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Inflammatory Bowel Disease Phase 2 Binary Endpoint NCT03201445

Study to Evaluate the Testicular Safety of Filgotinib in Adult Males With Moderately to Severely Active Inflammatory Bowel Disease: Complete Statistical Analysis

This randomized phase 2 trial examined sperm-concentration changes in adult males with moderately to severely active inflammatory bowel disease receiving filgotinib or placebo. The interpretation focuses on the Week 13 primary endpoint, its uncertainty, and the registry’s reporting limitations.

Trial start: 2017-07-11  ·  Enrollment: 139  ·  Sponsor: Lakefront Biotherapeutics NV
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 Study to Evaluate the Testicular Safety of Filgotinib in Adult Males With Moderately to Severely Active Inflammatory Bowel Disease (NCT03201445), a randomized phase 2 study. The primary outcome is Percentage of Participants With a ≥ 50% Decrease From Baseline in Sperm Concentration at Week 13.

139
Enrollment
Phase 2
2
Arms
In the primary outcome
-7.4 pts
Risk difference
Filgotinib
-14.9 to 0.0 pts
95% CI
Two-sided
FeatureRegistry value
ClinicalTrials.gov identifierNCT03201445
PhasePhase 2
ConditionInflammatory Bowel Disease
AllocationRandomized
Design modelParallel
MaskingDouble
Enrollment139
Arms in the primary outcome2
Lead sponsorLakefront Biotherapeutics NV
Results postedYes

2. Clinical Question

Population

Adult males with moderately to severely active inflammatory bowel disease (IBD) were eligible. The primary analysis population was the Semen Analysis Set: randomized and treated participants with at least one dose of double-blind study drug and two semen samples eligible for calculation of a mean at baseline and at the Week 13 analysis visit.

Intervention

Filgotinib was given during the double-blind period through Week 13. Participants who met the stated response and sperm-decrease conditions could continue double-blind treatment through Week 26; the registry’s arm description is incomplete, so further details of the treatment pathways are not established by the record.

Comparator

The primary comparison was filgotinib versus placebo matched to filgotinib. At Week 13, 66 participants were listed in the filgotinib group and 67 in the placebo group for the primary endpoint.

Primary question

What percentage of participants had a decrease of 50% or greater from baseline in sperm concentration at Week 13? The trial’s stated primary objective was to evaluate the testicular safety of filgotinib in adult males with moderately to severely active IBD.

3. Trial Design

This was a randomized, double-blind, placebo-controlled phase 2 study with a parallel-group design. The registry lists 139 participants enrolled and the trial status as terminated. The recorded study start date is 2017-07-11, and the primary completion date is 2020-11-20. The reason for termination is not reported in the registry record.

The main comparison assigned participants to filgotinib or matching placebo during the double-blind phase through Week 13. The registry describes continued treatment through Week 26 for certain Week 13 responders who did not meet prespecified sperm-decrease thresholds. It also describes treatment changes for some other participants, but the arm descriptions are incomplete. The full treatment pathway, including details for all participants, is not reported in the registry record.

The primary endpoint was assessed from baseline to Week 13. Baseline sperm and semen values were defined as the mean of two evaluable samples at screening; the Week 13 value was the mean of two evaluable samples collected at that visit. The registry also lists secondary outcomes involving sperm concentration, total sperm count, total motility, and ejaculate volume, with measurements at Week 13 or Week 26.

Standard of Care is listed among the interventions, but no corresponding primary-analysis group is included in the posted Week 13 results. The registry says results may be pooled with a separate study in participants with other inflammatory conditions, with a combined planned total of up to approximately 250 participants. That planned pooling does not change the group sizes in the posted primary comparison.

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: Study had 5 parts: Part A: Double-Blind Phase (DB Phase; Day 1 up to Week 13); Part B: DB Phase (Week 13 up to Week 26); Open-label (OL) Phase (after Week 13 study visit for up to 13 weeks); Monitoring Phase (MP; up to 52 weeks); and Long-term Extension (LTE) Phase (after Week 26 or end of OL Phase for up to 195 weeks).

Part A DB Phase (Through Week 13)

StageFilgotinibPlacebo
STARTED6970
COMPLETED6867
NOT COMPLETED13

Reasons for not completing this period:

ReasonFilgotinibPlacebo
Lost to Follow-up10
Protocol Violation01
Withdrawal by Subject02

Part B DB Phase (Week 13 to 26)

StageFilgotinibPlacebo
STARTED4538
COMPLETED4238
NOT COMPLETED30

Reasons for not completing this period:

ReasonFilgotinibPlacebo
Adverse Event10
Progressive Disease20

OL Phase (13 Weeks)

StageFilgotinibPlacebo
STARTED2423
COMPLETED2220
NOT COMPLETED23

Reasons for not completing this period:

ReasonFilgotinibPlacebo
Adverse Event02
Withdrawal by Subject21

LTE: DB Study Drug (up to Week 195)

StageFilgotinibPlacebo
STARTED3834
COMPLETED85
NOT COMPLETED3029

Reasons for not completing this period:

ReasonFilgotinibPlacebo
Adverse Event910
Lost to Follow-up01
Physician Decision02
Withdrawal by Subject44
Pre-Specified Decrease In Sperm Parameters (Switched to MP)67
Study Terminated By Sponsor115

Analysis population for the primary outcome, as defined in the registry: The Semen Analysis Set included all randomized and treated (≥ 1 dose of double-blind study drug) participants who had 2 semen samples that were eligible for mean calculation at baseline and at the Week 13 analysis visit with the date of the first chronologic semen sample used for purposes of assigning analysis visit windows.

