VGX-3100 Delivered Intramuscularly (IM) Followed by Electroporation (EP) for the Treatment of HPV-16 and/or HPV-18 Related Anal or Anal/Peri-Anal, High Grade Squamous Intraepithelial Lesion (HSIL) in Individuals Seronegative for Human Immunodeficiency Virus (HIV)-1/2: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for VGX-3100 Delivered Intramuscularly (IM) Followed by Electroporation (EP) for the Treatment of HPV-16 and/or HPV-18 Related Anal or Anal/Peri-Anal, High Grade Squamous Intraepithelial Lesion (HSIL) in Individuals Seronegative for Human Immunodeficiency Virus (HIV)-1/2 (NCT03499795), a na phase 2 study. The primary outcome is Percentage of Participants With no Histologic Evidence of Anal or Anal/Peri-Anal HSIL and no Evidence of HPV-16/18 at Week 36.

2. Clinical Question

The question combines a tissue finding and a viral finding at the same assessment point. A participant would need to meet both parts of the endpoint to count as having the specified outcome. This is not the same as asking whether either finding improved separately, and the composite does not by itself show which component was or was not met by individual participants.

The study focuses on a defined group: people with a particular high-grade lesion and associated HPV types who were seronegative for HIV-1/2. Its findings, if reported, would describe outcomes in that study population under the study regimen. Because there was no concurrent comparator, the study question is about observed outcomes in the treated group, not a direct estimate of how outcomes differed from another intervention or from no treatment.

3. Trial Design

This was a phase 2, open-label study with a single group and no allocation to separate treatment arms. The record lists enrollment of 23 participants and marks the study as completed. The study start date was 2018-05-15, and primary completion was 2020-06-16. The brief study description anticipated approximately 24 participants, while the recorded enrollment was 23.

Participants received VGX-3100 by intramuscular injection followed immediately by electroporation with the CELLECTRA™ 5PSP device. The arm description specifies four 6 mg doses on Day 0, Week 4, Week 12, and Week 40. The study population was adult men and women who were HIV negative and had histologically confirmed anal or anal/peri-anal HSIL associated with HPV-16 and/or HPV-18.

Open-label means that the study was not masked. The record identifies no randomized allocation and no control arm. Consequently, observed outcomes describe the participants receiving the regimen, but there is no concurrent group in this trial for estimating a treatment-versus-control difference. Changes over time can be described if data are available, but without a comparator they cannot by themselves separate treatment effects from other explanations for change.

The primary endpoint was assessed at Week 36, and the record also lists secondary outcomes at Week 36 and later time points, including lesion counts at Weeks 36, 64, and 88. Those outcomes represent different questions and assessment schedules; their result values are not reported in the registry record. The planned sample-size justification, details of interim analyses, and full statistical analysis plan are not reported in the registry record.

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: A total of 48 participants were screened out of which 23 were enrolled to receive study drug.

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: mITT population included all participants who received at least 1 dose of VGX-3100+EP. 'Overall number of participants analyzed' indicates the number of participants with data available for outcome measure analysis.

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: mITT population included all participants who received at least 1 dose of VGX-3100+EP.

6. Primary Endpoint

The registry lists the primary outcome as Percentage of Participants With no Histologic Evidence of Anal or Anal/Peri-Anal HSIL and no Evidence of HPV-16/18 at Week 36, measured over Week 36.

The primary endpoint is the percentage of participants with both no histologic evidence of anal or anal/peri-anal HSIL and no evidence of HPV-16/18 at Week 36. It is a composite endpoint: both conditions must be satisfied for an analyzed participant to meet the endpoint. The registry describes the measure as a percentage and specifies a 95% confidence interval.

Histology assesses tissue findings, while HPV testing addresses evidence of the specified viral types. Combining these measures asks whether the two findings are absent together at the assessment time, rather than treating either one alone as sufficient. The endpoint is therefore tied to a defined time point and to the particular lesion sites and HPV types in the study question.

