Therapeutic Vaccination for Patients With HPV16+ Cervical Intraepithelial Neoplasia (CIN2/3): Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Therapeutic Vaccination for Patients With HPV16+ Cervical Intraepithelial Neoplasia (CIN2/3) (NCT00988559), a non-randomized phase 1 study. The primary outcome is Number of Participants With Related Serious Adverse Events.

2. Clinical Question

3. Trial Design

The registry record describes a Phase 1, completed, non-randomized, unmasked, parallel-group study. Enrollment was 132. The study started in 2009-09, and primary completion was in 2016-07. The stated purpose was to test the efficacy and safety of different routes of administration of a DNA vaccine in patients with HPV16-positive CIN2/3.

The brief summary says participants were enrolled in six treatment groups. It describes gene-gun delivery in the first two groups, intramuscular vaccination in groups 3 and 4, and intralesional vaccination in groups 5 and 6. The arm descriptions differ: they assign gene-gun delivery to groups 1 and 2, intramuscular injections to groups 5 and 6, and intralesional delivery to groups 3 and 4. They also describe an intralesional-delivery-plus-imiquimod group numbered 7. These descriptions are not fully consistent, so the group numbering and route assignments should be read cautiously.

The arm descriptions state that vaccination occurred at weeks 0, 4, and 8 before therapeutic resection of the lesion at week 15. For the group described as receiving imiquimod, application to the cervix is also specified at weeks 0, 4, and 8. The registry record does not report how participants were assigned to groups, whether allocation followed a prespecified sequence, or why different routes were selected.

Because allocation was non-randomized, differences between groups may reflect more than the delivery route or co-intervention. The record does not establish that the arms were comparable at baseline. Accordingly, the group results are best interpreted as descriptive safety counts rather than estimates from a controlled comparison.

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.

Before assignment: 132 subjects signed consents to be screened for eligibility * 93 subjects signed consents, but did not meet the eligibility criteria to start the study (screen failures) * 39 subjects were assigned to a treatment group in the study

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: Related Serious Adverse Events

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.

Population: Participants enrolled in the study who received at least one study intervention

6. Primary Endpoint

The registry lists the primary outcome as Number of Participants With Related Serious Adverse Events, measured over 9 months.

The primary endpoint counts participants with intervention-related serious adverse events, defined by CTCAE. Its stated timeframe is 9 months. The outcome is a participant count, so it records how many participants met the serious-adverse-event definition rather than the total number of event episodes. The registry record does not provide further details about event grading, attribution procedures, or the handling of multiple events in one participant.

Safety outcomes are central in a Phase 1 study, where documenting serious harms is an important part of evaluating an intervention. A serious event is distinct from an event that is merely recorded as an adverse event: seriousness is a classification, and relatedness concerns whether the event is judged connected to the intervention. The primary endpoint therefore depends on both the seriousness criteria and the attribution process.

The posted counts show zero related serious adverse events in each listed group. They do not establish that no adverse events occurred: the registry also reports other adverse-event counts. Nor do these counts, by themselves, establish that serious events are impossible or that risk is absent. The registry record does not report confidence intervals, a statistical comparison, or a detailed account of how adverse events were collected.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

What does a participant count represent?

The primary outcome is a count of participants with an intervention-related serious adverse event. It is not a count of every event episode. If one participant experienced more than one qualifying event, a participant-based endpoint would still count that person as a participant with an event. The registry record does not explain in further detail how repeated events were handled, but the outcome is explicitly described as the number of participants.

For a binary outcome, each participant is classified according to whether the specified event occurred during the stated timeframe. General statistical practice can summarize such an outcome by reporting the number with the event alongside the number assessed or at risk. These counts retain the observed data without implying a model-based comparison. The registry record does not report an adjusted analysis, a confidence interval, or a hypothesis test for the primary outcome.

How should zero observed events be understood?

Zero observed events means that no participants in the reported group met the endpoint definition in the posted data. It does not mean that the probability of the event is known to be zero. In general, an estimate based on a finite group has uncertainty, and a zero count can be compatible with a range of underlying risks. Confidence intervals can describe uncertainty around an estimate, but no such interval is reported in the registry record.

It is also important to distinguish a zero for the primary endpoint from the absence of all adverse events. The primary endpoint requires an event to be both serious and related to the intervention. The record separately gives counts for other adverse events, with participants affected in each listed group. A broader adverse-event count can therefore be nonzero while the serious, intervention-related endpoint count is zero.

Why does the design affect interpretation?

Random allocation is a design method intended to make treatment groups comparable, on average, with respect to measured and unmeasured characteristics. This study is described as non-randomized. In general, that means observed differences between groups can reflect differences in participants or other aspects of care, as well as differences in the assigned intervention. The record does not report an adjustment strategy that would address such differences.

