Peptide Vaccination for Patients at High Risk for Recurrent Melanoma: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Peptide Vaccination for Patients at High Risk for Recurrent Melanoma (NCT00059475), a randomized phase 2 study. The primary outcome is Immunologic Response Rate.

2. Clinical Question

The clinical motivation described in the registry is prevention of melanoma recurrence in people considered at high risk after surgical removal of disease. The trial’s primary endpoint is an immune-assay response, not recurrence itself. Consequently, the posted comparisons address whether participants showed the defined laboratory response; they do not directly report whether recurrence differed between groups. The registry lists adverse events as a secondary outcome, but the primary results concern immunologic response.

3. Trial Design

This is a randomized, phase 2, parallel-group study with no masking. The registry lists the study as completed, with a start date of 2003-04 and primary completion in 2010-05. The sponsor is the National Cancer Institute (NCI), and total enrollment is recorded as 138. The registry record does not describe the allocation sequence or explain how randomization was implemented.

The primary results give counts for four peptide regimens. The reference arm received MART-1: 27-35; the other arms used a modified MART-1 27-35 peptide, MART-1: 26-35 (27L), or modified MART-1 together with gp100. The registry descriptions specify injections every three weeks for four cycles for these peptide regimens. The record also describes high-dose bolus interleukin-2 after enrollment on each corresponding peptide arm. How participants entered those subsequent interleukin-2 cohorts, and how that relates to the randomization, is not reported in the registry record.

The primary outcome counts are not the full enrollment: the reported analyzed group sizes are 13.0, 13.0, 13.0, and 8.0 across the four peptide arms. The endpoint timeframe is 11 months. The registry notes that the number analyzed and the results are correct, but that immunologic response rate data are not available for all patients. The record does not report a participant flow account sufficient to explain the difference between enrollment and the endpoint analysis counts, nor does it give the trial’s original sample-size justification.

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.

Only the first 6 of 8 groups are shown.

Overall Study

Analysis population for the primary outcome, as defined in the registry: The number of participants analyzed and results are correct. We do not have the immunologic response rate data for all patients.

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.

Only the first 6 of 9 groups are shown.

6. Primary Endpoint

The registry lists the primary outcome as Immunologic Response Rate, measured over 11 months.

The primary endpoint is the number of participants with an immunologic response, measured through in vitro sensitization assays. A response was defined as at least a two-fold increase in vaccine-specific interferon gamma secretion in post-vaccination specimens compared with pre-vaccination specimens. Immunologic monitoring was planned through the stated 11-month timeframe.

This endpoint is used to assess whether vaccination is followed by a measurable immune response directed at the vaccine peptides. It is a laboratory outcome: it records an assay result rather than a clinical event such as melanoma recurrence or survival. A positive assay may therefore describe immune activity without establishing what happened to participants’ disease over time. The registry record does not report a primary clinical recurrence endpoint among the posted outcomes.

The posted primary results are counts of responders and analyzed participants for each listed peptide regimen. The reference arm had 7.0 responders among 13.0 analyzed participants; the modified MART-1 27-35 arm had 1.0 among 13.0; the MART-1 26-35 (27L) arm had 0.0 among 13.0; and the combined modified MART-1 plus gp100 arm had 0.0 among 8.0. The record explicitly notes that response-rate data are not available for all patients. These counts therefore describe the analyzed participants, not necessarily everyone enrolled or assigned to a regimen.

7. Results Posted in the Registry

• Adj-2 27-35 (27L) MART-1 (Mod9mer) Peptide Q3wks x 4: 7.7% (1/13) versus 53.8% (7/13) on control; risk difference -46.2 percentage points (95% CI -76.9 to -15.4), risk ratio 0.14 (0.02–1.00); unadjusted two-proportion z-test p = 0.011.
• Adj-2 MART-1: 26-35 (27L) (Mod10mer) Peptide Q3wks x 4: 0.0% (0/13) versus 53.8% (7/13) on control; risk difference -53.8 percentage points (95% CI -80.9 to -26.7); unadjusted two-proportion z-test p = 0.002.

