Chemoprevention of Prostate Cancer, HDAC Inhibition and DNA Methylation: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Chemoprevention of Prostate Cancer, HDAC Inhibition and DNA Methylation (NCT01265953), a randomized na study. The primary outcome is Change of Total Urine SFN (Sulforaphane) Metabolites.

2. Clinical Question

The registry frames the broader objective as identifying mechanisms by which compounds found in cruciferous vegetables alter gene expression through epigenetic modifications and may prevent prostate cancer development. It also states that investigators had found SFN inhibits histone deacetylase activity in human colorectal and prostate cancer cells. Those statements describe the rationale; the registered primary outcome is a urine metabolite measure, not a clinical prostate cancer outcome or a direct measure of gene expression. The posted results therefore address the measured metabolite change between arms, not whether prostate cancer was prevented or whether a particular biological mechanism was established.

3. Trial Design

The study is registered as NCT01265953 and is titled “Chemoprevention of Prostate Cancer, HDAC Inhibition and DNA Methylation.” Portland VA Medical Center is listed as the sponsor. The registry describes a randomized, triple-masked, parallel-group study and reports an enrollment of 98. The phase is listed as NA, and the status is completed. The start is recorded as 2011-07, and primary completion as 2015-10.

The parallel groups were SFN-rich broccoli sprout extract capsules and placebo capsules. The supplement arm description specifies four weeks of extract, with 200µmol of sulforaphane (SFN) daily as 2 capsules (1 capsule B.I.D.) daily. The placebo arm description specifies four weeks of placebo capsules with the same daily capsule schedule. The registry’s intervention list identifies a gelatin capsule containing microcrystalline cellulose as a dietary supplement intervention.

The primary outcome is continuous: change in total urine SFN metabolites, expressed as micromolar (µM) concentrations. Blood and urine specimens were collected before and after intervention. The outcome timeframe is recorded as baseline and 4-8 weeks following intervention, while the arm descriptions specify a four-week intervention. The registry does not explain the relationship between these time descriptions or provide further details about the timing of individual collections.

The primary outcome analysis includes 42 participants in the supplement arm and 44 in the placebo arm. The registry notes that not all subjects had urine samples for analysis, so the number in this analysis differs from the total enrollment. The allocation method, masking procedures, eligibility criteria, and original sample-size assumptions are not reported in the registry record. No inferential analyses are posted in the registry, and no secondary outcomes are posted.

4. Participant Flow and Accounting

The registry reports how participants moved through each stage of the study. All counts below are exactly as posted; missing counts are not inferred from other stages.

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: Not all subjects had urine samples for analysis, therefore, the total number of subjects in this urine analysis is different from total number of enrolled subjects.

5. Baseline Characteristics

The table reproduces the baseline characteristics posted in the registry, which describe the participants analysed at baseline and help show whether the randomized groups were comparable.

6. Primary Endpoint

The registry lists the primary outcome as Change of Total Urine SFN (Sulforaphane) Metabolites, measured over Baseline and 4-8 weeks following intervention.

The primary endpoint is the change in total urine SFN (sulforaphane) metabolites. It is described as a mean of a continuous measure, with micromolar (µM) concentrations as the unit. For each participant with available measurements, change is defined as the post-intervention level minus the pre-intervention level. A positive change therefore indicates a higher measured post-intervention value than the pre-intervention value; a negative change indicates a lower value.

Urine SFN metabolites are relevant to the study’s stated focus on sulforaphane exposure and mechanisms associated with compounds found in cruciferous vegetables. Measuring the change from baseline places the post-intervention measurement in the context of the participant’s own pre-intervention measurement. The comparison between randomized groups then describes how the reported average changes differed between the supplement and placebo arms.

