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Malaria Vaccine Phase 2 Binary Endpoint NCT02992119

Malaria Vaccine Safety and Immunogenicity Study in Healthy Adults: Complete Statistical Analysis

This analysis examines a randomized, parallel-group phase 2 study of RTS,S/AS01 vaccine schedules in healthy Thai adults. It focuses on serious adverse events through 29 days after the last vaccination and the precision and limits of the posted between-group comparisons.

Trial start: 2017-06-04  ·  Enrollment: 193  ·  Sponsor: University of Oxford
Scope of this record

This page provides an independent statistical analysis and educational interpretation of publicly reported results. ClinicalTrials.gov provides the official trial registry record. Numerical trial results on this page are restricted to the results posted in the ClinicalTrials.gov record; calculations added by Clinical Biostats are labelled as such.

1. Trial at a Glance

This page covers the registry results for Malaria Vaccine Safety and Immunogenicity Study in Healthy Adults (NCT02992119), a randomized phase 2 study. The primary outcome is Number of Participants Who Experience a Serious Adverse Events (SAEs) 29 Days After the Last Vaccination.

193
Enrollment
Phase 2
7
Arms
In the primary outcome
-5.3 pts
Risk difference
Group 2
-15.3 to 4.8 pts
95% CI
Two-sided
FeatureRegistry value
ClinicalTrials.gov identifierNCT02992119
PhasePhase 2
ConditionMalaria Vaccine
AllocationRandomized
Design modelParallel
MaskingNone (open label)
Enrollment193
Arms in the primary outcome7
Lead sponsorUniversity of Oxford
Results postedYes

2. Clinical Question

Population

The study concerns healthy Thai adults. The official title identifies this population, and the registry record lists the condition as Malaria Vaccine. The registry record does not report further participant characteristics in the primary outcome entry.

Intervention

The trial evaluated RTS,S/AS01 schedules, including standard and fractional doses, a double fractional dose, schedules combined with DHA-PIP+PQ, and a fractional two-dose schedule combined with DHA-PIP+PQ. The registry record labels the primary outcome as the number of participants experiencing serious adverse events 29 days after the last vaccination.

Comparator

The posted comparisons use Group 1, RTS,S/AS01B Fractional dose, as the reference group. Each listed comparison is against one of the other six groups. The registry record identifies the trial as randomized, with no masking and a parallel model.

Primary question

How many participants in each group experienced a serious adverse event during the stated observation period, and how do the observed event proportions compare with Group 1? The outcome description specifies ascertainment from the date of the first vaccination to 29 days after the last vaccination and classification according to MedRA. The endpoint is a safety measure; the posted primary outcome does not measure vaccine immunogenicity or malaria prevention.

3. Trial Design

The registry record describes a randomized, unmasked, parallel-group phase 2 study titled “Malaria Vaccine Safety and Immunogenicity Study in Healthy Adults.” Its official title specifies evaluation of RTS,S/AS01 in healthy Thai adults. The record lists an enrollment of 193 and a completed status. The recorded start date is 2017-06-04, and the primary completion date is 2018-02-20.

Seven groups received different vaccine schedules. They included RTS,S/AS01B fractional dose; double RTS,S/AS01E fractional dose; RTS,S/AS01E standard dose; standard or fractional RTS,S/AS01E with DHA-PIP+PQ; and a fractional two-dose RTS,S/AS01E schedule with DHA-PIP+PQ. These are the registry’s arm descriptions; the primary outcome results are reported by group rather than as an overall trial estimate.

Group 1 is the reference group for the posted comparisons. The outcome record gives Group 1 as 1 event among 19 participants. The other groups’ primary outcome entries give 0 events in Groups 2, 3, 6, and 7, and 1 event in Groups 4 and 5. Their listed group sizes are 20, 29, 30, 28, 30, and 30, respectively. The registry record does not report the randomization procedure, allocation concealment, masking rationale, or details of treatment delivery. It also does not report a more detailed protocol description or a statistical analysis plan.

The brief summary describes a rationale involving malaria elimination activities and the potential relevance of vaccine schedules in that setting. That rationale is context, not an outcome of this primary safety comparison. The registry record does not report a primary immunogenicity result in the posted outcome data.

