Table 2.

Significant regions of gain or loss in BAC arrays.

						NP		P neg		P dys
		Chr	Location	Cytoband	Gain/Loss	freq	foot pvalue	freq	foot pvalue	freq	foot pvalue	Genes of Interest
1	NP only	4	28Mb	4p15.1	gain	25.0%	0.002
		7	9Mb	7p21	loss	25.0%	0.034					NXPH1
		9	91Mb	9q22	loss	25.0%	0.010					SPIN1, SHC3
2	P neg only	11	64Mb	11q13	gain			20%	0.002			COX8A, BAD, NRXN2, MAP4K2
		15	19Mb	15q11.2	gain			20%	0.010
		2	25Mb	2p23	loss			20%	0.010			CENPO, ADCY3
3	P dys	6	20Mb	6p22	gain					20%	0.008	E2F3
		10	24Mb	10p12	gain					20%	0.002	ARHGAP21
		5	133Mb	5q31	loss					20%	0.048	SKP1, VDAC1, PPP2CA
		7	129Mb	7q32	loss					20%	0.044	MIR183
4	P neg & dys	2	230–231Mb	2q36	loss			30%	0.020	30%	0.004	FBXO36
		3	171Mb	3q26	loss			30%	0.010	30%	0.004	TNIK, PLD1, FNDC3B
		3	44Mb	3p21	loss			40%	0.020	30%	0.020	KIF15
		4	173Mb	4q34	loss			40%	0.020	50%	0.006	GALNTL6
		4	4–5Mb	4p16.2	loss			20%	0.010	40%	0.004	STX18
		15	69–70Mb	15q22	loss			50%	0.020	60%	0.004	MIR629
		16	6Mb	16p13	loss			30%	0.010	20%	0.124	A2BP1
5	NP & P	1	103–104Mb	1p21	loss	37.5%	0.004	40%	0.010	50%	0.004	COL11A1
		2	233Mb	2q37	loss	25.0%	0.002	20%	0.090	30%	0.004	ALPI
		3	8Mb	3p26	loss	37.5%	0.002	40%	0.020	30%	0.032	RAD18
		6	16–18Mb	6p22	loss	37.5%	0.004	40%	0.010	30%	0.002	ATXN1
		9	9Mb	9p23	loss	25.0%	0.054	30%	0.050	50%	0.004	PTPRD

Frequency of regions of copy gain and copy loss as detected by STAC analysis for UC non-progressors (n=9; left), and UC progressors (n=11) at non-dysplastic (middle columns) or dysplastic (right columns) sites as indicated by cytoband and genomic location (NCBI Build 36.3). Number of samples and relative percentage (in parentheses) are shown for each alteration per group. Data is grouped to reflect sites specific to one or more of the sample sets (non-progressor, NP; progressor, P; progressor (dysplasia), P dys). NS = p-value > 0.05; not significant.