This endpoint is a biomarker measure, not a count of prostate cancer cases, a diagnosis, or a measure of cancer prevention. The registry’s rationale discusses epigenetic modifications and possible prevention, but the posted primary outcome is specifically urine metabolite change. The registry does not report a direct measure of gene expression, histone deacetylase activity, or DNA methylation as the primary endpoint. Nor does the record report a clinical cancer outcome among the four outcome measures. Interpretation should therefore remain focused on the measured urine metabolite concentrations and the participants included in that analysis.

The registered timeframe is baseline and 4-8 weeks following intervention. The record describes the intervention as four weeks but does not give more detailed specimen-collection timing or explain the range in the outcome timeframe.

7. Results Posted in the Registry

• Supplement: mean 4.75 versus -0.02 on control; difference 4.77 (95% CI 3.52 to 6.02), standardized effect d = 1.65; z-test p = <0.001.

8. Statistical Interpretation

9. Statistical Methods Explained

The primary outcome is continuous, and the registry identifies the reported statistic as a mean. A mean summarizes the average observed change in each arm. Because change is defined as post-intervention level minus pre-intervention level, the sign carries direction: a positive value indicates an average increase from baseline, and a negative value indicates an average decrease. The mean does not show whether all participants changed in the same direction or whether the observations were tightly clustered.

What does the standard error describe?

The group results report standard errors. A standard error describes the sampling uncertainty of an estimated mean: it indicates how much the estimate would be expected to vary across repeated samples under a statistical model. It is not the standard deviation of individual participants’ measurements and does not directly tell how diverse participant responses were. The registry does not report standard deviations for the primary outcome, and the posted summaries do not allow individual-level patterns to be described.

The standard errors are 0.64 for the supplement mean and 0.01 for the placebo mean. A large difference between group standard errors can reflect differences in variability, sample size, or both. The registry does not provide enough information to distinguish among those possible explanations. It would therefore be inappropriate to infer the distribution of individual values from the means and standard errors alone.

How should the mean difference be read?

The comparison is the supplement mean minus the placebo mean, expressed as a mean difference of 4.77. This is an unadjusted recalculation from the posted arm summaries. “Unadjusted” means that the comparison does not account for additional covariates in a model. The registry does not report an adjusted estimate or a sponsor-conducted statistical analysis; its analyses count is zero. The recalculated comparison is consequently a summary-level estimate rather than a report of a posted model-based analysis.

The comparison’s 95% confidence interval is 3.515 to 6.025. A confidence interval describes uncertainty around an estimated effect under the assumptions used to calculate it. It is not a range containing a known proportion of individual participants’ results, nor does it mean that the true value has a stated probability of lying within the realized interval. The interval gives a sense of the precision of this estimated difference. Its limits are in the same direction as the point estimate, but statistical precision alone does not establish clinical importance or mechanism.

What does the p-value contribute?

The unadjusted p-value is <0.001. In general, a p-value measures how unusual data at least as incompatible with a specified null hypothesis would be if that hypothesis and the statistical assumptions held. Here, the null hypothesis for the comparison is no mean difference between arms. A small p-value is evidence against that null within the unadjusted comparison, but it is not the probability that the null hypothesis is true. It also does not quantify the size or importance of the effect; the estimate and confidence interval provide information about magnitude and precision.

The registry does not report whether the trial had a prespecified hypothesis-testing plan, whether outcomes were selected or ranked in advance, or whether any interim analyses were conducted. Such details are not reported in the registry record and cannot be inferred from the posted p-value. There are four outcome measures listed, but no secondary outcomes are posted and no analyses are listed.

Why can over-dispersion matter?

For continuous outcomes, dispersion describes how participant values vary around a mean. If observations are more variable than a statistical model assumes, standard errors may be too small and confidence intervals may be too narrow. This general issue is called over-dispersion relative to the assumed model. It is one reason analysts examine the distribution of measurements and the fit of the model rather than relying only on an average. The registry does not provide participant-level measurements, a distributional assessment, or a model fit assessment, so no conclusion about over-dispersion in this trial can be drawn.

