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Cystic Fibrosis Phase 1, Phase 2 Binary Endpoint NCT04596319

Ph 1/2 Study Evaluating Safety and Tolerability of Inhaled AP-PA02 in Subjects With Chronic Pseudomonas Aeruginosa Lung Infections and Cystic Fibrosis: Complete Statistical Analysis

This analysis examines the registry record for a randomized, placebo-controlled Phase 1b/2a study of inhaled AP-PA02 in people with cystic fibrosis and chronic pulmonary Pseudomonas aeruginosa infection. It focuses on the safety endpoint and the limits of the posted results for statistical interpretation.

Trial start: 2020-12-22  ·  Enrollment: 29  ·  Sponsor: Armata Pharmaceuticals, Inc.
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 Ph 1/2 Study Evaluating Safety and Tolerability of Inhaled AP-PA02 in Subjects With Chronic Pseudomonas Aeruginosa Lung Infections and Cystic Fibrosis (NCT04596319), a randomized phase 1, phase 2 study. The primary outcome is Incidence and Severity Treatment Emergent Adverse Events (TEAEs).

29
Enrollment
Phase 1, Phase 2
n/a
Arms
In the primary outcome
n/a
Effect
No re-analysis shown
n/a
95% CI
See limitations
FeatureRegistry value
ClinicalTrials.gov identifierNCT04596319
PhasePhase 1, Phase 2
ConditionCystic Fibrosis, Pseudomonas Aeruginosa, Pseudomonas
AllocationRandomized
Design modelParallel
MaskingTriple
Enrollment29
Arms in the primary outcomen/a
Lead sponsorArmata Pharmaceuticals, Inc.
Results postedYes

2. Clinical Question

The central question is whether treatment-emergent adverse events, including their severity, were observed during and after single or multiple ascending doses of inhaled AP-PA02 in participants with cystic fibrosis and chronic pulmonary Pseudomonas aeruginosa infection. The registry describes a placebo-controlled study, so safety observations are presented across AP-PA02 and placebo cohorts. The record does not report a single comparative estimate for the primary outcome, and the primary outcome is not reduced to one comparison.

Population

Participants with cystic fibrosis and chronic pulmonary Pseudomonas aeruginosa infection. The registry record gives total enrollment as 29, but the primary outcome population field is empty.

Intervention

Inhaled AP-PA02, described as an anti-pseudomonal bacteriophage therapeutic candidate. The study included single and multiple ascending dose cohorts; dose amounts are not reported in the registry record.

Comparator

Placebo, described as an inactive isotonic solution. The registry lists single-ascending-dose and multiple-ascending-dose placebo groups.

Primary question

What incidence and severity of treatment-emergent adverse events were recorded from Day 1 before dosing through the End of Study Visit, defined as 28 days after the last dose?

In statistical terms, the endpoint is principally descriptive: it records how many participants experienced events and their severity. The registry lists counts by cohort for serious events, other events, and deaths. It does not report an adjusted or unadjusted estimate comparing AP-PA02 with placebo, nor a confidence interval or a significance test for the primary outcome. These omissions mean the registry record supports a description of recorded events, but not a precise estimate of a treatment-versus-placebo difference.

3. Trial Design

The registry identifies this as a Phase 1b/2a, randomized, double-blind, placebo-controlled study with single and multiple ascending dose components. Its phase is listed as Phase 1 and Phase 2. The design is described as parallel, and masking is recorded as triple. The record does not explain which groups were masked under that description or provide the procedures used to maintain masking.

Enrollment was 29. The listed intervention was AP-PA02, described as an anti-pseudomonal bacteriophage, and the comparator was placebo, described as an inactive isotonic solution. The adverse-event groups include Cohort 1 SAD, Cohort 2 SAD, Amendment 5 MAD, Cohort 3 MAD, Cohort 4 MAD, SAD Placebo, and MAD Placebo. These labels distinguish single-ascending-dose and multiple-ascending-dose groups, but the registry record does not give dose levels or a complete account of cohort assignment and dosing.