Using a percentage makes the result a proportion of the analyzed population, rather than a measure of the average change in a continuous quantity. The confidence interval is intended to express uncertainty around that estimated proportion. The registry defines the endpoint and its population but does not report the number meeting it, the number analyzed for the endpoint, the percentage, or the interval. Thus, the endpoint's observed value and its precision cannot be assessed from the registry record.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

What does a percentage endpoint represent?

The primary endpoint is a percentage of participants meeting a defined condition at Week 36. In general, a percentage for a binary outcome describes the share of analyzed participants classified as meeting that outcome. Each participant is classified according to whether both components of the composite are present: no histologic evidence of anal or anal/peri-anal HSIL and no evidence of HPV-16/18. A participant who does not meet either required part would not satisfy the full composite definition.

The registry record does not report the number meeting the endpoint or the number analyzed for it. It therefore does not permit reconstruction of the percentage. Enrollment is not interchangeable with the endpoint analysis denominator: the record defines the modified intention-to-treat population as participants receiving at least one dose, and says that the number analyzed for an outcome includes those with data available for that outcome. The actual Week 36 denominator is not reported in the registry record.

What does the confidence interval add?

The primary measure is specified with a 95% confidence interval. In general, a confidence interval presents a range of values compatible with the observed data under the method used, expressing uncertainty around an estimate. Its width is informative about precision: a narrower interval generally reflects a more precise estimate than a wider interval, subject to the assumptions of the method. An interval does not describe the range of individual participant outcomes, and it does not establish a causal effect.

Neither the primary percentage nor its confidence interval is reported in the registry record. The interval method is also not reported in the registry record. No further claims about the estimate's precision or the method used to calculate its interval can therefore be made.

How does the single-group design shape interpretation?

In a single-group study, outcomes are observed among participants receiving the study regimen, without a concurrent control group in the trial. The design can describe what happened in the enrolled and analyzed group, if those results are reported. It does not supply a randomized between-group contrast. General statistical interpretation: random allocation to comparison groups can help balance factors that might otherwise influence outcomes; without that design feature, comparisons with an assumed or historical outcome are vulnerable to differences in participants, measurement, follow-up, and other circumstances.

This study was open label and had no masking. The registry record does not report a comparator arm. These design details are important when interpreting outcomes that involve clinical assessment or decisions about measurement. They do not establish whether any particular assessment was biased, but they leave no blinded comparison within the trial to assess that possibility.

Why distinguish the composite from its components?

The primary endpoint requires both the histologic and HPV-16/18 conditions. A composite can put multiple clinically relevant findings into a single outcome, but its overall percentage may conceal different patterns among its components. General explanation: an overall composite result can be driven more by one component than another, so component-level results help explain what contributed to the combined outcome. The registry lists separate secondary outcomes related to HSIL and HPV testing, but does not report their numerical results. The primary endpoint's components cannot be disentangled using the reported information.

What can be inferred from the listed planning assumptions?

The registry includes a description of sample-size planning illustrations based on a fraction of an observed effect, with a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. For non-time-to-event outcomes, such illustrations are expressed as participants per arm for a specified power. These are planning illustrations, not observed trial outcomes, and do not describe this study's single-group design. The illustration values are not reported in the registry record. The study's own sample-size justification is not reported in the registry record.

General explanation: a planning calculation asks how many participants might be needed under specified assumptions about the effect to detect, allocation, statistical threshold, and method. Its result depends on those assumptions. It is not an estimate of the effect observed in the trial and must not be described as observed power. Here, the planning description does not establish what assumptions were used to set enrollment in this study.

What analysis details remain unknown?

The record identifies the endpoint, its timeframe, a confidence interval, and the modified intention-to-treat population description. It does not report the statistical method for the primary endpoint, the interval calculation method, the approach to missing data, or the handling of multiple outcomes. Interim analyses and a full statistical analysis plan are not reported in the registry record. These omissions limit evaluation of how the planned analysis relates to the outcome definition and how robust the estimate would be to alternative analysis choices.