Randomization can support a fair comparison by allocating participants to groups, but the registry does not report the randomization sequence method, allocation concealment, or baseline characteristics. The label “randomized” alone does not supply those details. Similarly, “triple” masking is the registry’s masking classification; the identities of the masked parties and how masking was maintained are not reported.

Overall, the statistical summaries support description of the observed group means and the unadjusted difference for participants with urine data. They do not replace a prespecified analysis plan or provide information about missing-data methods, model assumptions, covariate adjustment, or clinical outcome effects. Those elements are not reported in the registry record.

10. Confidence Intervals and Precision

The unadjusted mean difference in change in total urine SFN metabolites is 4.77, with a 95% confidence interval from 3.515 to 6.025. The interval expresses uncertainty around the estimated difference, given the calculation’s assumptions. Its lower and upper limits are both positive, so the range of estimates compatible with this calculation is on the same side of zero as the point estimate. The unadjusted p-value is <0.001.

The interval’s width provides a practical indication of precision: narrower intervals indicate less uncertainty about the estimated mean difference, while wider intervals indicate more. Precision is not the same as importance. The registry does not report a threshold that would define a clinically meaningful change in this metabolite measure, so the confidence interval cannot determine whether the magnitude is clinically meaningful. It also cannot establish a biological mechanism or a cancer-prevention effect.

The estimate is based on 42 participants in the supplement group and 44 in the placebo group. Not all enrolled subjects had urine samples for analysis. The registry does not report why samples were unavailable, how missingness was handled, or whether the missing measurements could differ systematically from the observed measurements. The confidence interval therefore describes uncertainty for the posted unadjusted comparison, not all possible uncertainty associated with missing data or analysis choices.

The registry reports standard errors for group means but not standard deviations or individual participant values. Consequently, the interval should not be interpreted as describing the spread of individual responses. It also rests on a recalculation from summary statistics rather than a posted sponsor analysis. The registry lists no analyses and indicates no discrepancy. These details place the interval’s precision in context without changing the fact that it is an estimate of the difference in mean metabolite change.

11. Planning a Similar Trial: Sample Size

This is a planning illustration, not a re-evaluation of the original trial. It asks: if a new study wanted to detect a difference like the one observed, or a smaller one, how large would it need to be? It is deliberately not “observed power” of the finished trial, which is not a meaningful quantity.

The planning figures are participants per arm, not total events. They are illustrations based on the observed effect, not the trial’s own original design assumptions. The stated assumptions are a two-sided significance level 0.05, equal allocation between the two arms, and a normal approximation. The effect to detect is set to a stated fraction of the observed effect. The trial’s original sample-size justification and design assumptions are not reported in the registry record.

For the row planning for 100% of the observed effect, the illustration gives 6 participants per arm for 80% power and 8 participants per arm for 90% power. For 75% of the observed effect, it gives 11 participants per arm for 80% power and 14 participants per arm for 90% power. For 50% of the observed effect, it gives 24 participants per arm for 80% power and 32 participants per arm for 90% power.

In plain language, the 80% power column describes the approximate number of participants per arm that the planning calculation would require to have an 80% chance of detecting the specified effect under its assumptions. The 90% column makes the same type of illustration for a 90% chance. These are planning probabilities under a model, not guarantees about a future study. The observed trial enrollment and the numbers analyzed for the urine outcome are distinct from these illustrative figures.

The pattern reflects a general design principle: smaller effects are harder to distinguish from random variation, so detecting them generally requires more participants. The figures are not observed power and should not be read as a measure of whether this completed trial succeeded. They also do not show that the original trial was designed using the observed effect. No original sample-size rationale is reported in the registry record.

12. How the Sample Size Is Derived

Power is the probability that a study of a given size rejects the null hypothesis when a specific true effect exists. It depends on four things: the effect to detect, the variability of the outcome, the significance level (here a two-sided α of 0.05, so z_1−α/2 = 1.960) and the desired power (z_1−β = 0.842 for 80% and 1.282 for 90%).

