Microarray data for a positive fusion gene hit. (A) This theoretical example of a fusion gene has a crossing-over event between sequences in intron 2 of gene A and intron 3 of gene B. (B) If the genes A and B both have 10 exons, the microarray will contain 10 × 10 = 100 oligos to cover all chimeric exon-to-exon junction combinations for this particular fusion gene. The A2-B4 oligo detects the fusion transcript from part (A). (C) In true fusion events, the longitudinal profiles generated from intragenic oligos targeting each exon and exon-to-exon junction will provide independent confirmation.