Table 1.

Features of the CNVs studied in 39 subjects with 17p13.3 rearrangements

Individuala	CNV type	CNV size (Mb)	Distal repeat	Proximal repeat	Microhomology (bp)b	Notesc
10	DEL	0.595	AluSg/−	AluYk4/−	17	Alu–Alu (82.2%)
15	DEL	0.746	AluYk4/−	AluY/−	43	Alu–Alu (90.6%)
19	DEL	0.611	AluY/−	AluYb8/ −	32	Alu–Alu (88.6%)
30	DEL	0.563	AluSq/−	AluSp/−	27	Alu–Alu (86.24%)
BAB3106	DEL	0.545	–	–	6	NHEJ/MMEJ
1	DUP	0.512	AluSp/+	AluSp/+	52	Alu–Alu (89.94%)
3	DUP	0.742	–	L2/+	4	MMEJ/FoSTeS/MMBIR
5	DUP	15.161	L1PA5/−	L1PA5/−	17	LINE/LINE
7	DUP	0.37	AluSx1/+	–	6	MMEJ/FoSTeS/MMBIR
8	DUP	0.455	AluJr/+	AluSx1/+	6	Alu–Alu (78.2%)
9	DUP	0.206	–	–	N	MMEJ/FoSTeS/MMBIR
14	DUP	0.921	AluSx/−	AluSz/−	3	Alu–Alu (84.1%)
21	DUP	0.146	AluSx/+	–	2	MMEJ/FoSTeS/MMBIR
22	DUP	0.341	AluY/−	AluYk4/−	46	Alu–Alu (90.16%)
26	DUP	0.018	AluSq/+	AluY/+	33	Alu–Alu (87.37%)
29	DUP	0.879	AluSq2/−	AluSx3/+	2	MMEJ/FoSTeS/MMBIR
31	DUP	0.028	AluSq2/+	LIMB4/+	2	MMEJ/FoSTeS/MMBIR
36	DUP	0.413	–	AluSx/+	3	MMEJ/FoSTeS/MMBIR
BAB3054	DUP	0.092	AluSg/−	AluY/−	19	Alu–Alu (84.21%)
2_1	DUP–NML–DUP	Complex	AluY/+	AluSc8/+	29	Alu–Alu (91.5%)
2_2	DUP–NML–DUP	Complex	AluSc/+	AluSc/+	9	Alu–Alu (91.5%)
4_1	DUP–NML–INV/DUP	Complex	AluY/−	AluSx/+	6	FoSTeS/MMBIR
4_2	DUP–NML–INV/DUP	Complex	AluSg/−	AluSc/+	34	Alu–Alu (89.13%)
6_1	DUP–NML–INV/DUP	Complex	AluY/−	AluY/+	39	Alu–Alu (89.6%)
6_2	DUP–NML–INV/DUP	Complex	AluY/−	L2b/+	N	FoSTeS/MMBIR
BAB3886_1	DUP–NML–INV/DUP	Complex	AluY/−	AluSc5/+	29	Alu–Alu (87.91%)
BAB3886_2	DUP–NML–INV/DUP	Complex	–	L2/−	N	FoSTeS/MMBIR
27_1	DUP-TRP/INV-DUP	Complex	AluJb/+	–	N	FoSTeS/MMBIR
27_2	DUP-TRP/INV-DUP	Complex	LTR8/+	L1MC2/+	2	FoSTeS/MMBIR
28_1	DUP-TRP/INV-DUP	Complex	–	–	2	FoSTeS/MMBIR
28_2	DUP-TRP/INV-DUP	Complex	AluSg/−	AluSg/+	21	Alu–Alu (84.69%)
33_1	DUP-TRP/INV-DUP	Complex	AluSx3/−	AluSz/+	25	Alu–Alu (85.14%)
33_2	DUP-TRP/INV-DUP	Complex	–	(TGTG)n/+	2	FoSTeS/MMBIR
K2_1	DUP-TRP-DUP	Complex	AluSz/−	AluY/−	5	Alu–Alu (76.32%)
K2_2	DUP-TRP-DUP	Complex	AluSx/ −	AluSq/−	25	Alu–Alu (83.16%)
18	TRP	0.011	AluSq/−	AluSg/−	30	Alu–Alu (82.01%)
20	TRP	0.811	AluSx1/+	–	1	FoSTeS/MMBIR
23_1	Complex	Complex	MER103C/+	AluSg4/−	N	FoSTeS/MMBIR
23_2	Complex	Complex	–	–	2	FoSTeS/MMBIR
23_3	Complex	Complex	–	LIMC4a/−	N	FoSTeS/MMBIR
23_4	Complex	Complex	–	–	N	FoSTeS/MMBIR
23_5	Complex	Complex	AluSx/+	LIPREC2/+	N	FoSTeS/MMBIR
23_6	Complex	Complex	MARNA/+	LIME4a/+	N	FoSTeS/MMBIR
24	Complex	Complex	AluY/−	AluSq2/−	4	Parental pericentric inversion
17_1	DEL-NML-DEL	0.545	–	–	6	FoSTeS/MMBIR
17_2	DEL-NML-DEL	0.007	AluY/−	–	N	FoSTeS/MMBIR
11	Terminal DEL	2.92	N/A	L1MA4	0	Telomeric healing
12	Terminal DEL	5.06	N/A	AluSc/−	3	Telomeric healing
25d	Terminal DEL	2.574	N/A	N/A	N/A
35	Terminal DEL	1.964	N/A	–	4	Telomeric healing
38	Terminal DEL	1.379	N/A	–	2	Telomeric healing
BAB3291	Terminal DEL	2.46	N/A	AluJo/+	2	Telomeric healing
K1	Terminal DEL	2.46	N/A	AluSp/+	1	Telomeric healing

Abbreviations: /+, repeat locates on plus strand; /−, repeat locates on negative strand; Alu–Alu, Alu–Alu-mediated rearrangement; DEL, deletion; DUP, duplication; MMBIR, microhomology-mediated break-induced replication; FoSTeS, fork stalling and template switching; NHEJ, non-homologous end joining; MMEJ, microhomology-mediated end joining; N/A, not applicable.

^aFor individuals with complex CNVs, there may be more than one breakpoint junctions aligned.

^bNumber of bp of microhomology sequence not shown due to multiple template switches (indicated by N). For detailed breakpoint junction sequences alignment, see supplementary figures.

^cAlu–Alu, Alu–Alu-mediated rearrangement as defined by the generation of a chimeric Alu hybrid; Similarity of the sequence between Alu pairs that generate the chimeric Alu is also listed (also see Fig. 7).

^dWe could not map the breakpoint of individual 25 with a terminal deletion, and therefore its breakpoint is unknown, as indicated by N/A.