DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data

Table 5 Comparison of the performances of DeviCNV and previous tools using 16 CNVs confirmed by qPCR

Sample		qPCR confirmed CNV				DeviCNV	VisCap	XHMM	CODEX
Sample	Median read depth	Gene	NM	CNV	CNV size (kb)	DeviCNV	VisCap	XHMM	CODEX
GM17433	82.13	CPT1A	NM_001876	EX10 DUP	0.20	O^a	X	X	X
		CD3E	NM_000733	EX4 DEL	0.01	O	X	X	O
		GATM	NM_001482	EX9 DUP	1.10	O	X	X	X
GM24007	142.84	PTPRC	NM_002838	EX16–17	0.83	O	X	X	O
		LMBRD1	NM_018368	EX12 DUP	0.10	O	X	X	X
		SLCO1B3	NM_019844	EX4 DUP	0.14	O	X	X	O
		PAH	NM_000277	EX5 DEL	0.07	O	O	X	X
		NR0B1	NM_000475	EX1 DEL	1.18	O	O	X	O
NA00852	204.09	HBA2	NM_000517	EX2–3 DEL	0.59	O	X	O	X
NA01741	164.4	TG	NM_003235	EX20 DUP	0.22	O	X	X	X
NA01741	164.4	TG	NM_003235	EX 21 DUP	0.15	O	X	X	X
NA02227	278.98	CYP21A2	NM_000500	EX10 DUP	0.80	O	X	X	X
NA02659	608.46	HBA2	NM_000517	EX3 DEL	0.24	O	X	O	X
NA12217	269.08	GBA	NM_001005741	EX12–11 DUP	0.86	O	X	X	X
NA22496	137.24	GUSB	NM_000181	EX11 DUP	0.14	O	X	X	X
NA22496	137.24	G6PC	NM_000151	EX2 DUP	0.11	O	X	X	O

CNV copy number variation, EX exon, DEL deletion, DUP duplication
^aIndicates whether a known CNV was found using each tool. “O” means all CNVs were found, and “X” means they were not found at all

ISSN: 1471-2105