A gene expression ratio-based diagnostic test for bladder cancer

Figures & data

Table 1 Bladder cancer diagnostic genes

Probe set	Accession #	Fold-change training set Aa	P value training set A	Fold-change training set Ba	P value training set B	Gene symbol	Description
Expressed at relatively higher levels in benign bladder
200795_at	NM_004684	6.08	2.15 × 10^−^8	2.37	6.33 × 10^−^5	SPARCL1	SPARC-like 1 (mast9, hevin)
201497_x_at	NM_022844	24.08	4.18 × 10^−^8	6.36	2.01 × 10^−^7	MYH11	Myosin, heavy polypeptide 11, smooth muscle
201540_at	NM_001449	11.07	3.15 × 10^−^7	2.97	1.10 × 10^−^3	FHL1	Four and a half LIM domains 1
200974_at	NM_001613	8.79	5.20 × 10^−7	2.93	2.93 × 10^−4	ACTA2	Actin, alpha 2, smooth muscle, aorta
202555_s_at	NM_005965	18.36	2.02 × 10^−6	4.29	1.83 × 10^−5	MYLK	Myosin, light polypeptide kinase
210987_x_at	M19267	7.30	2.52 × 10^−6	2.85	3.52 × 10^−5	TPM1	Tropomyosin
203951_at	NM_001299	44.07	2.53 × 10^−6	7.30	4.44 × 10^−6	CNN1	Calponin 1, basic, smooth muscle
202274_at	NM_001615	23.47	3.18 × 10^−6	4.39	4.29 × 10^−5	ACTG2	Actin, gamma 2, smooth muscle, enteric
201058_s_at	NM_006097	16.97	3.52 × 10^−6	6.00	9.46 × 10^−6	MYRL2	Myosin regulatory light chain 2, smooth muscle isoform
202222_s_at	NM_001927	29.79	4.19 × 10^−6	11.36	1.73 × 10^−6	DES	Desmin
205547_s_at	NM_003186	10.32	4.24 × 10^−6	3.94	7.96 × 10^−5	TAGLN	Transgelin
207961_x_at	NM_022870	24.82	1.53 × 10^−5	6.28	1.74 × 10^−6	MYH11	Myosin, heavy polypeptide 11, smooth muscle
214752_x_at	AI625550	5.27	1.78 × 10^−5	2.95	4.53 × 10^−5	FLNA	Filamin A, alpha (actin-binding protein-280)
200621_at	NM_004078	6.75	2.94 × 10^−5	2.25	3.46 × 10^−4	CSRP1	Cysteine and glycine-rich protein 1
200859_x_at	NM_001456	6.53	3.18 × 10^−5	3.02	1.03 × 10^−4	FLNA	Filamin A, alpha (actin-binding protein-280)
205382_s_at	NM_001928	27.85	1.36 × 10^−4	2.51	3.48 × 10^−3	DF	D component of complement (adipsin)
202822_at	BF221852	2.68	5.55 × 10^−4	2.10	5.86 × 10^−5	LPP	LIM domain-containing preferred translocation partner in lipoma
205132_at	NM_005159	23.63	9.13 × 10^−4	5.34	4.77 × 10^−6	ACTC	Actin, alpha, cardiac muscle
Expressed at relatively higher levels in bladder cancer
217871_s_at	NM_002415	0.39	5.18 × 10^−^4	0.45	5.10 × 10^−^3	MIF	Macrophage migration inhibitory factor
213911_s_at	BF718636	0.44	5.49 × 10^−^3	0.45	4.01 × 10^−^5	H2AFZ	H2A histone family, member Z
213491_x_at	AL514285	0.45	7.62 × 10^−^3	0.38	1.75 × 10^−^5	RPN2	Ribophorin II
202428_x_at	NM_020548	0.48	8.09 × 10^−3	0.47	4.72 × 10^−3	DBI	Diazepam-binding inhibitor

a Notes: Average expression level in benign bladder specimens/average expression level in malignant bladder specimens; Genes in bold identified for further analysis.

Table 2 Accuracy of all ratio combinations in predicting tumor diagnosis in training sets A and B combined

	SPARCL1	MYH11	FHL1
MIF	91% (73/80)	89% (71/80)	90% (72/80)
H2AFZ	84% (67/80)	84% (67/80)	89% (71/80)
RPN2	91% (73/80)	94% (75/80)	90% (72/80)

Notes: Six diagnostic genes were identified in a training set of samples as described in the text. A total of nine possible expression ratios (column/row intersection) were calculated where both genes used to form the ratio possessed inversely correlated expression levels in both tissue types. Predictions are stated as the fraction diagnosed correctly.

Figure 1 Verification of expression level ratios as a diagnostic tool in bladder cancer. Quantitative RT-PCR was used to obtain gene expression levels for the six bladder cancer diagnostic genes and calculate the geometric mean of the five-ratio diagnostic test (SPARCL1/MIF, S PARCL1/RPN2, MYH11/RPN2, FHL1/MIF, FHL1/RPN2) in frozen samples of benign bladder urothelium (n = 13) and bladder cancer (n = 13). This test identified 26 of 26 samples and did not result in any false-negatives. Note that the y-axis is in log scale.