Formula

n is the number of participants in each arm, Δ is the difference in means to detect and σ is the common standard deviation.

Worked calculation for this trial

1. Observed difference Δ = 4.770; pooled standard deviation σ = 2.898.
2. n = 2 × (1.96 + 0.842)² × 2.898² / 4.770² = 5.8, rounded up to 6 participants per arm for 80% power.

The smaller-effect rows in the table above repeat the same calculation with the effect multiplied by 0.75 and 0.5 (for ratios, applied to the logarithm of the ratio).

R code

alpha <- 0.05
z_a   <- qnorm(1 - alpha / 2)          # two-sided
delta <- 4.77                      # observed difference in means
sigma <- 2.89811186480998                     # pooled standard deviation
n_per_arm <- function(power, frac = 1) {
  ceiling(round(2 * (z_a + qnorm(power))^2 * sigma^2 / (delta * frac)^2, 6))
}
for (f in c(1, 0.75, 0.5))
  cat(sprintf("%3.0f%% of observed effect: n per arm = %s (80%% power), %s (90%% power)\n", 100 * f,
              format(n_per_arm(0.80, f), big.mark = ","), format(n_per_arm(0.90, f), big.mark = ",")))

# Check against R's built-in function (t-based, so very slightly larger)
cat("power.t.test:", round(power.t.test(delta = delta, sd = sigma, power = 0.80)$n, 1), "\n")

# Simulation: exact two-sample t-test using simulated means and variances
set.seed(1265953)
n    <- n_per_arm(0.80)
reps <- 20000
m_diff <- rnorm(reps, delta, sigma * sqrt(2 / n))             # difference in sample means
s2     <- sigma^2 * rchisq(reps, 2 * (n - 1)) / (2 * (n - 1))   # pooled sample variance
tstat  <- m_diff / sqrt(s2 * 2 / n)
cat(sprintf("Simulated power at n = %s per arm: %.3f (%d replicates)\n", format(n, big.mark = ","), mean(abs(tstat) > qt(0.975, 2 * (n - 1))), reps))

Output from running the code

100% of observed effect: n per arm = 6 (80% power), 8 (90% power)
 75% of observed effect: n per arm = 11 (80% power), 14 (90% power)
 50% of observed effect: n per arm = 24 (80% power), 32 (90% power)
power.t.test: 6.9 
Simulated power at n = 6 per arm: 0.729 (20000 replicates)

The simulation draws many sets of group means and variances at the planned sample size and counts how often the two-sample t-test rejects the null. It should land close to the target power; at very small required sample sizes it can fall below it, because the normal approximation is rough there.

13. Multiplicity, Missing Data and Analysis Populations

The registry lists four outcome measures, but reports zero secondary outcomes and zero analyses. The posted record therefore does not provide a full analysis set or describe which outcomes were tested, how they were ordered, or whether a multiplicity adjustment was planned. When several outcomes or comparisons are tested, the chance of at least one small p-value can increase; methods such as adjustment or a prespecified hierarchy can address that general issue. Whether any such approach was used in this study is not reported in the registry record. The unadjusted p-value should not be assumed to account for other outcomes or analyses.

The registry explicitly notes that not all subjects had urine samples for analysis and that the number included in the urine analysis differs from total enrollment. The primary outcome group sizes are 42 in the supplement arm and 44 in the placebo arm, while total enrollment is 98. The reasons for unavailable urine samples, the timing or extent of missingness, and the number missing in each arm are not reported in the registry record. No imputation method, complete-case definition, sensitivity analysis, or other missing-data procedure is described.

Missing measurements can affect how well an observed-data comparison represents the randomized groups, particularly if availability is related to participant characteristics or outcome values. That is a general concern rather than a finding about this trial: the registry does not report information that would establish why measurements were missing or whether missingness was related to outcomes. The published summary cannot resolve this uncertainty.

