Reconstructing DNA copy number by joint segmentation of multiple sequences

BMC Bioinformatics

Table 1 Detection accuracy and computation time of four methods on simulated normal samples

CNV size	CNV type	PennCNV		CBS		Fused Lasso		Group Fused Lasso
		TPR	FDR	TPR	FDR	TPR	FDR	TPR	FDR
5	Deletion	83.80	4.92	78.20	0.68	63.93	1.74	64.27	1.83
	Duplication	58.53	4.67	11.67	10.26	20.00	37.76	39.87	14.33
10	Deletion	95.03	1.45	88.37	0.56	88.50	0.60	88.87	0.56
	Duplication	93.43	0.78	56.50	4.40	83.90	12.60	91.60	3.85
20	Deletion	94.63	0.58	90.50	0.39	90.80	0.47	90.83	0.47
	Duplication	96.13	0.92	86.22	3.58	92.77	4.95	94.98	2.13
30	Deletion	94.57	0.28	93.30	0.29	89.38	0.52	89.77	0.53
	Duplication	96.09	0.05	90.77	1.61	94.32	1.78	94.98	1.29
40	Deletion	97.83	0.59	97.58	0.09	97.28	0.19	97.28	0.19
	Duplication	94.61	0.46	92.77	0.98	93.94	1.15	94.63	0.75
50	Deletion	94.33	0.07	92.76	0.04	90.47	0.11	90.48	0.11
	Duplication	94.50	0.09	93.81	0.74	93.11	0.79	93.64	0.49
Overall Deletion		95.02	0.55	93.06	0.19	91.08	0.33	91.19	0.34
Overall Duplication		93.82	0.44	86.92	1.55	90.56	2.85	92.46	1.38
Overall		94.42	0.49	89.99	0.85	90.82	1.60	91.83	0.87
Time (sec.)		0.48 (0.01)		0.78 (0.69)		0.22 (0.13)		0.28 (0.05)

TPR and FDR are measured as the percentage of related SNPs. Overall accuracy is calculated by pooling all sequences with a given type of CNV. Also reported are the average and standard deviation of the number of seconds required for the analysis of one sequence.

ISSN: 1471-2105