Tumor and Vaccine Site With a Toll Like Receptor (TLR) Agonist: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Tumor and Vaccine Site With a Toll Like Receptor (TLR) Agonist (NCT00960752), a randomized phase 2 study. The primary outcome is Comparison of Immune Responses of Vaccine+R848 to Vaccine Alone.

2. Clinical Question

3. Trial Design

This was a randomized phase 2 study with a factorial model and no masking. The registry lists melanoma as the condition, an enrollment of 47, and a completed status. M.D. Anderson Cancer Center is listed as the sponsor. The recorded study start was 2010-05-20, and the primary completion date was 2020-07-20.

The interventions listed were gp100, MAGE-3, and R848 gel. The arm descriptions distinguish a vaccine-only group from groups receiving the vaccines with R848. One R848 group is specifically described as a metastatic melanoma group. These descriptions indicate that the study included more than the central vaccine-plus-R848 versus vaccine-alone contrast, but the registry record does not give a complete account of the factorial assignments or explain how all groups relate to one another.

The vaccine descriptions specify daily administration for 8 weeks. The vaccines were administered at separate sites, using intradermal and subcutaneous routes as described in the record. R848 gel was applied to the gp100 injection site immediately in the groups assigned to receive it. These are descriptions of the recorded interventions, not evidence about adherence or actual treatment received by each participant.

Randomization can reduce systematic differences between assigned groups, but it does not by itself ensure that the groups were comparable in every realized sample. No allocation procedure, concealment method, stratification factors, or details of the factorial contrasts are reported in the registry record. Masking was listed as none. The record does not report the statistical analysis plan, sample-size justification, or the primary comparison results. The absent primary analysis limits what can be learned from the design about the immune-response contrast.

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: 47 participants enrolled on study, 1 participant screen failure, 1 participant stopped prematurely due to toxicity.

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: The original PI is no longer in the institution. Due to the absence of the original PI is no longer in the institution and the data is unavailable. The analysis for the primary outcome measure the comparison of immune responses of vaccine+R848 to vaccine alone is not available. All efforts were made to retrieve data.

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 Comparison of Immune Responses of Vaccine+R848 to Vaccine Alone, measured over 8 weeks.

The primary endpoint was a classification of T-cell immune response at 8 weeks. The registry describes measurement by a tetramer or multimer assay using flow cytometry. Participants were categorized as immune responders or immune non-responders according to whether the specified gp100-directed CD8+ T-cell or MAGE3-directed CD4+ T-cell threshold was met. The recorded threshold is at least 0.1% for the relevant cell population.

This kind of endpoint converts an assay measurement into a categorical response status. In general, a prespecified threshold can make a biological measurement easier to summarize as a group comparison. It also discards information about how far an individual measurement lies above or below the cutoff. A participant just meeting the threshold and a participant with a much larger measured response can receive the same category. Conversely, small measurement variation near the threshold could change the category. These are general properties of threshold-based outcomes, not findings about participants in this trial.

The registry title for the outcome frames the intended comparison as immune responses to vaccine plus R848 versus vaccine alone. However, the record states that the primary analysis is unavailable because the original principal investigator was no longer at the institution and the data were unavailable. The number of responders in each group, the estimated contrast, and its uncertainty are not reported in the registry record. Therefore, the endpoint definition is available, but its comparative result cannot be evaluated from the recorded primary outcome.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

What does the endpoint classification mean?

The registry defines response through a laboratory assay and a threshold. A participant is classified as an immune responder when the recorded gp100 tetramer-positive CD8+ T-cell measurement reaches at least 0.1% or the MAGE3 multimer measurement reaches at least 0.1% in the specified CD4+ T-cell population. This is a binary outcome: the assay information is translated into responder or non-responder status. In general, binary outcomes are commonly summarized by counts and proportions, or compared through a model appropriate to categorical data. The registry record does not report the primary group counts, the analysis method, or any estimated comparison.

Thresholds make endpoint definitions operational, but they can affect interpretation. A threshold can simplify a complex assay result and facilitate a prespecified classification. At the same time, categorization can obscure variation within each response category and make results sensitive to measurements close to the cutoff. The registry does not report assay reproducibility, handling of measurements at the boundary, or whether the threshold was specified before outcome data were reviewed. These matters therefore cannot be assessed for this study.

What does randomization contribute?

In general, random assignment is intended to balance prognostic factors across treatment groups on average. This supports comparison of assigned groups, especially when the analysis preserves the randomized assignment and outcome collection is sufficiently complete. Randomization does not guarantee balance in a particular trial, correct outcome measurement, or complete follow-up. The record identifies the study as randomized but does not report the sequence-generation method, allocation concealment, stratification, or analysis according to assigned group. The masking field is listed as none, so participants and study personnel were not masked according to the registry entry.

The study is also labeled factorial, and the arm descriptions include vaccine-only and vaccine-plus-R848 groups, including a group described as metastatic melanoma. Factorial designs can assess more than one intervention factor and may allow estimation of effects across combinations, subject to the design and analysis assumptions. The registry record does not explain the factor structure, which contrasts were prespecified, or how the metastatic group entered the analysis. It would therefore be inappropriate to reconstruct a factorial model or interpret every group comparison as part of the primary question.

