Complex structural variants in Mendelian disorders: identification and breakpoint resolution using short- and long-read genome sequencing

Table 2 Repetitive elements associated with cxSV reference breakpoints in the four participants

Participant	Breakpoint^a	Coordinate of breakpoint	Repetitive elements
P1	A3′-B5′	6:151443332	91% LTR/ERVL-MaLR
	B3′-C5′	6:154768570	32% DNA/hAT-Charlie
	C3′-D5′	6:154774047	75% LTR/ERVL-MaLR
	D3′-E5′	6:154778901	26% LINE/L2
	E3′-F5′	6:154778992	–
P2	A3′-B5′	1:244867200	70% SINE/Alu
	B3′-C5′	1:246064238	–
	C3′-D5′	1:246569871	45% SINE/MIR
	D3′-E5′	1:246816211	88% SINE/Alu
P3	A3′-B5′	9:80843698	82% LINE/L1 and 14% SINE/Alu
	B3′-C5′	9:80849462	59% LINE/L1
	C3′-D5′	9:80849760	63% LINE/L1
	D3′-E5′	9:80859678	86% LINE/L1
P4	A3′-B5′	X:17793009	–
	B3′-C5′	X:18074005	–
	C3′-D5′	X:18248955	41% SINE/Alu
	D3′-E5′	X:18532312	–

^aRefers to genomic segments as shown in Fig. 1. Repetitive elements, identified using RepeatMasker, represent the percentage of repetitive sequence for a 300 bp region of reference sequence flanking the breakpoint, as specified element: class/family