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("VGX-3100")
n      <- c(22)
events <- c(2)
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  VGX-3100  22  2  9.1  1.1  29.2  2.5  27.8  2.8  28.0

11. Multiplicity, Missing Data and Analysis Populations

The registry lists 12 outcome measures and one analysis. A primary endpoint is identified, alongside secondary outcomes covering adverse events, HSIL status, HPV-16/18 testing, LSIL or HSIL, progression to carcinoma, and lesion counts at specified follow-up times. The record does not report whether or how statistical testing across these outcomes was adjusted for multiplicity. The multiplicity strategy is not reported in the registry record.

General explanation: when several outcomes or comparisons are tested, the chance of finding at least one apparently notable result by chance can increase. A prespecified testing hierarchy or adjustment can address that issue, but the record does not establish that either was used. With no reported outcome values or inferential results for the listed measures, there is no basis for evaluating the impact of multiplicity on findings.

The registry defines the modified intention-to-treat population as all participants who received at least one dose of VGX-3100 plus electroporation. It also states that the overall number analyzed for an outcome indicates participants with data available for that measure. The number with available Week 36 primary endpoint data is not reported in the registry record. Neither the amount nor the reasons for missing outcome data are reported.

The method used to handle missing data is not reported in the registry record. General explanation: missingness can affect an estimate if participants with and without observed outcomes differ in ways related to the outcome. Analysis choices such as excluding people without measurements or assigning values under specified assumptions can lead to different interpretations. Without the missing-data method and the endpoint analysis denominator, the effect of missingness cannot be assessed.

The protocol's sample-size justification, interim analyses, and complete statistical plan are also not reported in the registry record. These details would help clarify which analyses were planned and how the primary result was intended to be interpreted, but their absence does not permit assumptions about what the investigators did.

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 serious adverse event terms

Most frequent non-serious adverse event terms

Serious events with the highest arm-level rate: ankle fracture (4.3%).

The adverse-event record lists 23 participants at risk for serious adverse events, with 1 participant affected, and 23 at risk for other adverse events, with 23 affected. It reports 0 deaths. Ankle Fracture is listed as a leading serious adverse event term, at 4.3%. These figures describe the safety entries in the registry record; they do not establish that an event was caused by the study regimen.

The record also lists a secondary outcome for participants with at least one local and systemic treatment-emergent adverse event during the 7 days following each dose, and another for participants with at least one adverse event. Numerical results for those outcome measures are not reported in the registry record. The summary counts above should not be taken as a complete account of event types, timing, severity, or relatedness.

General explanation: a serious adverse event is a classification based on seriousness criteria, not simply a synonym for a severe symptom. A count of participants affected is different from a count of individual events; one person may experience more than one event. The record does not provide enough detail to characterize individual cases, determine attribution, or assess patterns over time. The reported absence of deaths is specific to the registry's listed count and does not describe other safety outcomes.

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

The registry record establishes that this completed phase 2 study examined VGX-3100 administered intramuscularly followed by electroporation in a single group of adults with HPV-16 and/or HPV-18-related anal or anal/peri-anal HSIL who were seronegative for HIV-1/2. It defines a Week 36 primary endpoint requiring both no histologic evidence of HSIL and no evidence of HPV-16/18.

The record does not report the primary endpoint result, its analysis denominator, or its 95% confidence interval. It therefore does not show what percentage met the composite or how precisely that percentage was estimated. Secondary outcome results are likewise not reported in the registry record. No conclusion about the direction or size of an outcome should be drawn from the endpoint definition alone.

Even if a single-group outcome percentage were available, it would describe observed outcomes in the analyzed participants rather than a randomized contrast with a control group. This design cannot, by itself, establish how outcomes would have differed under another intervention or no intervention. The open-label, nonrandomized, single-group design is central to interpreting any result that may be reported elsewhere.

The safety entries report 1 participant affected by a serious adverse event among 23 at risk, 23 participants affected by other adverse events among 23 at risk, and 0 deaths. Ankle Fracture is listed at 4.3% among the serious terms. These entries do not establish causation, and they do not provide a full account of safety timing or attribution.

Overall, the registry record documents the study design, regimen, population, and intended outcome questions, but lacks the numerical efficacy results needed to interpret the primary endpoint. Statistical certainty, treatment comparisons, and causal conclusions cannot be derived from the endpoint description or enrollment count.

