Table 2.

Homozygous deletions in U-251 subclones.

Cell line	Chr	Cytoband	Start (bp on Chr)	Stop (bp on Chr)	# Probes	Deletion (mean log2 ratio)	P-value	Gene names
U-251MG	Chr9	P21.3	21908956	22148414	37	−2,598,488	0.000	C9orf53, CDKN2A, CDKN2BAS, CDKN2B
	Chr11	q11	55124730	55187341	12	−2,848,753	1.553e-161	OR4C11, OR4P4, OR4S2
U-251-4q12	Chr2	q22.1	141427652	142052932	119	−310,064	0.000	LRP1B
	Chr9	p21.3	21908956	22148414	37	−3,344,793	0.000	C9orf53, CDKN2A, CDKN2BAS, CDKN2B
	Chr10	q21.3	67748408	67784515	9	−4,727,192	5.978e-160	CTNNA3
	Chr11	q11	55124730	55187341	12	−4,244,455	7.253e-209	OR4C11, OR4P4, OR4S2
U-251N	Chr1	p33	51135519	51218298	18	−3,424,784	1.032e-151	FAF1, CDKN2C
	Chr2	q13	112607949	112672009	14	−3,144,469	8.919e-220	FBLN7
	Chr2	q22.1	14127652	142052932	119	−5,079,372	0.000	LRP1B
	Chr9	p21.3	21908956	22148414	37	−386,988	0.000	C9orf53, CDKN2A, CDKN2BAS, CDKN2B
	Chr10	q21.3	67748408	67784515	9	−434,557	2.586e-149	CTNNA3
	Chr11	q11	55124730	55187341	12	−4,281,094	4.431e-205	OR4C11, OR4P4, OR4S2
	Chr16	q23.1	77669056	77772300	22	−4,400,907	0.000	WWOX
U-251-FGA20gain	Chr2	q13	112607949	112672009	14	−299,373	6774e-186	FBLN7
	Chr2	q22.1	14127652	142052932	119	−440,903	0.000	LRP1B
	Chr9	p21.3	21908956	22148414	37	−3,257,158	0.000	C9orf53, CDKN2A, CDKN2BAS, CDKN2B
	Chr10	q21.3	67748408	67784515	9	−4,369,498	2.843e-140	CTNNA3
	Chr11	q11	55124730	55187341	12	−3,963,717	2.537ee-209	OR4C11, OR4P4, OR4S2
	Chr16	q23.1	77669056	77772300	22	−3,828,185	0.000	WWOX

White background, deletions common to all; black background, deletions common to 3 subclones; light gray background, common to U-251N and U-251-FGA20gain; dark gray background, proprietary to U-251N.