Fig. 3. Patterns and proposed mechanisms of structural variations.

a Chromothripsis, showing a shattering and subsequent repair process. Telomere crisis and/or micronuclei by chromosome mis-segregation may induce chromothripsis. b Chromoplexy, showing a “closed chain” (upper) in the Circos plot. This is a multi-chromosomal translocation (lower). c MMBIR by template switching of the replication machineries. d BFB cycle, showing subtelomeric copy number increases and fold-back inversions. Proposed mechanisms are shown below. e Different patterns of SVs in BRCA1- and BRCA2-mutant breast cancers. f Patterns and formation of DMs and neochromosomes. DNA fragments can self-ligate, forming a ring structure, and are amplified (DMs). Fragments capturing centromeres and telomeres become neochromosomes. g Patterns and processes of L1 retrotransposition in the cancer genome. h HPV integration and regional rolling-circle amplification