How should precision and significance be understood?

For a group comparison, an effect estimate describes the observed contrast, while a confidence interval conveys uncertainty around that estimate under the chosen statistical model. A significance test evaluates compatibility with a specified null hypothesis under its assumptions. These measures answer related but different questions. Statistical significance alone does not describe the size or practical meaning of an effect, and a non-significant result does not establish equivalence. Here, the primary estimate, uncertainty interval, and test result are not reported in the registry record. No inferential conclusion can be recovered from the endpoint definition or the fact that the trial was randomized.

For a binary outcome, the choice of effect measure matters. A difference in response proportions and a ratio of response proportions describe contrasts on different scales. Each can be accompanied by uncertainty estimates, and interpretation depends on the question and analysis plan. The registry does not report which measure was planned or used. No effect measure should be inferred from the outcome title.

What do the sample-size illustrations represent?

The sample-size material is described as a planning illustration based on an observed effect, with a two-sided significance level of 0.05, equal allocation between the two arms, and a normal approximation. The stated illustrations consider detecting a fraction of the observed effect. Such calculations describe hypothetical planning requirements under assumptions; they are not observed power and do not establish whether the completed study was adequately powered. The registry record does not report the sponsor's sample-size justification or the original design assumptions.

The primary analysis is unavailable, so the observed effect used for any such illustration cannot be evaluated from the recorded endpoint result. Any planning output should therefore be read as conditional on its stated assumptions, not as evidence that the trial detected or failed to detect an effect. A planning calculation cannot replace a reported estimate and its uncertainty.

General statistical considerations also include whether the outcome model matches the data, whether observations are independent, and whether the analysis accounts for the design. Over-dispersion matters in models for count data when variability exceeds what the assumed distribution allows; failing to account for it can make uncertainty estimates too small. That issue is a general methodological point, not a reported feature of this binary primary endpoint. No outcome model or diagnostic assessment is reported in the registry record.

10. Multiplicity, Missing Data and Analysis Populations

The trial record lists a primary immune-response outcome and a secondary outcome described as a composite of immune-cell infiltration for pDCs, mDCs, and NK cells in tumor biopsy samples. It does not report the analysis results for these outcomes. The primary comparison is expressly unavailable because the original principal investigator was no longer at the institution and the data were unavailable. The registry record does not report whether the secondary outcome was analyzed or how its components were combined.

Multiplicity arises when several hypotheses, outcomes, time points, or treatment contrasts are examined. In general, examining many comparisons can increase the chance of finding an apparently notable result by chance unless the analysis plan addresses that issue. The record does not report a multiplicity adjustment, a hierarchy of tests, or a prespecified strategy for interpreting multiple comparisons. The existence of a secondary outcome alone does not establish how multiplicity was handled.

The number of participants with evaluable primary endpoint data, the reasons for missing measurements, and the handling of missing data are not reported in the registry record. The record also does not specify the primary analysis population or whether participants were analyzed according to randomized assignment. These omissions limit assessment of possible bias and the denominator underlying any response estimate.

In general, missing outcomes can affect both the estimate and its precision, particularly when the probability of missingness is related to treatment or response. Different assumptions and methods for handling missing data can produce different results. No such assumptions or methods are reported, so their impact cannot be assessed. The unavailable primary analysis is a reporting gap; it is not evidence that the treatment groups had the same immune response.

11. Safety Results

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

Deaths

Other (non-serious) adverse events

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

Most frequent serious adverse event terms

Most frequent non-serious adverse event terms

Serious events with the highest arm-level rate: platelet count decreased (5.3%), thromboembolic event (5.3%).

The serious adverse event figures are descriptive counts among participants recorded as at risk in each group. Group 1 had 0 serious adverse events among 13 participants at risk; Group 2 had 0 among 13; and Group 3 had 2 among 19. The record reports 0 deaths in each group. These counts describe the registry's recorded safety data and do not, by themselves, establish whether an event was caused by a vaccine or R848.

The top serious terms are platelet count decreased and thromboembolic event, each reported as 5.3%. The registry does not provide further detail in this record about event timing, severity beyond the serious classification, recurrence, or treatment attribution. The listed percentages should be interpreted as the record reports them, not used to infer details that are absent.

Other adverse events affected 13 of 13 participants in Group 1, 9 of 13 in Group 2, and 9 of 19 in Group 3. These summaries are not the same as the serious-event counts. They do not describe event severity, duration, or the number of different event types experienced by each participant. In general, comparisons of safety counts require attention to follow-up duration, ascertainment, and differences in the groups. Those details are not reported in the registry record. The group described as metastatic melanoma should not automatically be treated as directly comparable to the other groups.