The record identifies Armata Pharmaceuticals, Inc. as sponsor. The study start date was 2020-12-22, primary completion was 2022-12-14, and status is completed. The primary outcome concerns the incidence and severity of treatment-emergent adverse events after single and multiple inhaled doses of AP-PA02. Its stated observation window begins on Day 1 before dosing and continues through the End of Study Visit, 28 days after the last dose, with the listed maximum observation periods differing between the single- and multiple-ascending-dose components.

Randomization can reduce systematic differences between treatment groups when implemented successfully, while masking can limit some forms of assessment or reporting bias. These are general design principles, not conclusions about how well those procedures operated in this trial. The registry record does not report the randomization method, allocation ratio, detailed eligibility criteria, or operational masking procedures.

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: Percentages were based on the number of subjects in the Safety Population in each treatment group. The Safety Population included all subjects who were administered at least 1 dose of study treatment.

Only the first 6 of 7 groups are shown.

Overall Study

StageCohort 1 SADCohort 2 SADAmendment 5 MADCohort 3 MADCohort 4 MADSAD Placebo
STARTED3323103
COMPLETED3323103
NOT COMPLETED000000

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.

CharacteristicUnitCohort 1 SADCohort 2 SADAmendment 5 MADCohort 3 MADCohort 4 MADSAD Placebo
Participants analysed3323103
Age, Customized: Age at screeningyears41.7 (SD 3.21)40.7 (SD 6.03)31.5 (SD 9.5)44.3 (SD 18.72)38.2 (SD 8.65)39.6 (SD 19.36)
Sex: Female, Male: FemaleParticipants230262
Sex: Female, Male: MaleParticipants102141
Ethnicity (NIH/OMB): Hispanic or LatinoParticipants000000
Ethnicity (NIH/OMB): Not Hispanic or LatinoParticipants000000
Ethnicity (NIH/OMB): Unknown or Not ReportedParticipants3323103
Race (NIH/OMB): American Indian or Alaska NativeParticipants000000
Race (NIH/OMB): AsianParticipants000000
Race (NIH/OMB): Native Hawaiian or Other Pacific IslanderParticipants000000
Race (NIH/OMB): Black or African AmericanParticipants000000
Race (NIH/OMB): WhiteParticipants3323103
Race (NIH/OMB): More than one raceParticipants000000
Race (NIH/OMB): Unknown or Not ReportedParticipants000000

6. Primary Endpoint

The registry lists the primary outcome as Incidence and Severity Treatment Emergent Adverse Events (TEAEs), measured over Day 1 pre-dose through End of Study Visit (28 days post last dose of study drug), up to 4 weeks for single ascending dose and up to 5.5 weeks for multiple ascending dose..

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

The primary endpoint is the incidence and severity of treatment-emergent adverse events (TEAEs) after single and multiple doses of inhaled AP-PA02. The outcome is measured as a count of participants. The timeframe begins on Day 1 before dosing and extends through the End of Study Visit, defined as 28 days after the last dose of study drug. The registry also describes the observation period as up to 4 weeks for single ascending dose and up to 5.5 weeks for multiple ascending dose.

Safety endpoints are used to describe events that occur during a study treatment period and the time specified for follow-up. Counting participants with an event gives a direct description of how many people were affected within each listed group. Severity adds information beyond whether an event occurred, because an event count alone does not describe its clinical seriousness. This is a general explanation of the role of such endpoints; it does not establish that every relevant event is captured or that groups are directly comparable.

The registry record names incidence and severity as the endpoint, but the posted primary outcome data do not provide a full severity breakdown or a single comparison between AP-PA02 and placebo. The adverse-event record separately lists serious events, other affected participants, and deaths by cohort. The population field for the primary outcome is empty, and no analysis is listed. Thus, the endpoint definition indicates what the study intended to assess, while the posted figures provide only a limited descriptive view of recorded safety events.

