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Malaria Phase 3 Registry Results NCT02699099

Immunogenicity and Safety Study of GSK Biologicals' Candidate Malaria Vaccine Given at 6, 7.5 and 9 Months of Age in Co-administration With Measles, Rubella and Yellow Fever (YF) Vaccines Followed by a Booster of the Malaria Vaccine.: Complete Statistical Analysis

This analysis examines a randomized Phase 3 study of the malaria vaccine candidate SB257049, focusing on anti-CS antibody concentrations after Dose 3 and selected secondary immunogenicity and safety results. The primary reported comparison is between the Coad and RTS,S groups.

Trial start: 2017-05-10  ·  Enrollment: 699  ·  Sponsor: GlaxoSmithKline
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 Immunogenicity and Safety Study of GSK Biologicals' Candidate Malaria Vaccine Given at 6, 7.5 and 9 Months of Age in Co-administration With Measles, Rubella and Yellow Fever (YF) Vaccines Followed by a Booster of the Malaria Vaccine. (NCT02699099), a randomized phase 3 study. The primary outcome is Anti-Circumsporozoite (Anti-CS) Antibody Concentrations, One Month Post Dose 3 of SB257049 (Primary Analysis).

699
Enrollment
Phase 3
2
Arms
In the primary outcome
n/a
Effect
No re-analysis shown
n/a
95% CI
See limitations
FeatureRegistry value
ClinicalTrials.gov identifierNCT02699099
PhasePhase 3
ConditionMalaria, Malaria Vaccines
AllocationRandomized
Design modelParallel
MaskingNone (open label)
Enrollment699
Arms in the primary outcome2
Lead sponsorGlaxoSmithKline
Results postedYes

2. Clinical Question

Population

Children who began vaccination at 6 months of age. The registry record describes an enrollment of 699 and a primary analysis population defined as the Per-Protocol set for immunogenicity.

Intervention

The Coad schedule included Vitamin A at 6 months, SB257049 at 6, 7.5 and 9 months, and yellow fever and combined measles-rubella vaccines at 9 months. A booster of SB257049 was scheduled 18 months after Dose 3.

Comparator

The primary comparison was with the RTS,S group. This group received Vitamin A at 6 months and SB257049 at 6, 7.5 and 9 months, with yellow fever and combined measles-rubella vaccines at 10.5 months. The registry record also describes a Control group with a later SB257049 schedule, but that group is not part of the reported primary comparison.

Primary question

What were anti-circumsporozoite (anti-CS) antibody concentrations one month after Dose 3 of SB257049, and how did the reported geometric mean ratio compare between the Coad and RTS,S groups?

The clinical question concerns an immune-response measure after a vaccine series given alongside other childhood vaccines. It is not a direct comparison of malaria illness or other clinical outcomes. The registry describes the study purpose as assessing immunogenicity, safety and reactogenicity when SB257049 was co-administered with Vitamin A, measles, rubella and yellow fever vaccines. The primary endpoint focuses specifically on anti-CS antibody concentrations at the stated post-dose time point. The reported primary analysis compares the Coad and RTS,S groups; the registry record does not report a primary anti-CS comparison with the Control group.

3. Trial Design

The registry record describes a randomized, parallel-group Phase 3 study with no masking. It lists 699 enrolled participants and a status of completed. The recorded start date is 2017-05-10, and the primary completion date is 2018-03-14. The study involved children who began vaccination at 6 months of age.

The Coad and RTS,S groups received SB257049 at 6, 7.5 and 9 months. Their schedules differed in the timing of the yellow fever and combined measles-rubella vaccines: these were given at 9 months in the Coad group and 10.5 months in the RTS,S group. Both groups were scheduled to receive an SB257049 booster 18 months after Dose 3, described as at 27 months of age. The Control group received Vitamin A and the yellow fever and combined measles-rubella vaccines at 9 months, followed by SB257049 at 10.5, 11.5 and 12.5 months and a booster 17.5 months after Dose 3, described as at 30 months of age.

