Safety Study of a Helper Peptide Vaccine Plus Pembrolizumab: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Safety Study of a Helper Peptide Vaccine Plus Pembrolizumab (NCT02515227), a na phase 1, phase 2 study. The primary outcome is Number of Participants With Dose-limiting Toxicities..

2. Clinical Question

The study was designed to evaluate safety, immunogenicity, and clinical activity of a helper peptide vaccine combined with PD-1 blockade. Its primary endpoint focuses on dose-limiting toxicity (DLT), a defined subset of adverse events used to characterize treatment safety. The registry description also identifies immune-related outcomes, including measures of T cells and immune signatures in the tumor microenvironment, responses to melanoma antigens, and antibodies specific to 6MHP.

The main question is descriptive: what number of participants met the study’s DLT definition? It is not a randomized comparison of the combination against pembrolizumab alone, vaccine alone, or another control. The cohort labels indicate whether participants were PD-1 antibody-naive or PD-1 antibody-experienced; they do not establish that differences between the cohorts are caused by prior treatment or by the study combination.

The registry record does not report the primary endpoint count. Consequently, the result for the number of participants with DLTs cannot be interpreted from the record summary. The adverse-event figures are a separate safety summary and should not be treated as the missing primary endpoint result.

3. Trial Design

This is a completed phase 1/phase 2 trial, listed as a single-group study with no masking. The allocation field is recorded as not applicable. Enrollment is listed as 22. The condition is melanoma, and the registry identifies the sponsor as Craig L Slingluff, Jr.

The treatment was a combination of 6MHP, a six-melanoma-helper-peptide vaccine, and pembrolizumab. The registry description states that 6MHP (200 mcg each peptide) was administered intradermally and subcutaneously on days 1, 8, 15, 43, 64, and 85. Pembrolizumab (200 mg) was administered intravenously every 3 weeks for up to 2 years, beginning on day 1. These are the planned schedules described in the record; they do not establish how long any individual participant received treatment.

The adverse-event data distinguish a PD-1 antibody-naive cohort and a PD-1 antibody-experienced cohort. Because this was not a randomized comparison, the cohorts should not be read as interchangeable treatment arms or as a controlled test of treatment effect. Their differing prior-treatment histories could be relevant to how outcomes are interpreted, but the registry record does not give participant-level details or an adjusted comparison.

The study started on 2016-10-06, reached primary completion on 2020-03-14, and is listed as completed. Its stated aims included safety and immune effects, with laboratory testing of blood, a lymph node, and tumor samples. The registry lists six outcome measures and zero analyses. The record does not report a statistical analysis plan, a sample-size justification, or further details about how the immune outcomes were analyzed.

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: DLT was defined as unexpected adverse event (AE) at least possibly related to treatment, and, for 6MHP, grade ≥3 hematological or non-hematological toxicity, except that vaccine site ulcers were considered DLTs if ulcer \>2cm, required antibiotics or debridement; and for pembrolizumab, required permanent discontinuation per specified guidelines. Also considered DLTs were selected grade ≥2 ocular AEs, and AEs that led to stopping treatment even if they did not meet prespecified DLT criteria.

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 Number of Participants With Dose-limiting Toxicities., measured over 30 days after the last administration of study drug..

The primary endpoint is the number of participants with dose-limiting toxicities during treatment with the combination of pembrolizumab and 6MHP. It is assessed 30 days after the last administration of study drug. This is a participant count, not a rate of events per unit of treatment time or a measure of the total number of adverse events.

The registry defines DLT as an unexpected adverse event at least possibly related to treatment. For 6MHP, the description includes grade ≥3 hematological or non-hematological toxicity, with a special rule for vaccine-site ulcers: an ulcer is a DLT if it is >2cm, requires antibiotics, or requires debridement. The registry text also begins to describe a pembrolizumab-specific criterion, but that part of the definition is incomplete in the record. The full criterion is not reported in the registry record.

A defined DLT endpoint is used in early-phase research to summarize serious or otherwise protocol-specified toxicities of concern. It focuses interpretation on events meeting the study’s threshold rather than treating every adverse event as dose-limiting. A count is most informative when its definition, observation period, and denominator are clear. Here, the observation window and much of the definition are described, but the registry record does not report the number meeting the endpoint or provide the associated analysis population.

