Nikoghosyan et al. BMC Cancer 2010, 10:607 http://www.biomedcentral.com/1471-2407/10/607 Sample Size Determination The sample size is calculated on the basis of the follow- ing assumptions: LPFS rate 5 years after radiation therapy of 70% 1) for proton therapy, hazard l1 = 0.0713, and 80% for carbon ion therapy, hazard l2 = 0.0446 (hazard ratio = 1.599). Recruitment period of 5 years, with constant accrual rate of 20% patients per year and a follow-up time of 8 years. One interim analysis according to a group sequen- tial design with two stages. Formula of Schoenfeld [20,21] used for the calculation of the number of accumulated events. For a two-sided logrank test with an overall two-sided significance level of 0.05 (including interim and final analyses) and power of 0.80, 143 events are required. The critical values and the test characteristics of the group sequential test design were calculated for an O’Brien and Fleming type alpha spending function. The computation assumes equal allocation to the two groups (n2/n1 = 1). Assum- ing an accrual time of 5 and a maximum observation time of 13 years a total of 319 patients is expected to yield the necessary number of events if the accrual rate is constant. Under these assumptions, the time point of the interim analysis should be 7 years after the first patient is entered. The ADDPLAN, Version 4.0 calcula- tor was used for the sample size estimation. With the assumption that approximately 7% of the patients will be lost to follow-up a total of 344 patients will be needed to accumulate 143 events. Analysis Populations and General Considerations Analysis populations will be defined as follows: The ITT population will include all patients who are randomised, with radiation therapy administration designated according to initial randomisation, regard- less of whether patients receive study treatment or receive a different treatment from that to which they were randomised. This will be the primary population for evaluating all efficacy endpoints as well as subject characteristics. The safety population consists of all subjects who received at least one dose of irradiation administration designated according to actual study treatment received. The PP population will consist of all subjects of the ITT population who completed the particle therapy, have at least 2 post-baseline assessments regarding the primary endpoint without pre-specified (in the statistical analysis plan), selected major protocol deviations thought to impact on efficacy analysis. Page 7 of 9 The statistical analysis will be done as soon as the database has been declared to be complete and accurate and has been locked. The details of the analysis will be laid out in the statistical analysis plan, which will be finalized and approved prior to the database lock. It has to be authorized before by the biometrician and the principle investigator. Missing values will not be replaced or imputed. For patients with incomplete fol- low-up, time to last follow-up date will be used as the censoring time in the analysis of time-to-event data. Efficacy Analysis Primary efficacy analysis LPFS is defined as the time from date of randomisation to local recurrence or death from any cause in the absence of documented local disease progression. LPFS will be censored on the date of the last tumour assess- ment on study for patients who do not have local tumour progression and who do not die while on study. A log-rank test (two-sided) will be used to compare LPFS between the two treatments. The LPFS-rates will be derived from the Kaplan Meier estimate [22] and the confidence intervals will be calculated using Green- wood’s formula. Secondary efficacy analyses A sensitivity analysis will be performed on the primary efficacy endpoint to assess the impact of protocol devia- tions using the per protocol analysis set. A hazard ratio with 95% confidence interval for the experimental arm relative to control arm will be esti- mated by proportional hazard regression [23-25] with treatment, gender, age (< 30, ≥ 30 years), tumour size (< 70 ml, ≥ 70 ml), compression of OAR (yes/no) as cov- ariates. A logistic regression analysis [26] will be carried out to identify relevant prognostic factors. Benefit from intervention (yes or no) will be defined as belonging to the patients groups (low-risk, high-risk group) which lay above the 50% percentile of LPFS. The analyses of OS, PFS and metastasis free survival will be conducted using log-rank test. The Kaplan-Meier method will be used to obtain the estimates of the survi- val functions and the 95% confidence intervals will be estimated using Greenwood’s formula. Covariates will not be included in the calculation. All of these secondary analyses will be conducted at the 0.05 level of significance. Descriptive statistics will be provided for all other sec- ondary endpoints. Additional exploratory analyses will be used as appropriate. Generally, results will be given by summaries of the data as indicated above together with the test statistics and their associated p-values. Appropriate confidence intervals of estimates of effect will be given to quantify the degree of uncertainty of the point estimates.