Mutation spectrum of Drosophila CNVs revealed by breakpoint sequencing

Table 1 Comparison of the types of CNV breakpoints identified in Drosophila and humans.

Type of breakpoint	Drosophila		Human (Conrad et al.)^a		Human (Kidd et al.)^b		Molecular mechanism(s)
	n	%	n	%	n	%
Blunt	223	35	58	19	82	11	NHEJ
Microhomology	262	41	151	50	289	39	MMEJ, replication-associated repair
Blunt and large stretches of sequence identity (³20 bp)	2	0.3	3	1	219	29	SSA, NAHR, replication-associated repair
Inserted/deleted bases	143	22	81	27	153	21	NHEJ, replication-associated repair
Inserted/deleted bases and microhomology	14	2	9	3	3^c	0.4	MMEJ, replication-associated repair
Total	644		302		743

The dataset of Conrad et al. refers only to deletions while the dataset of Kidd et al. includes both deletions and insertions. Excluded from both datasets of human CNVs were those variants classified as VNTRs (variable number of tandem repeats) and as transposable elements insertions. Further excluded from the dataset of Conrad et al. were 13 deletions that were also associated with inversions. Because Conrad et al. required only 1 bp of identical sequence to call a breakpoint as being associated with microhomology, we re-classified the entire dataset so that only deletions associated with at least 2 bp of identical sequence at the breakpoint were classified as being associated with microhomology.

ISSN: 1474-760X