8. Statistical Interpretation

9. Statistical Methods Explained

What does the risk difference describe?

The risk difference compares the proportion with the endpoint in one arm with the proportion in a reference arm. In these results, the endpoint is a positive immunologic assay. A negative estimate means the response proportion was lower in the named comparison arm than in the reference arm. The reported estimates are -0.462 for modified MART-1 27-35 and -0.538 for MART-1 26-35 (27L). They are unadjusted comparisons based on the analyzed groups, not adjusted estimates accounting for other participant characteristics.

Risk differences are expressed on an absolute scale: they describe the distance between the two response proportions. They do not state the relative change, and they do not directly measure recurrence or another clinical outcome. The corresponding confidence intervals communicate uncertainty about the underlying difference, given the observed data and the statistical approach used. The registry record does not identify the method used to calculate those intervals.

How should the p-values be read?

The unadjusted p-values are 0.011 for modified MART-1 27-35 versus the reference arm and 0.002 for MART-1 26-35 (27L) versus the reference arm. In general, a p-value describes how compatible the observed data are with a specified null model, assuming that model and the analysis assumptions hold. It is not the probability that the null hypothesis is true, and it does not measure the size or clinical importance of an effect.

These p-values are explicitly unadjusted. The registry record does not report a multiplicity strategy, so it is not possible to determine whether or how the sponsor accounted for multiple arm comparisons or outcomes. They should therefore be read as the posted unadjusted results rather than as evidence that a family-wise error rate or another multiplicity target was controlled.

What do the response counts add?

The counts make the basis of the endpoint comparison visible: 7.0 of 13.0 analyzed participants responded in the reference arm, compared with 1.0 of 13.0 in the modified MART-1 27-35 arm and 0.0 of 13.0 in the MART-1 26-35 (27L) arm. The combined modified MART-1 plus gp100 arm recorded 0.0 of 8.0. The registry’s note that response data are not available for all patients is important: the denominator for each posted result is the analyzed group, not the full enrollment. The reason participants lack endpoint data is not reported in the registry record.

In general, a binary endpoint reduces each participant’s assay result to whether the defined response threshold was met. This is straightforward to interpret, but it discards information about the magnitude of immune response beyond the positive or negative classification. The registry record does not report assay-level values, the distribution of changes in interferon gamma, or additional details about handling measurements that could not be classified.

Why do small groups matter?

Each primary arm has a limited analyzed group size, ranging from 8.0 to 13.0 participants. In general, estimates from small groups can be sensitive to the outcomes of individual participants and can have substantial uncertainty. The confidence intervals are consequently essential alongside the point estimates and p-values. The registry record does not report a sample-size justification for the original trial, so the analyzed group sizes cannot be evaluated against a stated target for the primary endpoint.

General statistical methods can also be affected by missing outcome information. If response availability differs across arms or is related to participants’ likely assay responses, an analysis restricted to participants with results may not represent all those enrolled. The registry record notes that data are unavailable for all patients but does not report the amount or pattern of missingness by reason, or an analysis addressing its potential effect. This is a limitation of interpretation, not evidence about why data are missing.

What analysis details are absent?

The registry record does not report the test or model used for the sponsor’s primary comparisons, an adjustment strategy, an interim-analysis plan, or a detailed statistical analysis plan. It also does not report whether the comparison set was prespecified. General principles such as choosing an analysis before seeing outcomes and accounting for multiple comparisons can help readers assess statistical credibility, but the record does not allow those design features to be verified.

The registry includes simple planning illustrations based on observed effects. These are hypothetical sample-size calculations under stated assumptions, not a description of the original trial design. They should not be confused with retrospective power calculations or treated as evidence that the study had a particular probability of detecting its observed result. The original design assumptions are not reported in the registry record.