The study is also described as unmasked. In general, knowledge of group assignment can affect reporting, assessment, or attribution of outcomes, particularly when judgments are involved. The registry record does not describe blinding of outcome assessors or a process for determining whether serious adverse events were intervention-related. These points do not show that outcome assessment was biased; they identify information needed to assess how event classification was conducted.

What can be inferred from the listed analysis information?

The registry record reports two outcome measures and zero analyses. The listed primary endpoint and secondary lesion outcome therefore have no posted inferential results in the record. No p-values, confidence intervals, adjusted estimates, or formal comparisons are reported. Without these, readers should not interpret the group counts as demonstrating a statistically established difference or equivalence.

General statistical interpretation separates estimation from testing. An estimate describes the observed data or a model-based quantity; an uncertainty interval expresses how imprecisely that estimate is determined under specified assumptions; a test evaluates evidence against a stated null hypothesis. The registry record does not report these inferential elements for the posted outcomes. The event counts remain useful descriptively, but their uncertainty and comparative meaning are not quantified in the registry record.

What do planning calculations mean?

Any sample-size planning illustration based on an observed effect is hypothetical, not an account of the trial’s observed power. The stated planning assumptions are a two-sided significance level of 0.05, equal allocation between two arms, a normal approximation, and an effect to detect expressed as a fraction of the observed effect. Such calculations depend on those assumptions and on the effect used as the planning reference. They are not evidence that the trial was designed around that target or that the target was achieved.

For a binary outcome, planning estimates expressed as participants per arm concern the number needed under an assumed effect and analysis framework. They do not describe the enrollment actually achieved or the number of participants who experienced an event. The registry record does not report a trial-specific sample-size justification, and the planning assumptions should not be mistaken for one.

More generally, over-dispersion is relevant when the variability in data exceeds what a statistical model assumes. It can make uncertainty estimates too narrow if not accounted for. This is a general concept; the primary endpoint is a participant count for a binary event, and the registry record does not report an over-dispersion analysis or a model-based estimate.

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("PMED Delivery - Groups 1 and 2", "IM Injections - Groups 5 and 6", "Intralesional Delivery - Group 3 and 4", "Intralesional Delivery + Imiquimod - Group 7")
n      <- c(10, 11, 11, 7)
events <- c(0, 0, 0, 0)
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  PMED Delivery - Groups 1 and 2  10  0  0.0  0.0  30.8  0.0  27.8  0.2  28.5
ARM  IM Injections - Groups 5 and 6  11  0  0.0  0.0  28.5  -0.0  25.9  0.2  26.5
ARM  Intralesional Delivery - Group 3 and 4  11  0  0.0  0.0  28.5  -0.0  25.9  0.2  26.5
ARM  Intralesional Delivery + Imiquimod - Group 7  7  0  0.0  0.0  41.0  0.0  35.4  0.3  36.9

11. Multiplicity, Missing Data and Analysis Populations

The registry record lists two outcome measures: the primary count of participants with related serious adverse events and the secondary outcome of absence of a CIN2/3 lesion by week 15. It reports zero analyses. Consequently, no outcome-specific estimates, uncertainty intervals, or tests are posted for interpreting the lesion outcome, and no formal comparison across treatment groups is reported for the primary outcome.

When a study assesses multiple outcomes or makes multiple comparisons, the chance of at least one apparently unusual result can increase. General approaches to multiplicity include prespecifying a primary comparison or adjusting the interpretation of tests. The registry record does not report a multiplicity strategy, a hierarchy among analyses beyond the primary and secondary outcome labels, or any interim analyses. No such approach should be assumed.

The record does not report how missing outcome data were handled, how many participants were missing each outcome, or whether analyses used all enrolled participants or a defined analysis population. The group-specific numbers at risk are posted for the adverse-event results, but they do not establish the completeness of data for every outcome. In general, missingness can affect interpretation if participants with unavailable data differ from those with recorded outcomes. The registry record does not describe an imputation method, sensitivity analysis, or follow-up completeness assessment.

The registry record also does not report a statistical analysis plan or the prespecified handling of protocol deviations. These omissions limit assessment of whether the posted outcomes and analyses follow a prespecified plan. They do not establish that a particular method was or was not used; the information is not reported in the registry record.

12. 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 non-serious adverse event terms

For the primary safety endpoint, the registry record reports zero participants with intervention-related serious adverse events in each listed group during the stated 9-month timeframe. The corresponding numbers at risk are 10, 11, 11, and 7 for the four named groups. These are observed group counts, not estimates of comparative safety.

The record separately reports other adverse events affecting 10 of 10 participants in PMED Delivery - Groups 1 and 2, 11 of 11 in IM Injections - Groups 5 and 6, 10 of 11 in Intralesional Delivery - Group 3 and 4, and 7 of 7 in Intralesional Delivery + Imiquimod - Group 7. These counts should not be read as serious events or as intervention-related serious events. The registry record does not list the terms for these other events.