Other adverse-event counts should not be substituted for the DLT result. The registry’s general adverse-event summaries cover a different categorization and do not indicate which events met the primary endpoint criteria.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

A count endpoint records how many participants meet a specified event definition during a stated observation period. It differs from an event count, which may include multiple events per participant, and from a rate, which relates events to time at risk. The primary endpoint is explicitly a number of participants with DLTs, assessed 30 days after the last study-drug administration. Its interpretation depends on the DLT rules and on which participants were evaluated.

What does a DLT definition do?

A DLT definition sets a threshold for classifying certain adverse events as dose-limiting. That classification is narrower than simply asking whether any adverse event occurred. The registry description identifies unexpected events considered at least possibly related to treatment and gives toxicity criteria for 6MHP, including a grade threshold and specific conditions for vaccine-site ulcers. It also starts a pembrolizumab-specific criterion, but the text is truncated. As a result, readers cannot reconstruct the full endpoint definition from the registry record.

Precise endpoint definitions matter because changing a threshold can change which events count. Timing matters as well: an event outside the stated assessment window may be handled differently from one within it. The primary outcome’s window is specified relative to the last administration of study drug, but the record does not state the number of participants assessed or how incomplete follow-up was handled.

How should a participant count be read?

A participant count is a descriptive summary. Its meaning depends on the count and the relevant population denominator. The primary endpoint count is not reported in the registry record, so neither a proportion nor an uncertainty interval for DLTs can be interpreted. No such value should be inferred from the serious or other adverse-event summaries, because those categories are not necessarily equivalent to DLT.

In general, a confidence interval expresses the range of values reasonably compatible with data under a specified statistical method. For a count or proportion, an interval can help convey uncertainty beyond the observed value alone. It does not correct for selection, confounding, incomplete outcome reporting, or a mismatch between the study design and the question being asked. No confidence interval for the primary endpoint is reported in the registry record.

What can the cohort summaries establish?

The safety summaries separate participants by PD-1 antibody experience. These labels describe cohort membership; they do not represent randomized assignment. In a non-randomized setting, groups may differ for reasons other than the intervention under study. General statistical comparisons between non-randomized groups can therefore be confounded by baseline characteristics, prior treatment, or other factors. The registry record does not provide an adjusted analysis that addresses such differences.

The serious-event and other-event figures are counts of participants, not a severity profile or an event-frequency distribution. For example, a count of participants with at least one event does not reveal how many events occurred within those participants. Nor does it identify the type, duration, or treatment relationship of each event. The registry lists no top serious-event terms. That absence does not supply detail about non-serious events or the primary endpoint.

What do the planning calculations represent?

Sample-size calculations are prospective planning tools: they describe how many participants might be required under a chosen design and set of assumptions to detect an effect of interest. They are not measures of the trial’s observed success. The stated illustration uses a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. It varies the target effect as a fraction of the observed effect. The calculations are not the trial’s own design justification, and the registry record does not report that justification.

Equal allocation between two arms is a hypothetical setup in this context, not a description of this single-group trial. The record also warns that the study is not a randomized comparison and its cohorts are not like-for-like controls. Thus, sample-size illustrations should not be used to imply that the study was powered for a causal comparison or that the stated assumptions match actual enrollment and analysis. They are not observed power. No extra statistical conclusion follows from a planning calculation alone.

Why can over-dispersion matter?

In general, over-dispersion occurs when observed variability exceeds what a statistical model assumes. If a model underestimates variability, uncertainty intervals may be too narrow and tests may be too optimistic. This concept is most relevant to outcomes modeled as counts or rates; the primary endpoint is a participant count. The registry record does not report a model for the primary endpoint, a dispersion estimate, or a method for addressing over-dispersion. It would therefore be inappropriate to claim that a particular count model or correction was used.

Overall, the available methods information supports a description of the endpoint, treatment schedule, and broad design only. The analysis plan, missing-data procedures, and full endpoint definition are not reported in the registry record. Those absences limit assessment of how robustly the posted results answer the stated safety question.

10. Exact Estimates for Each Arm

No two-arm comparison is shown for this trial, but each arm's result can still be summarized with exact interval estimates computed from the posted counts. The Clopper-Pearson interval is exact and conservative; the Wilson interval is a common closer-to-nominal alternative; the Bayesian credible interval uses a uniform Beta(1, 1) prior. For small groups the three can differ noticeably.

