Table 1.

Percentage frequencies of the most common copy number events in LGD, HGD and SCC samples

	LGD	HGD	SCC	P value
3p loss	28.95	72.46	0.72	0.3994
4p loss	13.16	44.93	0.33	0.9453
5q loss	23.68	69.57	0.56	0.9787
9p loss	26.32	65.22	0.50	0.7044
11 pq loss	18.42	50.72	0.36	0.7893
18q loss	7.89	42.03	0.50	0.0646
3q gain	36.84	68.12	0.60	0.2041
5p gain	39.47	62.32	0.51	0.0428
7 pq gain	39.47	47.83	0.50	0.0067
8q gain	50.00	57.97	0.59	0.0009
12p gain	7.89	31.88	0.36	0.2404
Expected	12	38	30

The p values that each event differs from the expected frequencies were calculated from the overall fraction of genome altered and total sample number for each group using a chi-squared test. As 11 regions were tested, p values below 0.0045 are considered significant