4. Participant Flow and Accounting

The registry reports how participants moved through each stage of the study. All counts below are exactly as posted; missing counts are not inferred from other stages.

Only the first 6 of 7 groups are shown.

Overall Study

StageGroup 1 RTS,S/AS01B Fractional DoseGroup 2 Double RTS,S/AS01E Fractional DoseGroup 3 RTS,S/AS01E Standard DoseGroup 4 RTS,S/AS01E + DHA-PIP+PQ Standard DoseGroup 5 RTS,S/AS01E Fractional DoseGroup 6 RTS,S/AS01E + DHA-PIP+PQ Fractional Dose
STARTED212130303030
COMPLETED192029303030
NOT COMPLETED211000

5. Baseline Characteristics

The table reproduces the baseline characteristics posted in the registry, which describe the participants analysed at baseline and help show whether the randomized groups were comparable.

Only the first 6 of 8 groups are shown.

CharacteristicUnitGroup 1Group 2Group 3Group 4Group 5Group 6
Participants analysed212130303030
Age, Categorical: <=18 yearsParticipants000000
Age, Categorical: Between 18 and 65 yearsParticipants212130303030
Age, Categorical: >=65 yearsParticipants000000
Sex: Female, Male: FemaleParticipants121116171716
Sex: Female, Male: MaleParticipants91014131314
Race and Ethnicity Not CollectedParticipants——————
feverParticipants000000

6. Primary Endpoint

The registry lists the primary outcome as Number of Participants Who Experience a Serious Adverse Events (SAEs) 29 Days After the Last Vaccination, measured over 29 days after last vaccination.

ElementRegistry entry
Result typeCount Of Participants
Measure of spreadnot applicable
UnitParticipants
Endpoint classificationBinary Endpoint

The primary endpoint counts participants who experienced a serious adverse event. The registry title specifies the period as 29 days after the last vaccination, while the outcome description defines the observation window as beginning on the date of the first vaccination and continuing to 29 days after the last vaccination. Events are classified according to MedRA.

A participant count is a binary-outcome summary: each participant is categorized as having experienced at least one qualifying event or not having experienced one during the specified period. It is not an event rate per unit of follow-up time, and it does not describe the number of separate events each affected participant may have had. The registry record does not provide further details about event adjudication or whether repeated events in the same participant were handled in a particular way.

Serious adverse events are used as a safety outcome because they capture events meeting the trial’s serious-event classification, rather than every symptom or medical occurrence. This endpoint does not by itself establish that an event was caused by vaccination. Nor does it measure immune response, infection, or protection against malaria. The registry record lists no primary endpoint population description beyond the group-level counts, so additional eligibility or analysis-population details are not reported in the registry record.

7. Results Posted in the Registry

Risk difference: Group 2

-5.3

95% CI: -15.3 to 4.8 percentage points

Recalculated from the posted summary statistics

Primary outcome by arm, with 95% confidence intervals
Primary outcome by arm with 95% confidence intervals0.05.410.816.321.727.1Group 1 (n=19)Group 2 (n=20)Group 3 (n=29)Group 4 (n=30)Group 5 (n=30)Group 6 (n=30)Group 7 (n=28)% of participants (95% CI)
Treatment effect versus the control arm
Forest plot of risk difference (percentage points) vs control (95% CI)Group 2Group 3Group 4Group 5Group 6Group 7-17-11-5.590.286.1412risk difference (percentage points) vs control (95% CI)

8. Statistical Interpretation

Clinical Biostats interpretation

The primary outcome entries show 1 participant with a serious adverse event in Group 1, 1 in Group 4, and 1 in Group 5. They show 0 in Groups 2, 3, 6, and 7. These are small event counts, so the observed pattern is sparse. The registry record does not establish from these counts whether an event was attributable to vaccination.

The posted pairwise comparisons use Group 1 as the reference. For Groups 2, 3, 6, and 7, each risk difference is -0.053, with a confidence interval from -0.153 to 0.048. For Groups 4 and 5, each risk difference is -0.019, with a confidence interval from -0.139 to 0.100. In each comparison, the interval includes zero. These intervals therefore include values consistent with no difference in observed risks, as well as values in either direction. They are broad relative to the point estimates, so the comparisons do not pin down a precise between-group difference.

