Table 1. Translocation breakpoints as identified by Whole-Genome Mate-Pair Sequencing and validated by Sanger sequencing (hg19).
| Translocation junctions as estimated by WG-MPS | Junction Length | Translocation breakpoint position as defined by SS | Disrupted Genes | Insertions/deletions (+ strand) | Microhomology (+ strand) |
|---|---|---|---|---|---|
| Case 1—Female with hearing loss | |||||
| chr1:74499775–74500253 | 479bp | chr1:74500101–74500108 | LRRIQ3 | AATTCA duplication | AATTC |
| chrX:82675876–82676282 | 407bp | chrX:82676074–82676079 | ~87kb upstream POU3F4 | GAATT duplication G deletion |
GAATT |
| Case 2—Female with mild to moderate intellectual disability | |||||
| chr6:16754266–16755111 | 845bp | chr6:16754305–16754306 | ATXN1 | ND | - |
| chr7:120530428–120531641 | 1214bp | chr7:120530522–120530523 | - | ND | G |
| chr7:124121849–124122971 | 1123bp | chr7:124122363–124122371 | - | ATCTTTT deletion T insertion |
- |
| chr8:129588349–129589617 | 1269bp | chr8:129589008–129589009 | - | ND | CTGG |
| chr8:132602314–132603246 | 933bp | chr8:132602994–132602995 | - | - | - |
| chr8:132899241–132900431 | 1191bp | chr8:132899713–132899714 | - | T insertion | - |
| chr8:132937706–132938936 | 1231bp | chr8:132938698–132938699 | EFR3A | ND | - |
| chr12:24016019–24017286 | 1268bp | chr12:24016112–24016113 | SOX5 | ND | C |
| chr12:27177142–27177824 | 682bp | chr12:27177486–27177487 | MED21 | ND | - |
| chr12:55357036–55357802 | 767bp | chr12:55357553–55357554 | TESPA1 | ND | CCAG |
| chr12:65386366–65387285 | 920bp | chr12:65386836–65386837 | - | ND | - |
| chr12:68784020–68784572 | 553bp | chr12:68784362–68784363 | - | ND | - |
| Case 3—Female with dysmorphic facial features and speech delay | |||||
| chr4:118195375–118197310 | 1936bp | chr4:118195456–118195460 | - | AGG duplication | G |
| chr9:14104333–14104994 | 662bp | chr9:14104378–14104384 | NFIB | GTCTA deletion | - |
The junction length, disrupted genes, as well as insertions/deletions and microhomology at the breakpoint junctions are also given. In Case 2, only those translocation breakpoint junctions mapped to the base-pair level are included in Table 1. Due to the highly repetitive regions at most chromothripsis rearrangement breakpoints in Case 2, validation was not feasible for all breakpoint junctions, and hence, possible insertions/deletions could not be determined in most cases. (bp = base-pairs; dn = de novo; WG-MPS = Whole-Genome Mate-Pair Sequencing; ND = not determined; SS = Sanger sequencing)