Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants

Table 2 Sequence characteristics of join-points in the breakpoint junctions from this study and meta-analysis of aggregate data¹

Product of rearrangement join-point	Frequency (~%, count/sum)
Product of rearrangement join-point	This study	Aggregate data¹
Join-points with 1 bp match	5.3% (3/57)	6.3% (10/159)
Microhomology > 2 bp	26.3% (15/57)	22% (35/159)
Microhomeology²	33.3% (19/57)	32.1% (51/159)
Alu-Alu	5.3% (3/57)	7.5% (12/159)
LINE-LINE	1.75% (1/57)	1.9% (3/159)
Blunt	3.5% (2/57)	5.7% (9/159)
Insertion³	22.8% (13/57)	23.9% (38/159)
Others⁴	1.75% (1/57)	0.6% (1/159)

¹The aggregate dataset consists of 148 sequenced breakpoint junctions from this study and previously published SV mutagenesis studies involving copy number gains at the Xq22 locus
²Re-interpreted data according to new definition of microhomeology. We re-analyzed breakpoint junction data from previous published studies [15, 21, 24, 32, 33]. Although in some cases both a microhomology and a microhomeology occur, microhomologies were not counted when we found microhomeologies at join-points
³Small insertion (1 to 20 bp) or larger insertion with unknown origin (> 20 bp)
⁴Rearrangement mediated by two highly identical directly oriented sequences (LCRs or self-chains)

ISSN: 1756-994X