The unadjusted p-values are 0.299 for Group 2, 0.212 for Group 3, 0.739 for Group 4, 0.739 for Group 5, 0.204 for Group 6, and 0.22 for Group 7. A p-value describes how compatible the observed data are with a specified no-difference model under the calculation’s assumptions; it is not the probability that a treatment has no effect. The registry record does not report an adjustment for multiple comparisons or a sponsor-specified inferential analysis for these comparisons. These p-values should therefore be read as unadjusted comparisons, not as a complete multiplicity-controlled analysis.

The entries describe the observed serious adverse event counts during the recorded follow-up window. They do not establish equivalence or prove that schedules have the same safety profile. Conversely, the fact that some groups have no recorded events does not establish absence of risk. With sparse binary outcomes, a small change in the number of observed events can materially alter the estimated group difference. The posted confidence intervals express that uncertainty.

The primary endpoint is safety-focused. Although the trial title and brief summary refer to immunogenicity, the registry record does not report a primary immunogenicity result in these outcome entries. These safety figures therefore cannot answer questions about immune response or malaria prevention. The study’s randomized design is relevant to comparisons, but details needed to assess the randomization process, analysis population, missing observations, and handling of multiple outcomes are not reported in the registry record.

9. Statistical Methods Explained

The primary endpoint is binary: the registry reports counts of participants who experienced a serious adverse event. A binary outcome distinguishes participants with an event from those without one during the specified observation period. The group results are counts, rather than continuous measurements such as laboratory values or time-to-event estimates.

What does the risk difference describe?

A risk difference compares the observed event proportions between two groups by subtracting one group’s proportion from the other’s. In the posted comparisons, Group 1 is the reference. The negative estimates correspond to lower observed event proportions in the comparison groups than in Group 1: Group 1 has 1 event among 19 participants, while the comparison groups have either 0 events or 1 event among their listed participants. A risk difference is an absolute contrast on the probability scale, not a relative ratio.

The posted risk difference is -0.053 for comparisons with Groups 2, 3, 6, and 7, and -0.019 for comparisons with Groups 4 and 5. The latter comparisons have an event recorded in both groups, while the former have an event recorded in Group 1 and none in the comparison group. Because event counts are sparse, these estimates are sensitive to the limited number of observed events and should not be treated as stable measurements of a broader population effect.

How should the confidence intervals be read?

A confidence interval describes a range of values compatible with the data and the method used to calculate the interval. It conveys uncertainty around an estimate; it is not a guarantee that the true value lies inside the range. The registry record does not report the confidence level or the specific method used for the posted intervals. The intervals for Groups 2, 3, 6, and 7 run from -0.153 to 0.048. Those for Groups 4 and 5 run from -0.139 to 0.100. All include zero, and they also extend to values on both sides of zero. Thus, the point estimates alone do not convey the full uncertainty.

What do the p-values contribute?

The reported p-values are unadjusted: 0.299, 0.212, 0.739, 0.739, 0.204, and 0.22 for Groups 2 through 7, respectively. In general, a p-value evaluates how unusual data at least as discrepant as those observed would be under a specified statistical model. It does not quantify the size or clinical importance of a difference, and it is not the probability that the null hypothesis is true. The record does not report a prespecified significance threshold, an adjustment for the multiple group comparisons, or the model details behind these p-values.

What can the planning illustrations tell us?

The registry record includes planning illustrations for Groups 4 and 5 based on the observed effect. These are not observed trial sample sizes and are not a measure of observed power. Under the stated assumptions—two-sided significance level 0.05, equal allocation between the two arms, and a normal approximation—the illustrations list participants per arm for 80% and 90% power. For planning for 100% of the observed effect, the entries are 1,733 and 2,320; for 75% of the observed effect, they are 3,247 and 4,345; and for 50% of the observed effect, they are 7,674 and 10,273. The record states that the target effect is the stated fraction of the observed effect.

These values are illustrative calculations based on the observed comparison, not evidence that the trial was designed to detect that effect. Planning based on a sparse observed event pattern can be especially uncertain because the estimated effect itself is imprecise. The registry record does not report the trial’s own sample-size justification or the assumptions used in its original design. It also does not report interim analyses. Those design features cannot be inferred from the planning illustrations.