The reported primary endpoint is an immunogenicity measure from the Coad and RTS,S groups. The group-level primary estimates use 207 participants in the Coad group and 213 in the RTS,S group. These endpoint-specific analysis counts are not the same description as the overall enrollment: the registry describes the primary analysis population as a Per-Protocol set for immunogenicity, with eligibility, protocol-compliance and elimination criteria. The complete population definition is not reported in the registry record.

The registry identifies ANOVA for the primary geometric mean ratio analysis and the Miettinen and Nurminen method for the posted secondary comparisons. Details of allocation implementation, masking beyond the designation of none, sample-size justification, and any interim analyses 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.

Overall Study

StageCoad GroupRTS,S GroupControl Group
STARTED231236232
COMPLETED223233226
NOT COMPLETED836

Reasons for not completing this period:

ReasonCoad GroupRTS,S GroupControl Group
Adverse Event102
Lost to Follow-up010
CONSENT WITHDRAWAL NOT DUE TO ADV. EVENT724

Analysis population for the primary outcome, as defined in the registry: Analysis was performed on the Per-Protocol set for immunogenicity defined for the primary analysis (Month 4.5), which included all evaluable subjects meeting all eligibility criteria, complying with protocol defined procedures, with no elimination criteria during the study. Subjects with incomplete vaccination course or blood sampling outside protocol windows were eliminated.

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.

CharacteristicUnitCoad GroupRTS,S GroupControl GroupTotal
Participants analysed231236232699
Age, ContinuousMonths6.3 (SD 0.3)6.3 (SD 0.3)6.3 (SD 0.3)6.3 (SD 0.3)
Sex: Female, Male: FemaleParticipants116119113348
Sex: Female, Male: MaleParticipants115117119351
Race/Ethnicity, Customized: BLACK OR AFRICAN AMERICANParticipants231236232699

6. Primary Endpoint

The registry lists the primary outcome as Anti-Circumsporozoite (Anti-CS) Antibody Concentrations, One Month Post Dose 3 of SB257049 (Primary Analysis), measured over At one month post Dose 3 of SB257049 (Month 4).

ElementRegistry entry
Result typeGeometric Mean
Measure of spread95% Confidence Interval
UnitEU/mL
Endpoint classificationnot reduced to a single comparison

The primary endpoint is the concentration of anti-circumsporozoite antibodies one month after Dose 3 of SB257049, identified as Month 4. Concentrations are expressed in ELISA units per milliliter (EU/mL). Anti-CS antibody response is an immunogenicity measure: it describes the antibody response observed after vaccination, rather than directly counting malaria cases or measuring another clinical outcome.

The registry reports geometric mean concentrations (GMCs) for the Coad and RTS,S groups, each with a 95% confidence interval. A geometric mean is used for measurements that are analyzed on a multiplicative scale; it summarizes the central level of the measurements after accounting for their distribution on that scale. A confidence interval expresses the uncertainty around an estimated group summary. It is not a range containing a fixed proportion of individual participants.

The primary comparison is reported as a geometric mean ratio, with an ANOVA-based 95% confidence interval. A ratio describes the relative scale of the two group summaries, rather than their absolute difference in EU/mL. The registry record does not state the non-inferiority margin or the full decision rule for the primary analysis. The endpoint can therefore be read as a comparison of antibody concentrations at a specified time point, but not as a complete account of the clinical interpretation or the trial’s formal success criteria.

7. Why No Re-analysis Is Shown

Reported as posted, not recalculated. Values missing or not estimable for a two-arm comparison (other endpoint). A result is recalculated only when the posted data support a clean two-arm comparison, so no result is shown beyond what the sponsor posted.

8. Statistical Interpretation

Clinical Biostats interpretation

At one month after Dose 3, the posted geometric mean anti-CS concentration was 452.9 EU/mL in the Coad group and 422.5 EU/mL in the RTS,S group. The corresponding 95% confidence intervals were 409.9 to 500.4 EU/mL and 382.9 to 466.2 EU/mL. The reported geometric mean ratio was 0.93, with a 95% confidence interval from 0.81 to 1.07. No p-value is reported for this analysis.

