Intrachromosomal rearrangements detected by PQ-COBRA –FISH. (A) An inversion of chromosome 12 in a normal carrier. In this balanced rearrangement, the distal region of the long arm is positioned on the end of the short arm of the rearranged chromosome. The segment of the short arm transferred to the long arm of the inv(12) could not be detected by us, nor in the original study by conventional cytogenetics or FISH with distal markers (Speleman et al 1993). (B) A der(1), composed exclusively of 1q material in a cervical cancer cell line with a complex karyotype. For each normal and rearranged homolog, the sequence of display is ratio image, the q arm paint (second binary label) and the thresholded image of the q-arm paint.