The record identifies a randomized parallel design, but does not give analysis methods for missing data, covariate adjustment, clustering, or subgroup analyses. The binary endpoint itself does not require an over-dispersion discussion in the way a count model might: the posted outcome is a participant-level event count. More generally, over-dispersion matters when observed variability in count data exceeds what a model assumes; that issue cannot be assessed from this endpoint description or the posted summaries.

10. Confidence Intervals and Precision

The risk-difference intervals are wide in relation to their point estimates. For Groups 2, 3, 6, and 7, the estimate is -0.053 and the interval runs from -0.153 to 0.048. For Groups 4 and 5, the estimate is -0.019 and the interval runs from -0.139 to 0.100. Each interval includes zero and allows for differences in either direction. The posted comparisons therefore leave substantial uncertainty about the size and direction of the underlying between-group differences.

These intervals are especially important because the observed event counts are sparse: the primary outcome entries show 1 event in Group 1, 1 in Group 4, and 1 in Group 5, with 0 in the other groups. Sparse outcomes offer limited information for estimating a risk difference. The confidence interval is more informative about precision than the point estimate alone, but its interpretation also depends on the calculation method. The registry record does not report the confidence level or interval method.

The p-values are also unadjusted, and the registry record does not report how multiplicity was handled. They should not be used as substitutes for the estimated differences and their intervals. The record does not report a prespecified threshold for interpreting these comparisons.

The planning illustrations list participants per arm for 80% and 90% power under stated assumptions and fractions of the observed effect. They are prospective planning illustrations, not observed power and not evidence of the precision achieved in this trial. The registry record does not report the sample-size justification used for the trial itself. In particular, the planning values do not resolve the uncertainty in the observed effect on which they are based.

11. Multiplicity, Missing Data and Analysis Populations

The primary outcome record gives one endpoint and pairwise comparisons of each group against Group 1. With several comparisons, the chance of at least one apparently unusual result can increase if each comparison is interpreted separately without accounting for multiplicity. The posted p-values are explicitly unadjusted. The registry record does not report a multiplicity adjustment, a familywise error strategy, or a hierarchy for testing the comparisons. It also does not report whether other planned primary or secondary comparisons were made.

The record lists 0 posted secondary outcomes and 0 posted analyses. This does not establish that no additional analyses were conducted; it means the registry record does not report them in these fields. The trial title and summary refer to immunogenicity, but no secondary outcome results are posted in the registry record. The detailed statistical plan, including any prespecified analysis populations and handling of protocol deviations, is not reported in the registry record.

The primary outcome entries list group sizes, while the adverse-event group entries give different numbers at risk for some groups. The record does not explain these differences or identify the analysis population used for each presentation. It does not report missing outcome counts, reasons for missingness, imputation methods, or sensitivity analyses. As a result, the effect of missing or differently available observations cannot be assessed from the registry record.

Randomization is reported, but the allocation procedure and concealment are not reported in the registry record. The record also does not report covariate adjustment, subgroup analysis plans, interim analyses, or a detailed statistical analysis plan. These omissions limit assessment of whether the posted comparisons follow a prespecified approach and whether the uncertainty estimates account for all relevant design features.

12. Safety Results

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

ArmParticipants with serious adverse eventsParticipants at riskPercentage
Group 11214.8%
Group 20210.0%
Group 30300.0%
Group 41303.3%
Group 51303.3%
Group 60300.0%
Group 70310.0%
Participants with at least one serious adverse event
Serious adverse events by armGroup 14.8%Group 20.0%Group 30.0%Group 43.3%Group 53.3%Group 60.0%Group 70.0%% of participants with at least one serious adverse event

Deaths

ArmDeaths (participants affected of at risk)
Group 10 of 21
Group 20 of 21
Group 30 of 30
Group 40 of 30
Group 50 of 30
Group 60 of 30

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 5% reporting threshold.