10. Confidence Intervals and Precision

The confidence intervals indicate the range of effects that remain compatible with the posted data under the interval method used. For modified MART-1 27-35 versus the reference arm, the risk difference is -0.462 and its interval extends from -0.769 to -0.154. For MART-1 26-35 (27L) versus the reference arm, the estimate is -0.538 and its interval extends from -0.809 to -0.268. Both intervals lie below zero, consistent with fewer observed assay responses in those comparison groups in the posted analysis.

These intervals are broad, so the precise size of the difference remains uncertain. The point estimates alone should not be read as exact effects. The observed groups are small, with 13.0 participants in the reference arm and in each of the two comparison arms covered by these intervals. In general, limited sample information produces less precise estimates, and uncertainty can remain substantial even when an interval does not include zero.

The intervals concern the immunologic response endpoint, not recurrence or survival. A confidence interval does not capture every source of uncertainty: it does not, by itself, address incomplete response availability, unreported analysis choices, or possible multiplicity. The registry record does not report a confidence interval for the combined modified MART-1 plus gp100 arm. Its count of 0.0 responses among 8.0 analyzed participants is descriptive, but the record does not post a corresponding comparison interval or p-value.

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 sample-size illustrations translate the observed response differences into hypothetical group sizes under stated assumptions. For this binary endpoint, the entries are participants per arm, not total events. The illustrations use a two-sided significance level of 0.05, equal allocation between the two arms, and a normal approximation. The effect to detect is set to the stated fraction of the observed effect. These assumptions describe the illustrations, not the trial’s original planning, whose assumptions are not reported in the registry record.

The 80% power column gives the participants per arm in the hypothetical design corresponding to an 80% chance of detecting the specified effect under those assumptions, if that effect and the assumptions were correct. The 90% power column gives the corresponding group size for a 90% chance. These are planning targets rather than observed results, and they are not observed power.

Rows planning for 100% of the observed effect use the full observed difference; the 75% and 50% rows plan for smaller effects. Smaller effects are harder to distinguish from random variation, so they require more participants per arm to reach the same target power. For the modified MART-1 27-35 comparison, the registry’s illustration lists 15 participants per arm for 80% power and 19 for 90% power at 100% of the observed effect; at 75%, the figures are 30 and 39; at 50%, they are 71 and 95. These are illustrations based on the observed effect, not the original design justification. The trial’s own sample-size assumptions are not 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, p₀ and p₁ are the control and treatment proportions, and p̄ is their average.

Worked calculation for this trial

1. Control proportion p₀ = 0.538; treatment proportion p₁ = 0.077; average p̄ = 0.308.
2. First term: z_1−α/2 × √[2p̄(1−p̄)] = 1.96 × 0.6527 = 1.2793.
3. Second term: z_1−β × √[p₀(1−p₀) + p₁(1−p₁)] = 0.842 × 0.5653 = 0.4757.
4. n = (1.2793 + 0.4757)² / (-0.4615)² = 14.5, rounded up to 15 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
p0 <- 0.538461538461538                          # control proportion
p1 <- 0.0769230769230769                          # treatment proportion
n_per_arm <- function(power, frac = 1) {
  q1 <- p0 + (p1 - p0) * frac               # smaller effect = fraction of the observed difference
  pbar <- (p0 + q1) / 2
  z_b <- qnorm(power)
  ceiling(round((z_a * sqrt(2 * pbar * (1 - pbar)) + z_b * sqrt(p0 * (1 - p0) + q1 * (1 - q1)))^2 / (q1 - p0)^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 (unrounded n per arm)
cat("power.prop.test:", round(power.prop.test(p1 = p0, p2 = p1, power = 0.80)$n, 1), "\n")

# Simulation: how often does the z-test reject at the 80%-power sample size?
set.seed(59475)
n    <- n_per_arm(0.80)
reps <- 20000
x0 <- rbinom(reps, n, p0); x1 <- rbinom(reps, n, p1)
ph <- (x0 + x1) / (2 * n)
z  <- ((x1 - x0) / n) / sqrt(ph * (1 - ph) * 2 / n)
cat(sprintf("Simulated power at n = %s per arm: %.3f (%d replicates)\n", format(n, big.mark = ","), mean(abs(z) > z_a, na.rm = TRUE), reps))