7. Why No Re-analysis Is Shown

Reported as posted, not recalculated. Primary outcome has several categories or time points; not reduced to one comparison. 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

The posted data are best read as cohort-level safety counts rather than as a treatment-effect estimate. They list participants at risk and participants affected by serious events, other events, and deaths within the named cohorts. No deaths are listed in any cohort. Serious events are listed for Cohort 4 MAD, where 1 participant was affected among 10 at risk; the other named groups list 0 serious events. For other events, the registry lists 1 affected participant among 3 at risk in Cohort 1 SAD, 1 among 3 in Cohort 2 SAD, 1 among 2 in Amendment 5 MAD, 0 among 3 in Cohort 3 MAD, and 5 among 10 in Cohort 4 MAD. The SAD Placebo group lists 2 affected among 3 at risk, and the MAD Placebo group lists 4 among 5 at risk.

These observations are not a direct numerical comparison of a single AP-PA02 group against a single placebo group. The active-treatment cohorts are separated by dose-stage labels, and the registry does not provide a pooled estimate or a specified contrast. Participants in different cohorts may also have different exposure patterns; the detailed dose levels and other cohort characteristics are not reported in the registry record. Consequently, interpreting differences between counts as evidence of a treatment effect would go beyond what the posted data establish.

The serious-event counts are sparse: most listed cohorts have no affected participant, while one cohort has an event recorded. In general, when the number of participants is small and events are uncommon, an observed count can be highly sensitive to a small change in the number of affected participants. A zero count in a small group does not establish that the underlying risk is zero. This is a general statistical point, not a trial-specific estimate of risk.

The record lists small intestinal obstruction as a serious adverse-event term, with 10.0% shown for that term. The displayed term should be interpreted within the limitations of the registry entry: the record does not provide a comparative estimate, a confidence interval, or fuller context about event timing, recurrence, or attribution. It should not be treated as proof that the study drug caused the event.

Overall, the registry supports a description of the safety counts recorded in the listed cohorts during the stated observation window. It does not report a formal statistical analysis of the primary outcome. Comparative uncertainty, including the precision of any difference between treatment and placebo, is therefore not quantified in the registry record.

9. Statistical Methods Explained

For a safety endpoint expressed as participants with an event, the basic descriptive quantity is a count within each group. The number at risk provides the group size against which that count is interpreted. The registry lists these quantities for serious events and other events in the named cohorts, alongside deaths. These figures answer a descriptive question: how many participants in each listed group were recorded as affected? They do not, on their own, answer whether an observed difference between groups is statistically distinguishable from chance or attributable to treatment.

What a group comparison would require

A treatment comparison would need a clearly defined contrast, such as a specified AP-PA02 cohort against a specified placebo cohort or a justified combination of cohorts. The registry record does not report such a primary-outcome comparison. It lists zero analyses for the outcome, and the primary outcome is not reduced to one comparison. No p-value, confidence interval, or adjusted estimate for the primary endpoint is reported in the registry record.

In general, a confidence interval describes a range of values compatible with the data and a stated statistical model. It conveys uncertainty as well as the direction and scale of an estimated effect. A narrow interval indicates greater precision than a wide interval, all else equal. Without an interval or an estimate of the between-group difference, readers cannot use the registry record to assess the precision of a treatment contrast. This general explanation does not supply a missing estimate.

Why sparse safety counts need care

General statistical reasoning is especially important when event counts are small. A count of zero in a cohort means that no affected participants were recorded in that group during the specified period; it does not show that the event cannot occur. Likewise, one or more observed events do not establish that treatment caused them. Small groups generally yield imprecise estimates, and the observed count may change substantially in relation to group size if a small number of events differ. The registry does not provide interval estimates to express this uncertainty.

Randomized allocation is a general method for limiting systematic differences between groups, but randomization does not ensure that small groups will have identical characteristics. The record states that allocation was randomized but does not report the method, allocation ratio, or baseline characteristics needed to examine group comparability. The cohort labels also distinguish dose-stage groups. Without detailed exposure and cohort information, pooling those groups or comparing them as if they were interchangeable would require assumptions not reported in the registry record.

