involving a first gene, which includes potential breakpoints for the translocation, and a second gene, which includes potential breakpoints for the translocation, the first and second genes being located on first and second chromosomes, respectively, the method comprising:

• (a) contacting, under hybridization conditions, a chromosomal preparation with a set of probes comprising first and second nucleic acid probes;
• wherein said chromosomal preparation comprises the first and second chromosomes;
• wherein the first probe bears a first label and is hybridizable to an untranslocated form of the first chromosome at a region located outside the first gene and no further than 1 Mb from the outermost known centromeric breakpoint associated with the translocation;
• wherein the second probe bears a second label different from the first label and is hybridizable to an untranslocated form of the second chromosome at a region located outside the second gene and no further than 1 Mb from the outermost known telomeric breakpoint associated with the translocation;
• wherein
• (i) if the first and second chromosomes have undergone the reciprocal chromosomal translocation, the first and second probes hybridize to a derivative chromosome formed via the translocation, such that both the first and second labels appear on the derivative chromosome;
• whereas
• (ii) if the first and second chromosomes have not undergone the reciprocal chromosomal translocation, the first and second probes hybridize to their respective chromosomes, such that only the first label appears on the first chromosome and only the second label appears on the second chromosome;
• (b) detecting a pattern of hybridization for the first and second probes;
• (c) determining from the pattern whether the first and second probes appear on the derivative chromosome or appear separately on the first and second chromosomes, respectively, thereby determining the presence or absence of the reciprocal chromosomal translocation.