Output from running the code

100% of observed effect: n per arm = 15 (80% power), 19 (90% power)
 75% of observed effect: n per arm = 30 (80% power), 39 (90% power)
 50% of observed effect: n per arm = 71 (80% power), 95 (90% power)
power.prop.test: 14.5 
Simulated power at n = 15 per arm: 0.852 (20000 replicates)

The simulation draws many pairs of event counts at the planned sample size and counts how often the two-proportion z-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 posts two unadjusted comparisons against the reference arm, with p-values of 0.011 and 0.002. It does not report a multiplicity adjustment or explain how the number of peptide arms and outcomes was considered in the analysis. When multiple comparisons are made, the chance of at least one apparently unusual result can increase; statistical methods may address this, depending on the analysis plan. The posted record does not say whether any such method was used outside the displayed unadjusted results. The combined modified MART-1 plus gp100 arm has no reported comparison estimate or p-value.

Outcome completeness is a separate concern. The registry states that the number analyzed and results are correct, but that immunologic response rate data are not available for all patients. The endpoint counts cover 13.0 participants in each of three arms and 8.0 in the combined-peptide arm, while enrollment is 138. The registry record does not report why data are unavailable, the missing-data pattern by arm, or whether any method was used to address missing outcomes. It also does not report an analysis population definition beyond the stated analyzed counts.

The posted information does not establish whether participants were analyzed according to randomized assignment, whether the endpoint analyses were prespecified, or whether there were interim analyses. Each of these details can affect how a trial result is interpreted; none should be inferred from the presence of randomized allocation alone. The registry record does not report the original statistical analysis plan or the sample-size justification. The numerical planning illustrations are separate from those missing protocol details and should not be treated as evidence of the sponsor’s original design decisions.

14. Safety Results

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

Other (non-serious) adverse events

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

Most frequent serious adverse event terms

Most frequent non-serious adverse event terms

Serious events with the highest arm-level rate: nodal arrhythmia (50.0%), cardiac troponin i increased (50.0%), creatine phosphokinase increased (50.0%).

The registry lists serious adverse events for peptide groups and corresponding high-dose interleukin-2 cohorts. The serious-event figures give the number at risk and the number affected. In the peptide-only cohorts, the posted serious-event count is 0 among 33 for MART-1: 27-35, 0 among 24 for modified MART-1 27-35, 0 among 33 for MART-1: 26-35 (27L), and 0 among 34 for the combined modified MART-1 and gp100 regimen. The corresponding interleukin-2 cohorts have different, smaller denominators; one serious adverse event is recorded among 2 participants in the cohort following MART-1: 26-35 (27L), while the other listed interleukin-2 cohorts record none among their stated at-risk participants.

These figures describe the registry’s event counts in the listed groups; they do not establish comparative safety. The serious-event terms listed most prominently are nodal arrhythmia, cardiac troponin I increased, and creatine phosphokinase increased, each reported as 50.0%. The registry excerpt does not give their numerators or link each term to a specific group, so those percentages need to be interpreted with caution. The record does not report deaths in these safety entries. These counts also do not replace the broader adverse-event outcome, which includes non-serious events.

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

The posted results show that immunologic responses were recorded in the reference MART-1: 27-35 arm and less often in the two comparison arms with reported statistical comparisons. The response counts were 7.0 among 13.0 analyzed participants in the reference arm, 1.0 among 13.0 in the modified MART-1 27-35 arm, and 0.0 among 13.0 in the MART-1 26-35 (27L) arm. The combined modified MART-1 plus gp100 arm also recorded 0.0 responses among 8.0 analyzed participants. The first two comparisons with the reference arm have negative risk-difference estimates and unadjusted p-values as.

These findings concern an immune-assay definition, not whether melanoma recurred. The registry’s study description frames recurrence prevention as the clinical motivation, but recurrence results are not reported in the primary outcome information. The endpoint therefore cannot establish that a peptide regimen prevented recurrence, prolonged survival, or produced another clinical benefit. Nor do the observed counts alone establish why response patterns differed.