The confidence interval describes uncertainty in the ratio estimate. It includes values on either side of the no-difference value for a ratio, so the point estimate alone should not be treated as a precise account of the possible relative response. The interval also does not establish equivalence: an equivalence conclusion depends on prespecified margins and a decision rule, and those details are not reported in the registry record. The reported analysis is labeled non-inferiority, but its margin and full testing criteria are not stated.

The endpoint-specific analysis counts are smaller than the overall enrollment because the primary analysis used a Per-Protocol immunogenicity population and required evaluable measurements. The registry describes that population as including evaluable subjects meeting eligibility criteria and protocol procedures, with no elimination criteria during the study. The remaining population-definition text is incomplete in the registry record. Reasons for any exclusions or missing antibody measurements are not reported in the registry record.

Several secondary immunogenicity outcomes concern antibody responses to measles, rubella and yellow fever vaccination. Their posted results offer additional descriptions of immune responses, but they are not substitutes for the primary anti-CS endpoint. The registry lists 37 secondary outcomes, while the number of outcomes alone does not establish how many were prespecified as confirmatory or how their analyses were prioritized. Secondary comparisons conducted without adjustment for multiple testing are more vulnerable to chance findings across a collection of tests.

The recorded safety results include serious adverse event counts, other adverse event counts and deaths for the three groups. These descriptive figures should be read in the context of the populations at risk and the registry’s incomplete reporting of event definitions, follow-up windows and attribution. They do not, by themselves, establish whether an event was caused by a vaccine or whether group differences are statistically reliable.

Overall, the primary data provide an estimate of the relative anti-CS antibody response at the stated time point, with a confidence interval that conveys uncertainty. They do not alone answer questions about clinical protection, durability beyond the measured time point, or the comparative safety of the schedules.

9. Statistical Methods Explained

The primary endpoint is reported using geometric mean concentrations and a geometric mean ratio. These summaries are suited to measurements interpreted on a multiplicative scale. The GMC describes a group’s central antibody concentration on that scale, while the ratio compares the two groups’ summaries. The primary group estimates are accompanied by 95% confidence intervals, and the registry identifies ANOVA as the method used to calculate those intervals.

What does a confidence interval convey?

In general, a confidence interval conveys the uncertainty of an estimate under the statistical model and analysis procedure used. A narrower interval indicates greater precision than a wider interval, while neither interval guarantees that the true value lies within its particular endpoints. The primary ratio interval extends from 0.81 to 1.07. Since a ratio’s no-difference value lies within that interval, the posted estimate does not pin down the relative response to one side of that value. The registry record does not report the non-inferiority margin needed to judge this interval against the trial’s formal criterion.

Why use a geometric summary?

Antibody concentrations are positive measurements and may vary multiplicatively. A geometric mean summarizes their central tendency after a logarithmic transformation, then returns the result to the original measurement scale. In general, this can make a group summary more appropriate when ratios are meaningful and the transformed data meet the model assumptions. The registry identifies ANOVA for the primary analysis, but does not report the model specification, covariates, transformation details, diagnostics or handling of values below assay limits. Those details are not reported in the registry record.

How should the secondary comparisons be read?

The posted binary secondary endpoints count participants meeting a seroconversion or seropositivity definition. Their sponsor-reported analyses use the Miettinen and Nurminen method and describe differences in percentage with 95% confidence intervals. This method estimates a difference between two proportions while accounting for the uncertainty in those proportions. The registry also includes simple unadjusted recalculations for selected comparisons. Such recalculations are not adjusted for baseline factors or other design features unless those are explicitly included; no such adjustment is described for the recalculations.

A confidence interval for a difference in proportions gives a range of values compatible with the observed data under the method’s assumptions. When the interval includes no difference, the estimate is not sharply separated from no difference at the stated confidence level. This does not prove that the groups are identical. Likewise, a p-value is a measure of how compatible data are with a specified null model; it is not the probability that the null hypothesis is true, nor is it a measure of clinical importance. The unadjusted p-values in the recalculations should be interpreted as exploratory when many outcomes are considered.

Why can over-dispersion matter?