Endpoint and observation window

The stated endpoint combines incidence and severity of treatment-emergent adverse events. The registry’s group counts distinguish serious events from other affected participants, but the posted information does not give a complete severity distribution for the primary endpoint. The specified observation window runs from Day 1 before dosing through the End of Study Visit, 28 days after the last dose; the record also states up to 4 weeks for single ascending dose and up to 5.5 weeks for multiple ascending dose. Event counts should be understood in relation to that observation period, not as a measure of events over an unspecified longer duration.

The registry record does not report definitions or adjudication procedures for treatment-emergent events, missing-outcome handling, or the analysis population. It also does not describe an interim analysis, statistical testing plan, or adjustments for multiple comparisons. These details matter in general because outcome definitions, participant inclusion, incomplete follow-up, and the number of statistical tests can affect interpretation. Their absence does not establish that procedures were or were not used; it means they are not reported in the registry record.

Planning calculations and observed results

General sample-size calculations estimate the number of participants that may be needed under selected assumptions. The registry describes a planning illustration based on a fraction of the observed effect, using a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. Such illustrations are not observed power and do not show that a study was designed with those assumptions. The registry record does not report the trial’s own sample-size justification or a statistical plan connecting a target sample size to the primary safety endpoint. Safety studies may also focus on describing events rather than testing a single efficacy contrast, so a planning calculation should not be read as evidence of a confirmed treatment effect.

Because the posted primary outcome lacks an analysis estimate and its uncertainty, statistical interpretation should remain descriptive. The cohort counts are useful for identifying what the registry records, but they cannot establish comparative safety with a quantified degree of precision.

10. Multiplicity, Missing Data and Analysis Populations

The registry record does not report a statistical plan addressing multiplicity, meaning the consequences of evaluating multiple outcomes, groups, doses, or time points. The study includes single and multiple ascending dose cohorts, and the primary outcome refers to both incidence and severity of treatment-emergent adverse events. It is not reported whether a hierarchy of outcomes, a primary comparison, or any adjustment for multiple testing was planned. Without that information, the statistical status of any particular comparison cannot be determined from the record.

Missing-data methods and analysis populations are also not reported in the registry record. The primary outcome population field is empty. The posted adverse-event counts include numbers at risk for each group, but the registry does not explain how participants with incomplete follow-up, missing event assessments, or withdrawal were handled. It also does not state whether the counts follow an intention-to-treat, safety, or other analysis population.

These omissions matter in general because the set of participants included and the handling of incomplete observations can affect the interpretation of event frequencies. Similarly, examining many comparisons without a prespecified strategy can increase the chance of findings that appear notable by chance. Those are general statistical considerations, not claims about analyses performed in this trial. The registry record does not report whether interim analyses occurred or how the endpoint analyses were conducted.

11. Safety Results

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

ArmParticipants with serious adverse eventsParticipants at riskPercentage
Cohort 1 SAD030.0%
Cohort 2 SAD030.0%
Amendment 5 MAD020.0%
Cohort 3 MAD030.0%
Cohort 4 MAD11010.0%
SAD Placebo030.0%
MAD Placebo050.0%
Participants with at least one serious adverse event
Serious adverse events by armCohort 1 SAD0.0%Cohort 2 SAD0.0%Amendment 5 MAD0.0%Cohort 3 MAD0.0%Cohort 4 MAD10.0%SAD Placebo0.0%MAD Placebo0.0%% of participants with at least one serious adverse event

Deaths

ArmDeaths (participants affected of at risk)
Cohort 1 SAD0 of 3
Cohort 2 SAD0 of 3
Amendment 5 MAD0 of 2
Cohort 3 MAD0 of 3
Cohort 4 MAD0 of 10
SAD Placebo0 of 3