Interpretation is also bounded by incomplete response data, small analyzed groups, unreported multiplicity handling, and missing details about the analysis plan and original sample-size justification. The registry record does not report enough information to determine how the unavailable outcomes might affect the comparisons. The results should be understood as a limited account of observed immunologic responses in the analyzed participants, rather than a complete evaluation of clinical effectiveness or a definitive comparison across all regimens.

16. Why This Trial Matters Statistically

This trial illustrates why the choice of endpoint matters. Its primary measure is a defined laboratory response to peptide vaccination, while the clinical motivation is recurrence prevention. Those are distinct questions: an assay can indicate immune activity, but the endpoint by itself does not establish a difference in recurrence. Keeping that distinction explicit prevents a biomarker result from being overstated as a clinical outcome.

The record also illustrates the importance of presenting absolute group counts alongside comparative statistics. The numbers of analyzed participants and responders make clear what the risk differences and p-values are based on. Confidence intervals add information about precision that a point estimate or significance test alone cannot convey. Here, the limited analyzed group sizes and interval widths make the uncertainty relevant to the interpretation.

Finally, this example highlights the need for transparent reporting of missing outcomes, multiplicity, and planned analyses. The registry acknowledges that immunologic response data are not available for all patients, but does not explain the missingness or report a strategy for addressing it. It also reports unadjusted comparisons without describing multiplicity handling. These gaps do not erase the posted findings, but they restrict how confidently they can be generalized or interpreted. The registry’s planning illustrations can show how assumed effect size relates to hypothetical sample size, while remaining separate from the unreported original design rationale.

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 primary outcome data do not cover all enrolled participants: the registry explicitly states that response-rate data are not available for all patients. Although it reports analyzed counts for each peptide group, the reason for missing results, the timing of missingness, and its distribution across all assigned participants are not reported in the registry record. This limits assessment of how representative the analyzed results are.

Only two comparisons have posted risk differences and unadjusted p-values. The combined modified MART-1 plus gp100 arm has response counts but no reported comparison estimate or p-value. The record does not explain the selection of comparisons, adjustment for multiple testing, or whether a prespecified analysis plan guided reporting. It also does not report the trial’s sample-size justification, interim analyses, or the statistical method used for the posted estimates.

The response endpoint is an assay measure rather than recurrence, and the primary result does not report recurrence outcomes. While the registry describes high-dose interleukin-2 cohorts after peptide-arm enrollment, how those cohorts relate to the randomized comparison is not reported in the registry record. The endpoint analysis groups are small, and the eligible population was restricted by melanoma status and HLA-A*0201 tissue type. These features limit what the results can say about other populations or clinical outcomes. The safety entries also provide event counts without full context for the listed serious-event terms, including no term-specific numerators in the record.

18. Related Tutorials

19. Related Statistical Calculators

20. Sources

• ClinicalTrials.gov: Peptide Vaccination for Patients at High Risk for Recurrent Melanoma — NCT00059475.
• Registry record last updated 2012-10-23; status last verified 2012-10.
• Results first posted 2012-08-14.
• 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

NCT00059475 is a completed, randomized phase 2 parallel-group study sponsored by the National Cancer Institute (NCI). It enrolled 138 participants and compared peptide immunization regimens in people at high risk for recurrent melanoma. The primary endpoint was immunologic response, defined by an increase in vaccine-specific interferon gamma secretion in post-vaccination specimens relative to pre-vaccination specimens.

The reference peptide arm recorded 7.0 responses among 13.0 analyzed participants. The modified MART-1 27-35 arm recorded 1.0 among 13.0, the MART-1 26-35 (27L) arm recorded 0.0 among 13.0, and the combined modified MART-1 plus gp100 arm recorded 0.0 among 8.0. Two comparisons with the reference arm have posted unadjusted estimates and p-values. The registry notes that response data are unavailable for all patients. Recurrence outcomes, the original sample-size justification, and several analysis details are not reported in the registry record.