Schematic of Proximal and Distal Breakage Intervals, Segmental Duplicons, and Genes in Class I and Class II AS Deletions. A) Breakage intervals exhibit variability at the proximal end in Class I deletions (BP1: WJK67, WJK36, WJK70) and uniformity at the proximal end in Class II deletions (BP2: WJK18, WJK24, WJK35). Breakage intervals at the distal ends (BP3) show heterogeneity within both Class I and Class II deletions. The symbols '+' and '-' indicate the probe is intact or deleted on the abnormal homolog. Breakage interval sizes are indicated in kilobases (Kb). D15S18 is a marker that is deleted in Class I and intact in Class II AS cases . B) Distinct duplicon blocks at the proximal (B-1) and distal (B-II) ends of the deletion are arranged in inverted orientation, and are separated by 5.96 Mb and 6.20 Mb in Class I patient samples WJK67 and WJK70. The proximal breakage interval for WJK36 does not involve a duplicon region. Panels B-III and B-IV: Class II patient samples, WJK18 and WJK24, overlap two pairs of duplicon blocks in the same orientation on the antisense DNA strand (< <) at the proximal and distal ends and are separated by 5.55 Mb and 5.38 Mb. WJK35 overlaps duplicon blocks separated by 5.09 Mb and are in the same orientation on the sense DNA strand (> >). In each panel (top to bottom), the genomic positions of paralogous segmental duplicons with their intrachromosomal distances (Mb) (orange), and genes (including isoforms) that are disrupted or deleted in the breakage intervals (blue or black) are indicated.