Analytical validation of the Oncotype DX prostate cancer assay – a clinical RT-PCR assay optimized for prostate needle biopsies

Table 5 Analytical precision for normalized gene expression and GPS

Gene Assay / Score	Precision SD reference normalized Cp	Lower 95% CL, Cp	Upper 95% CL, Cp
ARF1	0.08	0.07	0.10
ATP5E	0.15	0.13	0.18
AZGP1	0.14	0.12	0.16
BGN	0.11	0.09	0.13
CLTC	0.07	0.06	0.09
COL1A1	0.10	0.08	0.11
FAM13C1	0.10	0.09	0.12
FLNC	0.11	0.09	0.13
GPS1	0.08	0.07	0.09
GSN	0.10	0.09	0.12
GSTM2	0.13	0.11	0.15
KLK2	0.08	0.07	0.09
PGK1	0.08	0.07	0.10
SFRP4	0.11	0.10	0.13
SRD5A2	0.20	0.17	0.23
TPM2	0.10	0.09	0.12
TPX2	0.21	0.18	0.25
GPS	1.86	1.60	2.20

Analytical precision (assay variation within a given RNA input level ) of the 17 Oncotype DX prostate gene assays and GPS was derived from 10 different FPE prostate cancer samples that were run 9 times each: 3 replicates at each of 3 different RNA inputs: 5 ng, 10 ng and 20 ng (target). The within RNA input level sources of variation include instruments (qPCR and Tecan liquid handling robots), reagents lots (oligonucleotides, preamplification master mix and qPCR master mix), operator and time (processing spanned 2 calendar weeks).

ISSN: 1471-2164