In general, over-dispersion occurs when observed variability exceeds what a statistical model assumes. It can make standard errors too small and confidence intervals too narrow if the model does not account for the extra variability. This concept is relevant to count and proportion models, but the registry record does not state that over-dispersion was assessed or that a particular over-dispersion adjustment was used in these analyses. No conclusion about the adequacy of such an adjustment can be made from the stated methods alone.

What do the planning illustrations mean?

Where planning illustrations accompany selected recalculations, they use the observed effect as a planning reference, with alternative scenarios based on fractions of that effect. The stated assumptions are a two-sided significance level of 0.05, equal allocation between two arms and a normal approximation. They are planning illustrations, not observed power and not evidence about the original trial’s sample-size rationale. The registry record does not report the trial’s own sample-size justification or its design assumptions.

The analysis populations and denominators vary by endpoint. This is expected when different laboratory measurements, visits or response definitions determine who can contribute to each analysis. However, the registry record does not fully describe missing-data methods, reasons for non-evaluability or sensitivity analyses. These omissions limit assessment of how robust the estimates are to missing or excluded observations.

10. Analyses Reported by the Sponsor

MethodEstimate95% CIP-value
ANOVAGeometric Mean Ratio 0.930.81 to 1.07not reported

The registry reports the sponsor’s primary analysis as an ANOVA-based geometric mean ratio of 0.93, with a 95% confidence interval from 0.81 to 1.07. It is labeled as a non-inferiority analysis. The registry record does not give a p-value, the non-inferiority margin, or the complete formal decision rule. Those missing details prevent an independent determination of whether the prespecified non-inferiority criterion was met based only on the posted information.

The primary result displayed in the posted data is the same sponsor-reported analysis; no separate recalculated primary estimate is listed. The secondary outcomes include sponsor-reported Miettinen and Nurminen estimates and, for selected comparisons, simple unadjusted recalculations from posted summary statistics. Those recalculations are distinct from the sponsor’s analysis: they are not adjusted analyses and should not replace the reported method. The registry record does not identify a discrepancy between the sponsor analysis and the recalculations.

For interpretation, the sponsor’s reported method and estimate are the principal account of the analysis. The recalculations can provide a transparent check on selected summaries, but they cannot reproduce unreported model details or analysis decisions. Differences in methods, estimands, denominators or rounding can also affect a comparison between an unadjusted recalculation and a sponsor-reported result. The registry does not provide enough detail to assess every such possibility.

11. Multiplicity, Missing Data and Analysis Populations

The registry lists 39 outcome measures overall and 37 posted secondary outcomes. Considering multiple outcomes creates a multiplicity issue: when many hypotheses are examined, some results may appear notable by chance even if there is no underlying group difference. Statistical procedures can control this risk, but the registry record does not report a multiplicity adjustment, a hierarchy of secondary endpoints, or which secondary analyses were considered confirmatory. Unadjusted recalculated p-values should therefore not be interpreted as if they were protected against testing across the full set of outcomes.

Missing-data reporting is limited in the registry record. The primary analysis is described as a Per-Protocol set for immunogenicity, including evaluable subjects meeting eligibility criteria and protocol-defined procedures, with no elimination criteria during the study. The description is truncated after “Subjects with incomplete,” so the complete rules for handling incomplete observations are not reported in the registry record. Reasons for missing measurements, exclusions by group, imputation procedures and sensitivity analyses are also not reported in the registry record.

Because group counts vary across endpoint analyses, each estimate applies to the participants contributing data to that outcome and time point. The available record does not establish whether missingness was related to participant characteristics, vaccination, antibody response or adverse events. Without that information, the direction or size of any bias from missing data cannot be determined.

The registry does identify non-inferiority analyses for the primary endpoint and selected secondary outcomes. However, the primary non-inferiority margin and complete testing rule are not reported in the registry record. That omission matters because a non-inferiority conclusion depends not only on the observed estimate and confidence interval but also on the prespecified margin and analysis population. Details of interim analyses, if any, are not reported in the registry record.

