and leaf plot and explore the duration of timing of the imatinib therapy versus progression or mixed response using logistic regression and Kaplan-Meir survival method. CD133 mRNA Detection We performed two-step Real-Time RT-PCR first performed the RT-PCR to generate cDNA from patients, which can be used in Real-Time PCR to detect CD133 expression levels in samples. RT-PCR was performed in a total volume of 20 ml containing 0.5 ml of oligo and hexamers, 1 mg RNA, 2 ml 106Buffer, and 25 mM MgCl2, 10 mM dNTPs, 0.1 DTT, 40 U RNaseOUT and DCEP-treated ddH2O. The thermal cycle conditions included 10 min at 25uC, 50 min at 45uC and 70uC 15 min, followed by 40 cycles of 95uC for 45 sec and 60uC for 1 min and 72uC for 1 min. Real-Time PCR was performed in total volume of 50 ml containing 25 ml 16 SyberGreen Mix-buffer, 1 ml Rox Refeence Dye, 6 mM MgCl2, 100 mM KCl, 400 mM dATP, dCTP, dGTP and 400 mM dUTP, 40 mM Tris-HCl, 6 mM300 nM each primers, 2 ml 23300835 cDNA template for each reaction, followed 95uC for 10 min and 45 cycles of 95uC for 45 min, 55uC for 1 min and 72uC 45 sec. All reagents used for PCR were purchased from Invetrogen, or Stratagene, and using Stratagene MX-3000 Real-time PCR System. Data interpretation: the amount of target, normalized to an endogenous reference and relative to the positive control is defined by the Ct method. The formula is applied as follows: P-1206 manufacturer Target amount = 22Ct, where Ct =. The assays were run on duplicates in two separate experiments and averages of the two experiments were then used in the final analysis. Results Study enrolled 24 evaluable GIST patients in 2003. Their peripheral blood mononuclear CD133 mRNA and plasma VEGF level were assayed via real time RT-PCR assay and sensitive ELISA respectively. Mean CD133 mRNA levels for GIST patients was 615.17. Mean VEGF levels was 107.42 pg/ml. The results showed that the relative amount of CD133 mRNA expression was significantly lower in the post-treated patients as compared to those same pretreated 7 patients. The VEGF value was also lower in the plasma of treated patients than that of untreated. The pre- and post treatment CD133 mRNA and VEGF levels were shown in VEGF Detection We used a complete kit for the quantitative determination of human VEGF in plasma of patients. We established standard series using a recombinant human VEGF standard. Wash ELISA microtiter plates once with dd-H2O, add 200 ml /well PBS:2% BSA, incubate 1 hour at 37uC, wash 6 times with dd-H2O, add 50 ml/well plasma diluted in PBS:1%BSA. Then incubate for 2 hr at 4uC, wash 9 times with dd-H2O, add 50 ml/well anti-human IgG:HRP diluted in PBS:1% BSA, incubate for 28 hr at 23964788 4uC, wash 6 times with dd-H2O, wash once with carbonate buffer, add 50 ml/well working substrate solution, 
0.5 ml 4.0% OPD, 5 ml 30% H2O2, 1.0 ml 106 Substrate buffer, 8.5 ml dd-H2O. Incubate for 30 minutes at room temperature, add 25 ml/well 4.5N Sulfuric Acid. Read data at A450 nm by Packard SpectroCount and calculated to pg/ml for each sample by Packard I-Smart 2. The assays were run on duplicates in two separate experiments and averages of the two experiments were then used in the final analysis. Mean CD133 mRNA levels Paired Differences p value Before After 6.702 2.369 P = 0.048 Mean VEGF levels Before After 134.117 55.174 p = 0.002 paired sample test doi:10.1371/journal.pone.0055520.t002 CD133 Correlates with Response to Treatment Data Items Two Indicators: CD133 and VEGF Correlation Sig. 0.183 0.917 0.258 Average Ratio