R code and output

arm    <- c("6MHP + Pembrolizumab (PD-1 Antibody-naive Cohort)", "6MHP + Pembrolizumab (PD-1 Antibody-experienced Co")
n      <- c(6, 16)
events <- c(0, 3)
for (i in seq_along(n)) {
  ci <- binom.test(events[i], n[i])$conf.int          # Clopper-Pearson exact interval
  cr <- qbeta(c(0.025, 0.975), 1 + events[i], 1 + n[i] - events[i])   # Bayesian, uniform Beta(1,1) prior
  wi <- (function(x, n) { p <- x / n; z <- qnorm(0.975); d <- 1 + z^2 / n
    c((p + z^2 / (2 * n) - z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d, (p + z^2 / (2 * n) + z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d) })(events[i], n[i])
  cat(sprintf("ARM|%s|%d|%d|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f\n", arm[i], n[i], events[i], 100 * events[i] / n[i],
              100 * ci[1], 100 * ci[2], 100 * wi[1], 100 * wi[2], 100 * cr[1], 100 * cr[2]))
}

ARM  6MHP + Pembrolizumab (PD-1 Antibody-naive Cohort)  6  0  0.0  0.0  45.9  0.0  39.0  0.4  41.0
ARM  6MHP + Pembrolizumab (PD-1 Antibody-experienced Co  16  3  18.8  4.0  45.6  6.6  43.0  6.8  43.4

11. Multiplicity, Missing Data and Analysis Populations

The registry lists six outcome measures, including the primary DLT measure and secondary immune-related outcomes. When a study evaluates multiple outcomes, the chance of at least one apparently notable finding can increase if each is tested separately without a prespecified strategy. In general, multiplicity methods can control or contextualize that issue, but the registry record does not report whether any adjustment or hierarchy was planned. It also lists zero analyses, so no analysis-specific multiplicity approach is described.

The record does not provide the primary DLT count or its analysis population. The available adverse-event summaries do provide at-risk counts for their own categories, but those should not be assumed to define the population analyzed for the primary endpoint. The handling of participants with missing endpoint information, incomplete follow-up, or treatment discontinuation is not reported in the registry record.

In general, missing outcome data can affect interpretation if the likelihood of missingness is related to health status, treatment exposure, or the outcome itself. Without information on missingness and the analysis population, it is not possible to assess whether the reported counts cover everyone intended for evaluation or whether missing data could change their interpretation. No imputation, sensitivity analysis, or other missing-data procedure is reported.

The registry record also does not state whether the primary analysis followed an intention-to-treat principle, used an evaluable-participant population, or applied another analysis rule. These are important distinctions: different analysis populations can produce different summaries, especially when treatment exposure or follow-up varies. The record does not report a statistical analysis plan, so the intended handling of these issues remains unclear.

12. 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 5% reporting threshold.

Most frequent non-serious adverse event terms

The serious adverse-event summaries report zero affected participants in both cohorts: the PD-1 antibody-naive cohort lists 0 of 6 at risk, and the PD-1 antibody-experienced cohort lists 0 of 16 at risk. Deaths are also reported as 0 in each cohort. The record lists no top serious-event terms.

For the separate other-adverse-event category, the record reports 6 of 6 participants affected in the naive cohort and 16 of 16 in the experienced cohort. These counts mean that an event in that category was recorded for each participant in the respective at-risk group; they do not indicate the number of individual events or describe severity, duration, or relatedness.

These safety summaries are not the primary DLT result. DLT has a study-specific definition and assessment window, and its count is not reported in the registry record. Zero serious adverse events should therefore not be read as zero DLTs or as proof that no toxicity occurred. The registry record does not provide event-level detail that would allow a fuller safety profile to be reconstructed.

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

The record establishes that a completed phase 1/phase 2 study evaluated 6MHP with pembrolizumab in melanoma and that it included a primary safety endpoint based on dose-limiting toxicities. It also records serious and other adverse-event summaries for PD-1 antibody-naive and PD-1 antibody-experienced cohorts. These are descriptive details about the registered study and its posted safety counts.

The key limitation for interpreting the primary question is that the number of participants with DLTs is not reported in the registry record. As a result, the primary endpoint cannot be quantified from this information. The separate adverse-event summaries cannot replace it, because their categories and definitions may differ. Nor do the counts provide an estimate of comparative benefit or harm against another treatment.