ArmParticipants affected of at risk
Group 121 of 21
Group 221 of 21
Group 330 of 30
Group 429 of 30
Group 530 of 30
Group 629 of 30

Most frequent serious adverse event terms

Event termOrgan systemGroup 1Group 2Group 3Group 4Group 5Group 6
acute pharyngitisRespiratory, thoracic and mediastinal disorders0 of 210 of 210 of 301 of 300 of 300 of 30
DepressionPsychiatric disorders1 of 210 of 210 of 300 of 300 of 300 of 30
Acute sinusitisRespiratory, thoracic and mediastinal disorders0 of 210 of 210 of 300 of 301 of 300 of 30

Most frequent non-serious adverse event terms

Event termOrgan systemGroup 1Group 2Group 3Group 4Group 5Group 6
Injection site painInjury, poisoning and procedural complications20 of 2120 of 2130 of 3025 of 3029 of 3027 of 30
FatigueGeneral disorders18 of 2116 of 2124 of 3021 of 3019 of 3025 of 30
HeadacheNervous system disorders14 of 2113 of 2119 of 3014 of 3014 of 3017 of 30
PyrexiaGeneral disorders13 of 2113 of 2116 of 3014 of 3012 of 3016 of 30
MalaiseGeneral disorders9 of 215 of 218 of 3011 of 305 of 3014 of 30
Injection site reaction (pain)Injury, poisoning and procedural complications8 of 216 of 219 of 306 of 308 of 303 of 30
Injection site reaction (redness)Injury, poisoning and procedural complications2 of 2110 of 217 of 303 of 306 of 305 of 30
NauseaGastrointestinal disorders4 of 212 of 213 of 3012 of 303 of 306 of 30
Haemoglobin lowGeneral disorders2 of 211 of 217 of 306 of 303 of 304 of 30
DizzinessNervous system disorders1 of 212 of 212 of 304 of 304 of 308 of 30

Serious events with the highest arm-level rate: depression (4.8%), acute pharyngitis (3.3%), acute sinusitis (3.3%).

Do not overextend the safety comparison. Serious-adverse-event counts are safety observations, not efficacy outcomes, and should not be combined with the primary result into a single benefit-risk number.

The primary outcome entries report a serious adverse event in Group 1, Group 4, and Group 5, with 0 reported in Groups 2, 3, 6, and 7. The endpoint description covers the period from the first vaccination through 29 days after the last vaccination, and identifies MedRA classification. These are participant counts; they do not provide a detailed account of event severity, timing, recurrence, or attribution to vaccination.

The adverse-event group entries separately list serious-event counts at risk and affected. They show 1 serious event in Group 1, Group 4, and Group 5, and 0 in the other groups. They also report 0 deaths in every group. The at-risk counts in these entries do not always match the group sizes in the primary outcome entries, and the registry record does not explain the difference. The serious-event terms listed most often are Depression at 4.8%, acute pharyngitis at 3.3%, and Acute sinusitis at 3.3%. The record does not explain the relation of these terms to individual groups or to the primary endpoint counts.

A serious adverse event is not automatically caused by the intervention. The registry record does not provide causal attribution or an adjudication description. These figures describe what was posted, not a complete assessment of safety across all possible outcomes or follow-up periods.

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

The posted results describe a small number of serious adverse events during the specified observation period. The primary outcome entries show 1 event in Group 1, Group 4, and Group 5, and 0 in Groups 2, 3, 6, and 7. The comparisons estimate lower observed risks in the groups with no recorded events than in Group 1, while the groups with an event in both arms have smaller negative point estimates.

The confidence intervals are broad and include zero in every posted comparison. The data therefore do not precisely distinguish the group risks. This does not establish that the schedules are equivalent, and zero observed events in a group do not prove that the group has no risk. The unadjusted p-values also do not establish equivalence or provide a probability that a particular schedule is safe.

The endpoint measures serious adverse events, not vaccine-induced immune response or malaria outcomes. Although the trial title and summary refer to immunogenicity and malaria elimination context, those topics cannot be answered by these primary safety counts. The registry record does not report a posted immunogenicity result in the outcome data. The results also do not establish whether any event was caused by vaccination, because causal attribution is not reported.