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
Cohort 1 SAD1 of 3
Cohort 2 SAD1 of 3
Amendment 5 MAD1 of 2
Cohort 3 MAD0 of 3
Cohort 4 MAD5 of 10
SAD Placebo2 of 3

Most frequent serious adverse event terms

Event termOrgan systemCohort 1 SADCohort 2 SADAmendment 5 MADCohort 3 MADCohort 4 MADSAD Placebo
small intestinal obstructionGastrointestinal disorders0 of 30 of 30 of 20 of 31 of 100 of 3

Most frequent non-serious adverse event terms

Event termOrgan systemCohort 1 SADCohort 2 SADAmendment 5 MADCohort 3 MADCohort 4 MADSAD Placebo
headacheNervous system disorders0 of 30 of 31 of 20 of 31 of 101 of 3
chillsGeneral disorders0 of 30 of 30 of 20 of 32 of 100 of 3
infective pulmonary exacerbation of cystic fibrosisInfections and infestations0 of 31 of 30 of 20 of 31 of 100 of 3
chest discomfortGeneral disorders0 of 30 of 30 of 20 of 31 of 100 of 3
fatigueGeneral disorders0 of 30 of 30 of 20 of 31 of 100 of 3
painGeneral disorders0 of 30 of 30 of 20 of 31 of 100 of 3
pyrexiaGeneral disorders0 of 30 of 30 of 20 of 31 of 100 of 3
sialoadenitisInfections and infestations0 of 30 of 30 of 20 of 31 of 100 of 3
vulvovaginal mycotic infectionInfections and infestations0 of 30 of 30 of 20 of 31 of 100 of 3
ligament sprainInjury, poisoning and procedural complications0 of 30 of 30 of 20 of 31 of 100 of 3

Serious events with the highest arm-level rate: small intestinal obstruction (10.0%).

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 safety record lists, for each cohort, the number of participants at risk and the number affected by serious events, other events, and deaths. These are counts, not comparative estimates. For serious events, Cohort 4 MAD lists 1 affected participant among 10 at risk; each other listed cohort records 0. No deaths are listed. The other-event counts vary across the named groups, including the placebo cohorts, so they should be read separately rather than combined into a treatment-versus-placebo conclusion.

The registry identifies small intestinal obstruction as a serious adverse-event term and displays 10.0%. The record does not provide enough detail to establish causal attribution or to interpret that percentage as a comparative risk. Serious-event counts describe events meeting the record’s serious category; they do not summarize every aspect of severity or experience.

In general, a zero count in a small cohort does not prove absence of risk, and an event recorded after treatment does not by itself establish that treatment caused it. The registry does not report confidence intervals, event-level timing, or a formal comparison for these counts. Accordingly, the figures describe what was recorded in the stated follow-up period, with uncertainty and causality not quantified in the registry record.

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

The posted results mean that the registry contains cohort-level counts of serious events, other affected participants, and deaths for this study of inhaled AP-PA02 and placebo. Most cohorts list no serious events, while Cohort 4 MAD lists 1 affected participant among 10 at risk. The cohort-level counts also show other affected participants in both AP-PA02-labeled and placebo-labeled groups. No deaths are listed. These observations provide a descriptive account of recorded events during the stated study follow-up.

They do not, by themselves, establish a causal relationship between AP-PA02 and any event. They also do not establish that AP-PA02 is safer or less safe than placebo, because the registry does not provide a defined statistical comparison, an effect estimate, or an interval describing uncertainty. The different dose-stage cohorts are listed separately, and the registry record does not report enough detail to treat them as one homogeneous group or to combine their counts into a single comparative result.

In general, randomized and masked study designs can support more credible comparisons when their procedures are adequately implemented and the analysis is prespecified. The record reports randomized allocation and triple masking, but does not describe the implementation details or a statistical analysis of the primary outcome. This means those design labels should be recognized without assuming that they resolve the limitations of the posted counts.