The study did not use randomized allocation and has no like-for-like control group. Its cohort labels distinguish prior PD-1 antibody experience, but do not make the cohorts equivalent in other respects. Observed differences between cohorts, if considered, would not establish that prior treatment or the study combination caused those differences. The record does not report a comparative or adjusted analysis.

The immune outcomes describe intended areas of study, such as T-cell measures and immune signatures, but their results are not included in the registry record in the registry record. The listed aims alone do not show that a particular immune response occurred or that it translated into clinical activity.

Accordingly, the record supports a limited account of trial design and adverse-event categories, not a complete judgment of the combination’s safety or clinical activity. It does not provide the primary endpoint count, full DLT definition, analysis populations, or statistical plan needed for a more comprehensive interpretation. No treatment recommendation follows from these registry entries.

14. Why This Trial Matters Statistically

This trial illustrates why a clearly defined safety endpoint and a complete result are both needed. The registry specifies that the primary question concerns the number of participants meeting DLT criteria within a stated assessment window. But the count itself is not reported in the registry record. A well-defined endpoint without its result cannot answer the central descriptive safety question.

It also highlights the difference between adverse events in general and events classified as dose-limiting. The registry reports that participants in both cohorts experienced an event in the other-adverse-event category, while reporting no serious adverse events in those summaries. Neither category can be assumed to equal the DLT endpoint. This distinction is important when readers encounter several safety summaries for the same study.

The single-group design also limits what can be learned about comparative effects. Separate cohorts based on prior PD-1 antibody experience may be useful for describing the study population, but without randomization they do not create a controlled comparison. Statistical interpretation should match the design rather than treating cohort labels as if they were assigned treatment groups.

Finally, the record demonstrates the value of reporting analysis details alongside outcome counts. The full DLT criteria, analysis population, missing-data handling, and multiplicity strategy are not reported. Their absence limits reproducibility and makes it harder to assess uncertainty or the relationship between the endpoint definition and the posted safety summaries. These are general reporting concerns made concrete by this trial record.

15. 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.

Several limitations specific to this record constrain interpretation. Most importantly, the primary endpoint result—the number of participants with DLTs—is not reported in the registry record. The DLT definition is also incomplete: it describes criteria for 6MHP and begins a pembrolizumab-specific criterion, but does not provide the full text. The endpoint therefore cannot be fully reconstructed or evaluated against its result.

The study is listed as single-group, with allocation not applicable and no masking. The PD-1 antibody-naive and experienced cohorts do not constitute randomized, like-for-like control arms. Their adverse-event counts can be described separately, but the record does not support a causal comparison between them.

Adverse-event reporting is limited to participant counts in serious and other categories, along with deaths. The registry lists no top serious-event terms, and does not provide further event-level detail in the registry record. The other-event counts do not describe event number per participant, severity, duration, or relatedness. They should not be used as a substitute for the DLT outcome.

The record lists six outcomes and zero analyses but does not report the statistical analysis plan, sample-size justification, analysis population, missing-data procedures, or multiplicity strategy. It is also unclear from the registry record how many participants were assessed for the primary endpoint. These gaps limit evaluation of precision, completeness, and analytic choices. The listed planning assumptions are illustrations rather than evidence about the trial’s actual design or observed power.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Safety Study of a Helper Peptide Vaccine Plus Pembrolizumab — NCT02515227.
• Registry record last updated 2023-08-25; status last verified 2023-08.
• Results first posted 2023-08-25.
• 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.

19. Record Summary

NCT02515227 is a completed phase 1/phase 2, single-group study of the 6MHP helper peptide vaccine plus pembrolizumab in melanoma. Enrollment is listed as 22, and the record describes PD-1 antibody-naive and PD-1 antibody-experienced cohorts. The study started on 2016-10-06 and reached primary completion on 2020-03-14.

The primary endpoint is the number of participants with dose-limiting toxicities, assessed 30 days after the last study-drug administration. That endpoint result is not reported in the registry record. The separate safety summaries report zero serious adverse events and zero deaths in each cohort, while recording an other-category adverse event for every participant in each cohort’s at-risk group.

The record lists six outcome measures and zero analyses. It does not report the full DLT definition, analysis plan, missing-data handling, or analysis population. The non-randomized cohort summaries are descriptive and do not provide a controlled comparison of the combination against another treatment.