12. Safety Results

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

ArmParticipants with serious adverse eventsParticipants at riskPercentage
Coad Group6123126.4%
RTS,S Group6223626.3%
Control Group6623228.4%
Participants with at least one serious adverse event
Serious adverse events by armCoad Group26.4%RTS,S Group26.3%Control Group28.4%% of participants with at least one serious adverse event

Deaths

ArmDeaths (participants affected of at risk)
Coad Group2 of 231
RTS,S Group0 of 236
Control Group3 of 232

Other (non-serious) adverse events

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

ArmParticipants affected of at risk
Coad Group219 of 231
RTS,S Group221 of 236
Control Group207 of 232

Most frequent serious adverse event terms

Event termOrgan systemCoad GroupRTS,S GroupControl Group
Plasmodium falciparum infectionInfections and infestations21 of 23129 of 23621 of 232
GastroenteritisInfections and infestations16 of 23117 of 23613 of 232
PneumoniaInfections and infestations15 of 23112 of 23617 of 232
MalariaInfections and infestations6 of 2313 of 23611 of 232
SepsisInfections and infestations9 of 2312 of 2368 of 232
Otitis mediaInfections and infestations2 of 2315 of 2364 of 232
Urinary tract infectionInfections and infestations3 of 2312 of 2363 of 232
AnaemiaBlood and lymphatic system disorders0 of 2313 of 2364 of 232
Lower respiratory tract infectionInfections and infestations3 of 2313 of 2361 of 232
BronchiolitisInfections and infestations0 of 2313 of 2362 of 232

Most frequent non-serious adverse event terms

Event termOrgan systemCoad GroupRTS,S GroupControl Group
Upper respiratory tract infectionInfections and infestations143 of 231149 of 236168 of 232
GastroenteritisInfections and infestations103 of 231120 of 236119 of 232
PyrexiaGeneral disorders101 of 23195 of 23628 of 232
Respiratory tract infectionInfections and infestations67 of 23168 of 23684 of 232
MalariaInfections and infestations44 of 23151 of 23676 of 232
EnteritisGastrointestinal disorders37 of 23142 of 23654 of 232
PneumoniaInfections and infestations40 of 23133 of 23630 of 232
ConjunctivitisInfections and infestations26 of 23125 of 23631 of 232
Otitis mediaInfections and infestations20 of 23126 of 23630 of 232
DermatitisSkin and subcutaneous tissue disorders23 of 23125 of 23628 of 232

Serious events with the highest arm-level rate: plasmodium falciparum infection (12.3%), pneumonia (7.3%), gastroenteritis (7.2%), malaria (4.7%), sepsis (3.9%).

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 registry reports serious adverse events among 61 of 231 participants in the Coad group, 62 of 236 in the RTS,S group and 66 of 232 in the Control group. Other adverse events were reported for 219 of 231, 221 of 236 and 207 of 232 participants in those respective groups. Death counts were 2, 0 and 3, respectively. These are descriptive counts; they do not establish that an event was caused by a vaccine, and the registry record does not provide a comparative statistical analysis for these figures.

The listed serious-event terms include Plasmodium falciparum infection (12.3%), pneumonia (7.3%), gastroenteritis (7.2%), malaria (4.7%), sepsis (3.9%) and otitis media (2.1%). The registry record does not fully specify the denominator and reporting rules for these term-specific percentages, whether participants could contribute more than one event, or how event relatedness was assessed. The timing and follow-up window for the adverse event summaries are not reported in the registry record.

Serious adverse events, other adverse events and deaths are distinct descriptive categories and should not be conflated. The counts alone do not show the severity distribution of all events, establish a between-group difference, or determine causation. A complete safety interpretation would require the event definitions, follow-up period, exposure context and any prespecified statistical comparisons, which are not reported in the registry record.

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

The primary result describes anti-CS antibody concentrations one month after the third SB257049 dose in the Coad and RTS,S groups. The posted GMCs and ratio provide a summary of immune response at that measurement time. The 95% confidence interval around the ratio communicates uncertainty and includes the no-difference value for a ratio. The estimate should therefore be read alongside its interval, not as a precise statement that one schedule produced a greater or smaller response.

The result does not by itself establish whether the schedules are equivalent or whether a formal non-inferiority criterion was satisfied. The registry labels the analysis non-inferiority, but the margin and complete decision rule are not reported in the registry record. A confidence interval can only be interpreted against such a criterion when the criterion is known.