The study’s stated objective was to evaluate safety, tolerability, and phage recovery profile, while the listed primary endpoint is treatment-emergent adverse-event incidence and severity. The registry record does not report a comparative primary-outcome analysis or a result for phage recovery in the information summarized in the outcome record. Conclusions should therefore remain limited to the specific counts and endpoint description that are posted, rather than extending to unreported outcomes, longer-term effects, or clinical benefit.

13. Why This Trial Matters Statistically

Statistically, this trial illustrates the distinction between a study design that includes randomization and the information needed to interpret a comparative result. Random allocation and masking are relevant design features, but the registry’s posted safety figures are counts within separate cohorts. Without an explicitly reported comparison and uncertainty estimate, readers cannot judge the precision of a treatment-versus-placebo difference from these data.

The study also highlights the challenge of interpreting uncommon safety events in small groups. A small number of observed events can be important to describe, but the estimate of how often events occur is generally uncertain when group sizes are limited. A cohort with no recorded serious event should not be read as demonstrating that such events are impossible. Conversely, an event recorded in a treatment cohort does not alone establish causation.

Another statistical issue is the presence of several dose-stage cohorts and an endpoint that includes both incidence and severity. A clear analysis plan would explain which comparisons and outcome summaries were intended to answer the primary question and how multiple assessments were handled. Those details are not reported in the registry record. Their absence makes the posted results more suitable for cautious description than for a definitive inferential claim.

For clinical researchers and biostatisticians, the record is a useful example of why event counts, denominators, endpoint definitions, analysis populations, and uncertainty estimates all matter. Counts convey what was observed; design and analysis details determine how far the observations can support a comparison. Here, the available record allows the former to be described, while important parts of the latter are not reported.

14. Limitations

The registry record gives total enrollment as 29, but the primary outcome population field is empty. It does not report how many participants were assigned to each intervention overall, the randomization ratio, the randomization procedure, or baseline characteristics by cohort. The at-risk counts are listed within the adverse-event groups, but the record does not explain whether they represent all enrolled participants, all treated participants, or another safety population.

Although the primary endpoint includes incidence and severity, the posted outcome information does not provide a complete severity distribution or a single comparative estimate. No confidence interval, p-value, or formal analysis of the primary endpoint is reported. The record also does not explain event definitions, attribution procedures, or how missing follow-up was handled.

The cohort labels identify single- and multiple-ascending-dose groups, including an Amendment 5 MAD group, but dose amounts and detailed cohort histories are not reported. The record does not provide enough information to determine whether cohorts can appropriately be pooled or compared directly. Follow-up is described as extending to 28 days after the last dose, with different maximum durations listed for single and multiple ascending dose components; safety outside that stated window is not addressed by these figures.

Finally, the record does not report a statistical analysis plan, multiplicity strategy, interim analyses, or the trial’s own sample-size justification. These are limits on what can be concluded from the registry entry; they do not establish whether such procedures existed elsewhere. Interpretation should remain confined to the posted cohort counts and endpoint description.

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18. Record Summary

NCT04596319 is a completed Phase 1b/2a randomized, triple-masked, parallel, placebo-controlled study of inhaled AP-PA02 in participants with cystic fibrosis and chronic pulmonary Pseudomonas aeruginosa infection. Enrollment was 29. The registry lists single and multiple ascending dose cohorts, with AP-PA02 described as an anti-pseudomonal bacteriophage and placebo as an inactive isotonic solution.

The primary endpoint concerns incidence and severity of treatment-emergent adverse events from Day 1 before dosing through 28 days after the last dose. Cohort-level adverse-event counts are posted, and no deaths are listed. The record identifies small intestinal obstruction as a serious-event term and displays 10.0%.

No comparative primary-outcome analysis, confidence interval, or p-value is reported in the registry record. The analysis population, missing-data handling, multiplicity strategy, and statistical analysis plan are not reported. The available results therefore support descriptive interpretation of the listed safety counts, not a quantified treatment-versus-placebo conclusion.

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