Table.

Concordance of RB1 Status as Determined by Fluorescence In Situ Hybridization and Immunohistochemistry Compared to The Cancer Genome Atlas

Tumor ID	RB1 deletion by FISH	Copy number (log2 ratio)a	RB1 protein by IHCb, c	RB1 expression (log2 ratio)d	RB1 somatic mutatione	GBM Subtypef
08-0520	Homozygous	−2.406	0	−0.255	NA	N
08-0350	Homozygous	−2.146	0	−0.145	NA	P
08-0386	Hemizygous	−0.399	0	−0.33	NA	N
08-0389	Hemizygous	−0.682	0	0.093	Novel nonsense mutation	NA
08-0349	Hemizygous	−0.638	1	0.036	NA	N
08-0359	Hemizygous	−0.549	1	0.584	No	P
08-0347	Hemizygous	−0.473	1	0.544	No	P
08-0511	Hemizygous	−0.704	2	0.474	NA	C
08-0517	Hemizygous	−0.828	2	0.515	NA	P
08-0516	Hemizygous	−0.606	2	0.402	NA	NA
08-0357	Hemizygous	−0.571	2	0.735	NA	C
08-0246	Not Del	−0.322	1	0.835	No	C
08-0512	Not Del	−0.302	1	−0.7509	NA	M
08-0360	Not Del	−0.270	1	0.648	No	M
08-0375	Not Del	−0.050	1	0.691	No	C
08-0380	Not Del	−0.041	1	0.959	No
08-0518	Not Del	−0.036	1	1.006	NA	C
08-0356	Not Del	−0.032	1	1.061	NA	NA
08-0355	Not Del	−0.016	1	1.016	NA	C
08-0385	Not Del	NA	1	0.532	No	P
08-0345	NA	−0.080	2	1.333	NA	NA
08-0510	Not Del	−0.132	2	1.108	NA	M
08-0514	Not Del	−0.088	2	1.063	NA	C
08-0353	Not Del	−0.083	2	1.158	No	NA
08-0390	Not Del	−0.003	2	1.148	No	M
08-0522	Not Del	0.048	2	0.986	NA	M
08-0392	Not Del	−0.083	2	0.625	NA	M
08-0531	Not Del	−0.063	2	0.777	NA	C
08-0244	Not Del	−0.056	2	0.711	NA	NA
08-0521	Not Del	−0.004	2	0.591	NA	NA
08-0358	Not Del	−0.003	2	0.85	NA	C
08-0344	Not Del	0.020	2	0.615	No	P
08-0525	Not Del	0.041	2	1.399	NA	NA
08-0381	Not Del	NA	2	NA	NA	NA

CGH, comparative genomic hybridization; FISH, fluorescence in situ hybridization; GBM, glioblastoma; IHC, immunohistochemistry; NA, data not available; No Del, no deletion; RB1, Retinoblastoma Tumor Suppressor Protein; TCGA, The Cancer Genome Atlas.

^aCopy number [Tumor/Normal] data from TCGA, HMS.harvard HG-CGH-244A; gene deletion defined as [log₂(Tumor/Normal) less than or equal to −0.4 (fold change of copy number in tumor vs. normal less than or equal to 0.758)] (11).

^bMean IHC score for tumors with decreased RB1 copy number by array CGH was significantly different than the mean IHC score for tumors with intact RB1 (0.95 vs. 1.48, p<0.05; n=32).

^cThe mean IHC score for tumors with loss of RB1 transcript expression was significantly different than the mean IHC score for tumors with intact RB1 expression (0 vs. 1.42, p<0.00005; n=33).

^dExpression [Tumor/Normal] data from TCGA, AgilentG4502A_07; loss of RB1 expression defined as [log₂(Tumor/Normal) less than 0 (fold-change of expression in tumor vs. normal less than 1)].

^eSequencing data from TCGA, hgsc.bcm.edu (11).

^fGBM subtype as determined by Verhaak et al (18). P, proneural; N, M, Mesenchymal; C, Classical