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

The registry record documents a randomized phase 2 study of gp100 and MAGE-3 vaccines with or without R848, with an immune-response classification assessed at 8 weeks. It specifies the assay-based threshold that defined response and records safety summaries for the groups. It also says the primary comparison is unavailable because the original principal investigator was no longer at the institution and the data were unavailable.

Consequently, the record does not establish how many participants were classified as immune responders, whether response classifications differed between the vaccine-plus-R848 and vaccine-only groups, or how precise any difference would be. The absence of a reported analysis is not equivalent to a finding of no difference. Nor can the primary question be answered by the trial's completed status, its randomized design, or the intervention descriptions.

The safety counts indicate that serious adverse events were recorded in Group 3 and none were recorded in the other listed groups; no deaths were recorded. Those observations are descriptive. They do not alone show that a particular intervention caused or prevented an event, and they do not capture unreported details such as timing, attribution, or follow-up completeness. The other adverse-event counts likewise do not provide a full account of event types or severity.

In general, a trial result is most informative when it includes the group-specific outcome data, an effect estimate, an uncertainty interval, and a clear account of the analysis population and missing data. The registry record does not provide those elements for the primary endpoint. The responsible interpretation is therefore limited: the intended immune-response question and its measurement are described, but the comparative efficacy result cannot be determined from the record. These findings should not be extended beyond the recorded study population, interventions, endpoint, and available safety summaries.

13. Why This Trial Matters Statistically

This trial illustrates an important distinction between a well-defined research question and an interpretable result. The registry describes a randomized comparison of vaccine-plus-R848 against vaccine alone and gives a threshold-based definition of immune response. Yet it reports that the primary analysis is unavailable. A clear endpoint definition is useful for understanding what investigators intended to measure, but it cannot replace the observed group data or the statistical comparison.

For statistical interpretation, the missing primary analysis matters because the central quantities are absent: group response counts, an effect estimate, and a measure of uncertainty. Without these, it is not possible to judge whether the data suggest a difference, how large a difference might be, or how compatible the data are with a range of possible effects. The inability to estimate those quantities also prevents a direct evaluation of precision or statistical evidence.

The record also highlights the need to interpret design features in context. Randomization supports a planned group comparison, but does not eliminate concerns about incomplete outcome data, analysis populations, or differences between groups as implemented. The factorial label and the presence of a group described as metastatic melanoma further make it important to know which contrasts were planned. Those details are not reported in the registry record.

Finally, safety counts and immune-response outcomes answer different questions. The recorded adverse-event summaries can be described, but they do not fill the gap in the primary endpoint analysis. Statistically, transparent reporting of outcomes, denominators, uncertainty, and missing-data handling is necessary for readers to distinguish an unreported result from evidence of no effect. This record makes that distinction especially consequential.

14. 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 main trial-specific limitation is that the registry states the primary outcome analysis is unavailable. It attributes this to the original principal investigator no longer being at the institution and the data being unavailable. As a result, the record does not report the primary response counts, comparative estimate, uncertainty, or test result. This prevents statistical assessment of the stated primary question.

The registry does not report the primary analysis population, the number with evaluable assay measurements, reasons for missing endpoint data, or the method used to handle missingness. It also does not report the detailed statistical plan, sample-size justification, or multiplicity strategy. These omissions limit assessment of the analysis choices and of how robust any intended conclusion would have been.

Although the study is identified as randomized and factorial, the record does not provide the allocation procedure, the full factorial structure, or the planned role of each group in the primary contrast. One group is described as metastatic melanoma, which makes it important not to assume that every group was intended for direct comparison with every other group. No such broader interpretation can be supported by the available descriptions.

The intervention descriptions document intended administration, but the record does not report adherence, treatment received, or deviations from the described regimen. The safety summaries lack details about event timing, attribution, follow-up, and ascertainment. The record also lists a secondary immune-cell infiltration outcome without reporting its analysis. These limitations concern what can be evaluated from the registry record; they do not establish that the trial lacked these procedures or data outside the record.

15. Related Tutorials

16. Related Statistical Calculators

17. Sources

• ClinicalTrials.gov: Tumor and Vaccine Site With a Toll Like Receptor (TLR) Agonist — NCT00960752.
• Registry record last updated 2021-08-13; status last verified 2021-07.
• Results first posted 2021-08-13.
• 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.

18. Record Summary

NCT00960752 is a completed, randomized phase 2 study sponsored by M.D. Anderson Cancer Center, with melanoma listed as the condition and enrollment of 47. The registry describes gp100 and MAGE-3 peptide vaccines administered with or without R848 gel, including a group described as metastatic melanoma.

The primary outcome was an immune-responder classification assessed at 8 weeks using tetramer or multimer assays and a specified T-cell threshold. The registry states that the primary comparison is unavailable because the original principal investigator was no longer at the institution and the data were unavailable. Thus, no primary comparative result or precision estimate is reported.

Safety summaries record serious adverse events in Group 3 and none in Groups 1 and 2, with 0 deaths in each group. The record also lists other adverse events and two top serious-event terms. These figures are descriptive and do not establish causation. The registry does not report the analysis population, missing-data handling, or statistical analysis plan.