SC and LC Probes Developed for FISH. A) High resolution map of LC (red) and SC (green) probes. Proximal targets of probes 1 and 2 (arrowheads) in BP1 share 99% sequence identity to their distal BP3 targets (arrowheads). Probes 3, 4, 7, 8 and 10 are adjacent to duplicon regions. LC probes 5 and 6 mimic SC probes as each have one paralog target in BP2 and their other paralogs are divergent and distal of 15q11.2q13 or interchromosomal (see text). Probe 9 serves as a deletion control that targets a sequence ~20 Kb centromeric of MAGEL2. Probe lengths are reported in base pairs (bp). B) Metaphase FISH algorithm for delineating Class I and Class II deletions in 15q11.2q13. Probes 1 through 10 are color-coded. A schema of hybridization experiments is shown for Class I and II deletions. Different outcomes indicated by the presence (+) or absence (-) of an SC (green) or LC probe (red) prescribes the procedure for delineating boundaries of a breakage interval (unfilled box). If two paralogous LC targets are retained; this is indicated by a '++' symbol. Further refinement of a deletion interval requires either sequential application of additional SC probes or dual-color/dual-probe hybridization.