No death counts are posted. Death information is therefore not reported in the registry record; it should not be interpreted as a reported zero. The record also does not give confidence intervals or a comparative statistical analysis. Because allocation was non-randomized, the group counts do not support a like-for-like safety ranking.

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

The posted data describe the number of participants recorded with intervention-related serious adverse events in the listed groups. The observed count was zero in each group. This is a direct description of the registry results within the stated 9-month timeframe and endpoint definition. It is not a demonstration that serious adverse events cannot occur or that there is no risk.

The other adverse-event counts show that events outside the primary serious-and-related definition were recorded. Those broader counts should not be combined with the primary outcome or treated as evidence of a serious event. The record does not report event terms for those counts, so their clinical character cannot be described from the posted data.

The study also listed absence of a CIN2/3 lesion by week 15 as a secondary outcome. The registry record reports no analyses, so the posted outcome information does not establish the result of that lesion assessment or a difference between delivery routes. The stated study purpose includes efficacy and safety, but the available posted results described in the record do not provide an efficacy analysis.

Because treatment groups were non-randomized, differences in their outcomes would not by themselves establish that delivery route caused those differences. The inconsistent group descriptions add uncertainty about the relationship between group numbers and routes. The counts are therefore most appropriately treated as descriptive observations, with no claim of comparative superiority, equivalence, or efficacy.

Finally, the overall enrollment figure is 132, whereas the adverse-event groups have their own listed numbers at risk. The registry record does not explain how those reported safety populations relate to total enrollment. It also does not report missing-data handling, analysis populations, confidence intervals, or the statistical plan. These gaps limit how far the findings can be generalized or quantified.

14. Why This Trial Matters Statistically

This trial illustrates a statistical distinction that matters in early clinical research: an observed count is not the same as a precise estimate of risk. The serious-adverse-event counts are zero in each listed group, but the registry record does not report uncertainty intervals. Readers can describe what was observed without treating that observation as proof that an event is impossible or that the true risk is zero.

It also demonstrates why outcome definitions matter. The primary endpoint concerns participants with serious events judged related to the intervention. Other adverse events are reported separately. Keeping these categories distinct prevents a broad event count from being mistaken for the primary safety result and makes clear what the endpoint does, and does not, capture.

The non-randomized design is another important statistical feature. Without random allocation, group comparisons may be confounded by differences among participants or other factors. The record does not report baseline comparability or an adjusted analysis. Descriptive group counts remain informative, but they do not provide a secure basis for attributing differences to a particular route or treatment component.

Finally, the registry record lists a secondary lesion outcome but reports zero analyses. This gap highlights the difference between registering an outcome and posting an analyzed result. The record's inconsistent descriptions of group numbering and routes further show why clear intervention and arm reporting is necessary for interpreting results. Together, these features make cautious description more defensible than comparative claims.

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. First, the study is non-randomized and unmasked. The registry record does not report baseline characteristics by group or an adjusted analysis, so comparability across arms cannot be assessed from the posted information. The counts should not be treated as a controlled comparison.

Second, the group descriptions are inconsistent. The brief summary assigns intramuscular vaccination to groups 3 and 4 and intralesional vaccination to groups 5 and 6, while the arm descriptions assign those routes to the opposite numbered groups. The arm descriptions also include group 7, although the brief summary refers to six groups. These discrepancies make group labels and route mapping less clear.

Third, although total enrollment is 132, the listed numbers at risk for serious adverse events are smaller, and the registry record does not explain how those safety counts relate to enrollment. It does not report completeness of follow-up, missing outcome data, or analysis populations. The record also does not provide event terms for the other adverse-event counts or explain event attribution procedures.

Fourth, the registry record reports zero analyses. It does not give inferential results for the primary safety outcome or the secondary lesion outcome, nor does it report confidence intervals, a statistical analysis plan, or a trial-specific sample-size justification. Death counts are not reported in the record. These limitations do not establish that information was never collected; they mean it is not reported in the registry record.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Therapeutic Vaccination for Patients With HPV16+ Cervical Intraepithelial Neoplasia (CIN2/3) — NCT00988559.
• Registry record last updated 2018-07-09; status last verified 2018-07.
• Results first posted 2018-07-09.
• 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

NCT00988559 is a completed Phase 1, non-randomized, unmasked, parallel-group study with enrollment of 132. It examined routes of therapeutic DNA vaccination in patients with HPV16-positive CIN2/3. The registry record states that the study started in 2009-09 and reached primary completion in 2016-07.

The primary outcome was the number of participants with intervention-related serious adverse events, as defined by CTCAE, over 9 months. The posted count was zero in each listed group. Other adverse-event counts were also recorded. Absence of a CIN2/3 lesion by week 15 was listed as a secondary outcome, but the registry record reports zero analyses.

Group assignment was non-randomized, and descriptions of group numbering and routes are inconsistent. No comparative statistical analysis, confidence intervals, missing-data approach, or sample-size justification is reported in the registry record. The safety counts are therefore descriptive and do not establish comparative treatment effects.