Proximal and Distal AS/PWS Breakpoint Hotspots, Duplicon Structures, Genes, SC and LC Intervals in chromosome 15q11.2q13. Panel A shows genomic coordinates (x-axis) and relevant genes. Panel B depicts frequency (y-axis) of previously reported BAC (blue histograms) and oligonucleotide (green histograms) microarray breakage point hotspots. Five breakage regions (A-E) and Class I and Class II deletions are indicated. Panel C shows SC and LC intervals that are coincident with the breakage hotspots. LC and SC intervals developed for FISH probes are shown in red and green, respectively [for higher resolution, see Figure 2A]. LC and SC intervals, depicted as black bars, display the density of coverage along 15q11.2q13 and can be used for further refinement of breakage activity within the AS/PWS duplicon clusters. Intervals for probe development were selected based on their proximity to high breakage densities and the multiplex information obtained from both proximal and distal breakpoints of Class I and Class II deletions. Panel D shows clusters of segmental duplicons and their relative position to genes, breakage hotspots, and LC and SC intervals. Colors refer to degree of similarity among paralogous sequences - orange is > 99%, yellow is 98-99% and gray hues are 90-98%.