Table 2.

CNV calls for the RT-qPCR validated regions of 16 bladder cancer samples from Guo et al.³¹

Gene	Chromosome	Region Start	Region End	Call	Sample Name	XHMM	DECoNT-XHMM	ECOLE	ECOLEFT−SOMATIC
CDKN2A/B	9	20.3 m	24,1 m	DEL	B63_Cancer	No	No	No	Yes
CDKN2A/B	9	20.3 m	24,1 m	DEL	B112_Cancer	Yes	Yes	No	N/A
CDKN2A/B	9	20.3 m	24,1 m	DEL	B80-0_Cancer	No	No	No	Yes
CCDN1	11	69.8 m	69.8 m	DUP	B37_Cancer	No	No	No	Yes
CCDN1	1	69.8 m	69.8 m	DUP	B103_Cancer	No	No	No	Yes
DHFR	5	79.9 m	80 m	DUP	B15_Cancer	No	No	No	Yes
DHFR	5	79.9 m	80 m	DUP	B18_Cancer	No	No	No	Yes
DHFR	5	79.9 m	80 m	DUP	B19_Cancer	No	No	No	Yes
DHFR	5	79.9 m	80 m	DUP	B24_Cancer	No	No	No	N/A
DHFR	5	79.9 m	80 m	DUP	B34_Cancer	No	No	No	Yes
DHFR	5	79.9 m	80 m	DUP	B50_Cancer	No	No	No	Yes
ERBB2	17	35 m	35.2 m	DUP	B9_Cancer	No	No	No	Yes
ERBB2	17	35 m	35.2 m	DUP	B23_Cancer	No	No	No	Yes
ERBB2	17	35 m	35.2 m	DUP	B80_Cancer	No	No	No	N/A
ERBB2	17	35 m	35.2 m	DUP	B80-5_Cancer	No	No	No	Yes
ERBB2	17	35 m	35.2 m	DUP	B86_Cancer	No	No	No	Yes

The table lists the genes, regions, validated calls, and the predictions of each method. Note that ECOLE^FT−SOMATIC is fine-tuned on samples B112, B24, and B80. The calls of ECOLE^FT−SOMATIC for these samples are denoted as N/A as they are used during training. Bold denotes captured CNV.