14. Why This Trial Matters Statistically

This trial raises several statistical issues that matter when reading studies of lesion outcomes. The primary endpoint combines histology with evidence of HPV-16/18 at a defined follow-up time. The composite has a clear all-components requirement, but interpreting its percentage would require both the result and, ideally, information about each component. Without component-level estimates, an overall value could not show which part of the composite shaped it.

The single-group design makes the distinction between describing outcomes and estimating a treatment effect especially important. A percentage among participants who received the regimen would be a description of that group. It would not be a randomized comparison, and it would not isolate the influence of the intervention from other explanations. The open-label design is another relevant feature when considering how assessments were made.

Precision also matters in a study with enrollment of 23. The registry specifies a 95% confidence interval for the primary percentage, but does not report the estimate, interval, or endpoint-specific analysis count. Without those values, readers cannot judge how much uncertainty surrounds the result. The enrollment figure alone is not a measure of precision for the primary endpoint, because the number with data available for that outcome is not reported.

Finally, the record lists multiple secondary outcome measures but does not report a multiplicity approach or the results. It also omits the statistical analysis plan, missing-data methods, interim analysis details, and sample-size justification. These are not merely technical details: they affect how an outcome estimate should be interpreted, what claims can be made across multiple measures, and whether the analysis follows a prespecified plan. The record defines questions of statistical interest, but does not include the efficacy results needed to answer them.

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.

The principal limitation for statistical interpretation is that the registry record does not report numerical results for the primary endpoint. The Week 36 composite percentage, its 95% confidence interval, and the number analyzed for that outcome are absent. Numerical results for the listed secondary outcomes are also not reported. Consequently, the observed efficacy outcomes and their precision cannot be described.

The design was single group, open label, and had no allocation to a comparator. It therefore offers no concurrent control comparison within the study. This limits what can be inferred about differences attributable to the regimen. The design also does not provide a blinded comparison for the primary outcome assessment.

The study enrolled 23 participants; the brief description anticipated approximately 24. The registry record does not report the sample-size justification, so it is not possible to determine the planned precision target or the assumptions used for enrollment. Nor does the record report the primary analysis method or the method used to calculate the confidence interval.

The record's modified intention-to-treat definition includes participants who received at least one dose, while the number analyzed for each outcome is described as participants with available data. The Week 36 analysis denominator, missingness, reasons for missing data, and missing-data handling are not reported. These omissions prevent evaluation of potential bias from incomplete outcome data.

Multiplicity handling, interim analyses, and the full statistical analysis plan are not reported in the registry record. The listed safety figures also lack detailed information about event timing, relatedness, and individual event counts. These limitations restrict both efficacy and safety interpretation; they do not imply a particular unreported outcome.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: VGX-3100 Delivered Intramuscularly (IM) Followed by Electroporation (EP) for the Treatment of HPV-16 and/or HPV-18 Related Anal or Anal/Peri-Anal, High Grade Squamous Intraepithelial Lesion (HSIL) in Individuals Seronegative for Human Immunodeficiency Virus (HIV)-1/2 — NCT03499795.
• Registry record last updated 2023-07-14; status last verified 2023-07.
• Results first posted 2023-07-03.
• 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

NCT03499795 is a completed phase 2, open-label, single-group study sponsored by Inovio Pharmaceuticals. It enrolled 23 participants and examined VGX-3100 delivered intramuscularly followed immediately by electroporation with the CELLECTRA™ 5PSP device. The described regimen was four 6 mg doses on Day 0, Week 4, Week 12, and Week 40.

Eligible participants were adults seronegative for HIV-1/2 with histologically confirmed anal or anal/peri-anal HSIL associated with HPV-16 and/or HPV-18. The primary endpoint was the percentage with no histologic evidence of HSIL and no evidence of HPV-16/18 at Week 36, with a specified 95% confidence interval. The primary result and interval are not reported in the registry record.

The record lists 12 outcome measures and safety counts, including 1 participant with a serious adverse event among 23 at risk and 0 deaths. A full statistical analysis plan, missing-data approach, multiplicity strategy, interim analyses, and sample-size justification are not reported in the registry record.