Anti-CS antibody concentration is an immunogenicity outcome, not a direct measure of malaria incidence, clinical protection or duration of protection. The record also includes other immune-response outcomes, but their results cannot be collapsed into a single measure of vaccine effect. The reported safety counts are descriptive and do not establish vaccine causality or a statistically reliable safety difference.

The study compares schedules that differ in the timing of co-administered vaccines and includes a Control group with a later SB257049 schedule. The primary reported anti-CS analysis, however, is between the Coad and RTS,S groups. It does not directly answer every possible comparison among all three schedules. The registry record does not report the full statistical plan, missing-data analyses, or all details needed to assess selection into each endpoint analysis.

Accordingly, the posted information supports a focused reading of the measured antibody response and selected safety summaries. Broader conclusions about clinical benefit, long-term response, equivalence, causation or the overall balance of effects are not established by these summaries alone.

14. Why This Trial Matters Statistically

This trial illustrates why the statistical question must be matched to the endpoint. The primary outcome is a geometric mean antibody concentration, while selected secondary outcomes count participants meeting antibody response definitions. These measures describe different aspects of immunogenicity and use different scales. A ratio for a continuous concentration outcome cannot be read as interchangeable with a difference in response percentages.

The study also makes the analysis population important. Enrollment describes the trial as a whole, whereas the primary analysis uses a Per-Protocol immunogenicity set and secondary endpoints have their own evaluable participants. These denominators are tied to the endpoint and time point. Readers should not assume that every outcome uses the same participants or that group counts can be added to reconstruct a population total.

Non-inferiority interpretation depends on a prespecified margin, not just on whether a confidence interval crosses a null value. The registry labels the primary analysis non-inferiority but does not report the margin or complete decision rule. That gap is a practical reminder that an estimate may be numerically clear while the formal decision framework remains incompletely documented.

Finally, the broad secondary outcome set raises the importance of multiplicity and transparent prioritization. Multiple immune measurements can be informative, but unadjusted results warrant more cautious interpretation than a clearly specified primary analysis. The record’s combination of primary immunogenicity, additional antibody outcomes and safety summaries offers useful descriptive breadth while leaving important analysis details unreported.

15. Limitations

Several trial-specific limitations follow from the registry record. First, the primary analysis is restricted to a Per-Protocol immunogenicity population, but its complete definition is not available: the description ends after referring to subjects with incomplete information. The record does not state how many participants were excluded from each analysis for particular reasons or whether missing measurements were handled through imputation or sensitivity analyses.

Second, the non-inferiority label is not accompanied by the margin or full decision rule. Without that information, the reported ratio and confidence interval cannot independently establish whether the formal criterion was met. The registry also does not describe the trial’s sample-size justification or interim analysis plan.

Third, the primary reported comparison is between the Coad and RTS,S groups. Although a Control group is described, the posted primary result does not include that group. The schedules also differ in the timing of measles-rubella and yellow fever vaccination, and the control schedule places the SB257049 series later. The available results do not isolate the contribution of each schedule component.

Fourth, the registry lists numerous secondary outcomes, but multiplicity handling and confirmatory status are not reported. The selected recalculated comparisons are unadjusted and should be treated accordingly. Finally, adverse event definitions, follow-up windows, event attribution and term-specific percentage denominators are not fully described. These reporting gaps limit conclusions about missingness, formal non-inferiority, multiplicity and comparative safety.

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19. Record Summary

NCT02699099 is a completed, randomized, open-label, parallel-group Phase 3 study of SB257049 in children beginning vaccination at 6 months of age. The registry lists 699 enrolled participants. Its primary endpoint is anti-CS antibody concentration one month after Dose 3, reported as geometric mean concentrations and a geometric mean ratio for the Coad and RTS,S groups.

The reported ratio is 0.93, with a 95% confidence interval from 0.81 to 1.07. The registry labels the analysis non-inferiority but does not report the margin or complete decision rule. Secondary immunogenicity outcomes and descriptive safety counts are also posted. Interpretation is limited by incomplete reporting of the primary analysis population, missing-data handling, multiplicity procedures and safety follow-up details.

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