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. 2019 Dec 9;11:80. doi: 10.1186/s13073-019-0676-0

Fig. 3.

Fig. 3

CGRs detected by aCGH at the PLP1 locus. a Two duplications separated by CNRs were detected on aCGH in 9 individuals with PMD. The distance between the two duplications differs among these individuals, ranging from 16 to 7863 kb. In the schematic figure below each array, duplications are depicted in red and CNRs in gray. Three cases (BAB8940, BAB8955, and BAB8960) could be single duplications on the H2 inversion haplotype or could be two duplications with one TS involving reversal of the direction of replication between IRs LCRA1a and LCRA1b (Additional file 1: Figure S9); three (BAB8923, BAB8928, and BAB8965) have directly oriented DUP-NML-DUP structures (Additional file 1: Figures S6–1, S6–2 and S6–3); one has two tandem head to tail duplications (BAB8962; Additional file 1: Figure S6–4); and two (BAB8920, BAB8934) have DUP-NML-INV/DUP structures (Additional file 1: Figure S7). b A DUP-TRP-DUP pattern of rearrangement was detected on aCGH in three individuals with PMD (Additional file 1: Figure S10). Breakpoint junction analyses indicated that one of these individuals (BAB8964) probably has the previously reported DUP-TRP/INV-DUP pattern of rearrangement with inversion mediated by a TS between inverted repeats LCRA1a and LCRA1b. Based on aCGH data, BAB8970 probably has the same structure, although breakpoint junctions were not resolved (Additional file 1: Figures S10–1 and S10–2). Breakpoint junction analysis indicates that BAB8939 also carries a DUP-TRP/INV-DUP, but the inversion was not mediated by LCRA1a and LCRA1b (Additional file 1: Figure S10–3). Duplications are indicated in red, triplications in blue, and LCR blocks (LCRA1a and LCRA1b) in yellow. c Additional CGR patterns at the PLP1 locus were identified on aCGH. DUP-NML-DUP-NML-DUP rearrangement pattern in which duplications are separated by short CNRs (BAB8924, BAB8936, and BAB8959). In BAB8924, based on the sequenced breakpoint junction, this case may have two tandem head to tail duplications on the H2 haplotype that has an inversion within LCRA1a and LCRA1b (Additional file 1: Figure S12–1a) or may have three duplications with one TS between LCRA1a and LCRA1b resulting in an inversion (not shown). We were not able to resolve any breakpoint junctions in BAB8936 (Additional file 1: Figure S12–1b). Breakpoint junction sequencing in BAB8959 showed that the CGR based on aCGH may not have occurred during the same cell division (Additional file 1: Figures S12–2). One individual, BAB8931, exhibited DUP-NML-DEL pattern of rearrangement with a ~ 283-kb duplication (breakpoint junction in LCRA1a) followed by ~ 106 kb of CNR and then a ~ 16-kb deletion (breakpoint junction in LCRA1b). The most complex rearrangement in this study was observed in individual BAB8937 with a DUP-QUAD-TRP rearrangement pattern. In this case, duplication is followed by a quadruplication and then a triplication. The possible mechanism for such rearrangements is shown in Additional file 1: Figure S11. Duplications are indicated in red, CNRs in gray, deletion in green, triplication in blue, quadruplication in orange, and LCR blocks in yellow in the horizontal bar under each array