Translating tumor biology into personalized treatment planning: analytical performance characteristics of the Oncotype DX®Colon Cancer Assay

Table 4 Precision for non-normalized CT values

FPE RNA Pool	Gene	Total SD (C_T)	Overall C_T	Total % RSD (95% CI)
1	ATP5E	0.24	24.86	1
				(0.6, 3.3)
1	BGN	0.22	25.89	0.8
				(0.5, 1.8)
1	FAP	0.28	29.86	0.9
				(0.5, 3.0)
1	GADD45B	0.32	30.81	1.1
				(0.6, 3.6)
1	GPX1	0.22	25.7	0.8
				(0.5, 2.4)
1	INHBA	0.25	28.52	0.9
				(0.5, 2.7)
1	MK167	0.2	28.56	0.7
				(0.4, 1.9)
1	MYBL2	0.23	29.27	0.8
				(0.5, 1.8)
1	PGK1	0.28	27.61	1
				(0.6, 2.3)
1	UBB	0.19	25.68	0.7
				(0.5, 1.7)
1	VDAC2	0.25	27.68	0.9
				(0.6, 2.1)
1	MYC	0.26	27.62	0.9
				(0.6, 2.2)
2	ATP5E	0.23	25.87	0.9
				(0.5, 3.7)
2	BGN	0.2	26.66	0.8
				(0.5, 1.8)
2	FAP	0.25	30.28	0.8
				(0.5, 2.8)
2	GADD45B	0.3	30.6	1
				(0.5, 4.5)
2	GPX1	0.19	26.05	0.7
				(0.4, 2.8)
2	INHBA	0.23	29	0.8
				(0.4, 2.9)
2	MK167	0.19	29.63	0.6
				(0.4, 1.6)
2	MYBL2	0.23	30.77	0.8
				(0.4, 2.9)
2	PGK1	0.24	28.64	0.8
				(0.5, 2.8)
2	UBB	0.16	26.17	0.6
				(0.4, 1.6)
2	VDAC2	0.24	28.87	0.8
				(0.5, 2.2)
2	MYC	0.24	30.32	0.8
				(0.5, 2.5)

Two FPE RNA pools were created to provide homogeneous templates for measuring precision. FPE RNA pool 1 represents a sample with a RS in the low risk group (RS < 30) and FPE RNA pool 2 represents a sample with a RS in the high risk group (RS≥40). Using the standard 2 ng/well RNA equivalent, precision was assessed by estimating between-day, between-lot, between-7900 instrument, between-plate (within day), and within-plate variability components and total variability. Listed are the estimates of total variance for each gene and each of the two FPET pools using raw C_T values. All genes met the pre-specified acceptance criterion of 10% on the total %RSD.

ISSN: 1471-2407