The trial is recorded as randomized, which is relevant to the intended comparison of groups. However, the registry record does not report the allocation method, masking beyond stating none, analysis populations, missing-data handling, or a detailed prespecified statistical plan. Those omissions, along with sparse event counts and unadjusted multiple comparisons, limit how strongly the estimates can be interpreted. The findings are best read as descriptive group counts with uncertain comparative estimates, not as definitive evidence about differences in safety.

The planning illustrations are not findings from the trial and do not indicate observed power. They show how assumed effects related to the observed comparison map to planning sample sizes under stated assumptions. They do not change the uncertainty in the posted event counts.

14. Why This Trial Matters Statistically

This trial is statistically notable because it compares several vaccine schedules while the primary safety outcome is rare in the posted data. Such settings make the difference between an estimate and its precision particularly important. A point estimate can look like a clear separation when one group has no observed events, but the interval indicates how much uncertainty remains around that estimate.

The posted comparisons make this distinction visible. The estimated risk differences are negative, but all the confidence intervals include zero and extend to values on either side of it. The comparison estimates therefore should not be treated as precise evidence of group differences. The event counts are also too sparse to support broad conclusions about all serious adverse events or longer-term safety from these figures alone.

The design creates multiple pairwise comparisons against Group 1. Because the p-values are unadjusted and the registry record does not report a multiplicity plan, a single p-value cannot be interpreted as if it were the only comparison in a prespecified testing family. The record’s silence about the analysis plan is also important: randomization is reported, but the specific inferential procedures and analysis populations are not.

The planning illustrations demonstrate why sample-size planning depends on the effect one aims to detect and on the underlying assumptions. They are planning calculations based on the observed effect, not a record of the trial’s original design and not observed power. The registry record does not provide the trial’s own sample-size justification. This distinction matters when readers assess what the study was intended or able to establish.

Finally, the trial’s stated interest in safety and immunogenicity should not blur the scope of the posted primary endpoint. The reported endpoint is serious adverse events over a defined period. Statistical interpretation should remain tied to that outcome and its uncertainty.

15. Limitations

The primary outcome is based on sparse event counts, with 1 event recorded in three groups and 0 in the other groups. That limits the information available for estimating between-group differences. The posted confidence intervals are broad and include zero, so the comparative estimates are imprecise.

The registry record gives different group sizes for the primary outcome entries and the separate adverse-event group entries. For example, the primary outcome lists 19 participants for Group 1, whereas the adverse-event entry lists 21 at risk; other groups also have differences. The record does not explain how those denominators relate or which population each represents. No reconciliation should be assumed.

Although the trial is described as randomized, the registry record does not report the randomization method, allocation concealment, or analysis populations. It states that masking was none but does not provide further procedural detail. Missing data, reasons for any unavailable outcomes, and sensitivity analyses are not reported in the registry record.

The comparisons are unadjusted, and the record does not describe multiplicity control or a prespecified testing strategy. It also does not report a detailed statistical analysis plan, the confidence-interval method, the confidence level, or a significance threshold. The sample-size justification for the trial is not reported; the posted planning illustrations are based on observed effects and stated assumptions, rather than the trial’s own design.

The primary endpoint does not establish causality for adverse events. Event adjudication details and causal attribution are not reported in the registry record. The outcome entries also do not provide a posted primary immunogenicity result, despite the trial title’s reference to immunogenicity. Conclusions must therefore remain limited to the posted serious adverse event counts and their uncertain comparisons.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

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Use this trial's endpoint as a starting point for deeper study of effect measures, confidence intervals, and sample-size planning.

19. Record Summary

NCT02992119 is a completed randomized, unmasked, parallel-group phase 2 study of RTS,S/AS01 schedules in healthy Thai adults. The registry lists enrollment of 193, a start date of 2017-06-04, and primary completion on 2018-02-20. Seven groups received standard, fractional, double fractional, or DHA-PIP+PQ-combination schedules.

The primary outcome counts participants with serious adverse events from the first vaccination through 29 days after the last vaccination, with events classified according to MedRA. The posted entries show 1 event in Groups 1, 4, and 5 and 0 in Groups 2, 3, 6, and 7. Each posted risk-difference interval includes zero. The comparisons are unadjusted, and the registry record does not report a multiplicity plan, detailed statistical analysis plan, missing-data methods, or trial sample-size justification. No secondary outcomes are posted in the registry record.

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