BMC Bioinformatics

Table 5 Copy number estimation results obtained on 10K Array data of sample JEKO-1

From: Bayesian DNA copy number analysis

		mBPCR
gene region	FISH CN	${\hat{ρ}}^{2}$	${\hat{ρ}}_{1}^{2}$	CBS	CGHseg	HMM	GLAD	BioHMM	Rendersome
BCL6	3/2	2.97	2.99	2.97	2.90	2.92	2.92	3.14	2.92
C-MYC	ampl	12.11	9.35	10.27	10.27	13.95	9.82	8.26	13.10/3.11
CCND1	2	4.08	3.77	4.08	4.08	3.84	3.79	3.14	3.50
BIRC3	4/5	4.08	4.29	4.08	4.08	3.84	3.79	3.14	3.50
ATM	4	4.08	4.29	4.08	4.08	3.84	3.79	3.14	3.50/2.39
D13S319	4	3.72	3.59	3.57	3.72	3.62	3.58	3.14	3.43
LAMP1	4	3.41	3.82	3.41	3.41	3.62	2.49	3.14	3.43
TP53	2/3	2.81	3.00	2.83	2.50	3.52	2.93	3.14	2.93
MALT1	4	3.63	3.62	3.48	3.64	3.42	3.42	3.14	3.42
BCL2	4	3.63	3.62	3.48	3.64	3.42	3.42	3.14	3.42

On this noisy data, BioHMM and Rendersome often estimated the gene copy number wrongly, while this occurred only sometimes to CBS, HMM and GLAD. The method mBPCR with ${\hat{ρ}}_{1}^{2}$ correctly estimated the gene copy numbers, apart from CCND1 whose copy number was estimated by all methods differently from the FISH technique.

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