The registry record also does not describe the analysis population beyond noting the urine-sample limitation. It does not say whether the primary analysis followed intention-to-treat principles, included only participants who completed intervention, or used another population definition. The record does not report a protocol analysis set or an adjustment for baseline values beyond defining the outcome as a change score. These gaps limit assessment of the analysis strategy and its relationship to randomization. No conclusion about the use or absence of unreported procedures should be inferred from the registry entries alone.

14. Safety Results

The registry reports serious adverse events as affected participants divided by participants at risk.

Deaths

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 0% reporting threshold.

Most frequent non-serious adverse event terms

The registry reports serious adverse events for 50 participants at risk in the supplement group and 48 at risk in the placebo group. Serious adverse events affected 0 participants in each group. The record lists no serious adverse event terms. Deaths were 0 in both groups.

For other adverse events, 2 participants were affected in the supplement group and 1 in the placebo group. These are participant counts, not rates, and the registry does not provide details about the event types, severity, timing, or relationship to intervention. The at-risk counts for other adverse events are 50 in the supplement group and 48 in the placebo group.

These registry figures are limited to the categories and counts posted. A zero count for serious adverse events or deaths means none were reported in the relevant group in this record; it does not establish that no event of any kind occurred or that risks are absent. The record does not report how adverse events were collected, the observation period for safety reporting, or whether all participants contributed the same amount of follow-up. The safety counts should be read alongside those reporting limitations and not as a complete account of every possible event.

15. What the Result Does, and Does Not, Mean

The posted primary outcome shows a difference in mean change in urine SFN metabolites between the supplement and placebo groups. The supplement group’s mean change was 4.75 micromolar (µM), while the placebo group’s mean change was -0.02 micromolar (µM). The unadjusted recalculated mean difference was 4.77, with a 95% confidence interval from 3.515 to 6.025 and an unadjusted p-value of <0.001. These results describe the analyzed urine measurements.

They do not show that prostate cancer was prevented. The primary endpoint is a urine metabolite measure, not a cancer diagnosis or cancer-incidence outcome. The registry’s background rationale discusses epigenetic modifications and possible prevention, but the posted primary result does not directly demonstrate a change in gene expression, histone deacetylase activity, or DNA methylation. The registry does not post a secondary outcome analysis that would establish those mechanisms.

The findings also do not establish clinical benefit or harm. The registry does not report a clinically meaningful threshold for metabolite change, and a statistically distinct group mean is not by itself a measure of patient-important benefit. The adverse-event entries report no serious adverse events or deaths in either group, with other adverse events affecting 2 participants in the supplement group and 1 in the placebo group. Those counts do not establish that an intervention is free of risk.

Interpretation is limited to the participants with urine measurements: 42 in the supplement group and 44 in the placebo group. The record says that not all enrolled subjects had urine samples for analysis but does not report why data were unavailable or how missingness was handled. The comparison is an unadjusted recalculation from posted summaries, and the registry reports no analyses. Taken together, the results support a description of the measured metabolite changes in the analyzed groups, while leaving clinical outcomes, biological mechanism, missing-data effects, and broader applicability unresolved.

16. Why This Trial Matters Statistically

This study is statistically useful as an example of the distinction between a biomarker endpoint and a clinical outcome. The registered primary measure is change in urine SFN metabolites, which describes a biological measurement over time. The broader study rationale concerns epigenetic mechanisms and possible prostate cancer prevention, but those aims are not interchangeable with the primary endpoint. A result for a biomarker cannot by itself establish a change in cancer risk or a clinical outcome.

The record also illustrates why the analysis population matters. Enrollment was 98, but the urine analysis includes 42 participants in the supplement group and 44 in the placebo group. The registry explicitly states that not all subjects had urine samples for analysis. Without reported reasons for missing samples or details of the missing-data method, readers cannot assess whether the analyzed participants fully represent the randomized groups for this outcome.

