Abstract: Disclosed are methods and compositions for detecting a chromosomal rearrangement in a sample of nucleic acids. In an exemplary method, a first nucleic acid comprising a portion of a first chromosome, which may be detectably labeled, is attached to a substrate; a first portion of a test nucleic acid is hybridized to the first nucleic acid; a second nucleic acid comprising all or a portion of a second chromosome, which may be detectably labeled, is hybridized to a second portion of the test nucleic acid, thereby forming a trimolecular sandwich, and the hybridization of the test nucleic acid to both of the first and second nucleic acids is detected as an indication that the test nucleic acid comprises a chromosomal rearrangement. In particular embodiments, the first and second nucleic acids are derived from the same chromosome.