Steps in sequencing 18q terminal deletions for patient 1 (A-D) and data for the other patients (E-I). (A) CGH-array profile in custom slide showing 18q21.33 terminal deletion for P1. Below, a schematic view of the breakpoint junction. The box, designated as “telomere cap” indicates the telomere (TTAGGG)n sequence. Black arrows show location of PCR primers in different combinations (ATF3, ATF4, ATF5 with TelR2); (B) PCR result in agarose gel 1.5% showing the fragment amplification using the three pairs of primers in P1 and no amplification in the male control (C) and blank (B); (C) Sequencing result showing the breakpoint in 18q21.33 and the beginning of telomere sequences (underlined); Alignment of the PCR products to the normal 18q sequence (above) and telomere sequences (below) showing microhomology (yellow) of 3 bp for P1 (D); 2 bp for P2 (E); 1 bp for P3 (F); 2 bp for P5 (H) and 2 bp for P6 (I); and a complex rearrangement with an interstitial deletion with addition of 17 bp (red) followed by normal 18q sequence before the telomeric sequences, without microhomology, for P4 (G).