Table 1.

Mechanisms of CCR formation, involved genes and molecular signatures of joining points

	FoSTeS	MMBIR	Breakage-fusion-bridge cycle	Chromothripsis
Causes	stalled replication forks	DSBs	?	overactivity of SPO11, free radicals or ionizing radiation, covalent DNA damage interfering with resolution of Holliday junctions or defective cell cycle checkpoints
Basic mechanism	strand invasion by lagging DNA replication strand	joining of 2 open DNA strands	?	NHEJ and MMBIR
Enzymatic activities	DNA replication machinery	exonuclease-mediated resection	artemis-nuclease, gap-filling DNA polymerase, ligase 4	not studied
Associated CNVs	deletions, duplications, triplications	none	none	only losses, no duplications; pachytene stage of meiosis I
DNA fragment orientation	head-to-tail	head-to-tail	head-to-tail	randomly joined in head-to-tail, tail-to-tail and head-to-head orientations
Junction sequences	?	microhomologies, short deletions, non-templated insertions	small deletions due to NHEJ	losses of a few base pairs up to several kb, small insertions of non-templated sequences
Junction spacing	?	?	?	closely spaced
Key references	Hastings et al., 2009; Colnaghi et al., 2011	Hastings et al., 2009; Colnaghi et al., 2011	Scott and Pandita, 2006	Liang et al., 1998; Holloway et al., 2010; Truong et al., 2013

? = Not known.