Another statistical lesson is the difference between an effect estimate, its precision, and a p-value. The unadjusted recalculated mean difference is 4.77, its 95% confidence interval is 3.515 to 6.025, and the unadjusted p-value is <0.001. Each answers a different question: the estimate describes the contrast, the interval describes uncertainty, and the p-value assesses compatibility with a null comparison under assumptions. None alone establishes clinical importance.

Finally, planning illustrations based on an observed effect are not the same as the trial’s original sample-size justification. The registry does not report the original assumptions, and the planning figures depend on the observed effect and stated modeling assumptions. Keeping design rationale, observed results, and retrospective illustrations distinct helps avoid treating an observed result as evidence that the study was prospectively designed to detect it.

17. Limitations

• The posted summary statistics are the only data these results rest on; patient-level data, full protocols and statistical analysis plans are not available.
• Recalculated results are simple, unadjusted calculations from posted summaries. They do not replace the sponsor's prespecified analysis.

The registry record leaves important design and analysis details unspecified. It identifies the study as randomized, triple-masked, and parallel, but does not describe the randomization method, allocation concealment, which parties were masked, or how masking was maintained. Eligibility criteria and baseline characteristics are not reported in the record. These omissions limit assessment of group comparability and the conduct of allocation and masking.

The outcome timeframe is given as baseline and 4-8 weeks following intervention, while the arm descriptions specify a four-week intervention. The record does not explain the range in follow-up timing or provide a more detailed schedule for specimen collection. It also does not report whether urine samples were collected and processed under consistent procedures or whether laboratory personnel were masked.

The primary analysis uses participants with urine data, and the record says not all subjects had samples for analysis. Reasons for missing samples, missingness by arm, and the handling of missing data are not reported. The record provides standard errors but not standard deviations, participant-level distributions, or individual outcome values. These omissions prevent assessment of within-group variability and the assumptions behind the summary-level recalculation.

The registry lists no analyses and no secondary outcomes. It does not report an original sample-size justification, interim analyses, an analysis plan, covariate adjustment, or a prespecified approach to multiplicity. No clinical prostate cancer outcome is reported among the posted results. These are limitations of the available registry record; they do not establish that procedures were absent outside the record. The main result is consequently best understood as an unadjusted comparison of mean urine metabolite changes in the participants with available measurements.

18. Related Tutorials

19. Related Statistical Calculators

20. Sources

• ClinicalTrials.gov: Chemoprevention of Prostate Cancer, HDAC Inhibition and DNA Methylation — NCT01265953.
• Registry record last updated 2019-05-01; status last verified 2019-04.
• Results first posted 2017-07-14.
• Data retrieved from ClinicalTrials.gov on 2026-11-09.
• Group sizes, means, event counts and sponsor-reported p-values are reproduced as posted. Effect estimates, confidence intervals and p-values not attributed to the sponsor are independently calculated from the posted summary statistics.

21. Record Summary

NCT01265953 is a completed, randomized, triple-masked, parallel-group study sponsored by Portland VA Medical Center. Its title is “Chemoprevention of Prostate Cancer, HDAC Inhibition and DNA Methylation,” and enrollment is recorded as 98. The registered comparison is four weeks of SFN-rich broccoli sprout extract capsules versus four weeks of placebo capsules.

The primary outcome is change in total urine SFN metabolites, defined as post-intervention minus pre-intervention level. The analyzed group sizes are 42 for supplement and 44 for placebo. Their mean changes are 4.75 and -0.02 micromolar (µM), respectively. The unadjusted recalculated mean difference is 4.77, with a 95% confidence interval from 3.515 to 6.025 and p <0.001.

The registry notes that not all enrolled subjects had urine samples for analysis. It posts no analyses and no secondary outcomes. The primary result describes a urine biomarker comparison; the registry record does not report a clinical prostate cancer outcome.