5. Baseline Characteristics

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

Population: The Safety Analysis Set included all randomized participants who took ≥ 1 dose of double-blind study drug.

CharacteristicUnitFilgotinibPlaceboTotal
Participants analysed6970139
Age, Continuousyears36 (SD 8.5)34 (SD 8.4)35 (SD 8.5)
Sex: Female, Male: FemaleParticipants000
Sex: Female, Male: MaleParticipants6970139
Race/Ethnicity, Customized: Ethnicity – Not Hispanic or LatinoParticipants6868136
Race/Ethnicity, Customized: Ethnicity – Hispanic or LatinoParticipants112
Race/Ethnicity, Customized: Ethnicity – Not PermittedParticipants011
Race/Ethnicity, Customized: Race – American Indian or Alaska NativeParticipants202
Race/Ethnicity, Customized: Race – AsianParticipants373875
Race/Ethnicity, Customized: Race – Black or African AmericanParticipants101
Race/Ethnicity, Customized: Race – WhiteParticipants293160
Race/Ethnicity, Customized: Race – Not PermittedParticipants011
Sperm Concentrationmillion sperm cells/milliliter (mL)63.4 (SD 34.34)61.8 (SD 34.96)62.6 (SD 34.53)
Total Sperm Countmillion sperm cells/ejaculate190.6 (SD 107.08)171.1 (SD 100.74)180.8 (SD 104.02)
Sperm Total Motilitypercentage of motile sperm59.6 (SD 11.33)58.6 (SD 10.94)59.1 (SD 11.11)
Ejaculate VolumemL3.2 (SD 1.20)3.0 (SD 1.48)3.1 (SD 1.35)
Percent Normal Sperm Morphologypercentage of normal sperm41 (SD 6.4)41 (SD 5.5)41 (SD 6.0)

6. Primary Endpoint

The registry lists the primary outcome as Percentage of Participants With a ≥ 50% Decrease From Baseline in Sperm Concentration at Week 13, measured over Baseline to Week 13.

ElementRegistry entry
Result typeNumber
Measure of spreadnot applicable
Unitpercentage of participants
Endpoint classificationBinary Endpoint

The primary endpoint was the percentage of participants with a decrease of 50% or greater from baseline in sperm concentration at Week 13. It is a binary outcome: each participant either met the stated decrease threshold or did not. Sperm concentration is reported as a measure of sperm cells per milliliter, and the registry gives a normal range of at least 15 million sperm cells/mL.

For this endpoint, baseline was the mean of two evaluable semen samples collected at screening, and the Week 13 value was the mean of two evaluable samples collected at Week 13. Using means of two samples defines how the endpoint was constructed; it does not remove uncertainty arising from biological variation, missing samples, or the small number of participants who met the threshold.

In general, a threshold-based endpoint gives a direct count of participants crossing a prespecified level of change, which can be straightforward to interpret as an event proportion. It also discards information about the size of changes that do not cross the threshold. The registry’s stated primary objective concerns testicular safety, and this endpoint measures a specified sperm-concentration change over the Week 13 interval. The record does not report why this threshold or time point was selected.

7. Results Posted in the Registry

Risk difference: Filgotinib

-7.4

95% CI: -14.9 to 0.0 percentage points

Recalculated from the posted summary statistics

Primary outcome by arm, with 95% confidence intervals
Primary outcome by arm with 95% confidence intervals0.04.08.012.016.020.0Filgotinib (n=66)Placebo (n=67)% of participants (95% CI)
Treatment effect versus the control arm
Forest plot of risk difference (percentage points) vs control (95% CI)Filgotinib-16-13-9.17-5.71-2.261.20risk difference (percentage points) vs control (95% CI)

8. Secondary Efficacy Endpoints

The registry also posts results for secondary outcomes. For each outcome below, the endpoint type, the test applied to the posted summary statistics, the result and its interpretation are given in turn. Secondary endpoints are usually not adjusted for multiple testing, so they support rather than confirm the primary finding.

Secondary outcomeTypeEffect measureEstimate (95% CI)Planning size, 80% power
Percentage of Participants With a ≥ 50% Decrease From Baseline in Sperm Concentration at Week 26Binary EndpointRisk difference-2.9 pts (-13.8 to 8.0)1,129 per arm

Percentage of Participants With a ≥ 50% Decrease From Baseline in Sperm Concentration at Week 26

Treatment effect versus the control arm
Forest plot of risk difference (percentage points) vs control (95% CI)Filgotinib/DB Filgotinib (Res…Filgotinib/OL Filgotinib (Non…-18-13-7.06-1.384.309.98risk difference (percentage points) vs control (95% CI)

The registry lists secondary semen outcomes covering sperm concentration, total sperm count, total motility, ejaculate volume, and the Week 26 threshold-based sperm-concentration endpoint. Eleven secondary outcomes are posted. They extend the primary question across different semen measures and, for some measures, a later visit. The secondary results therefore provide additional outcome-specific information, rather than a single confirmatory answer to the primary safety question.

The overall interpretation should remain anchored to the Week 13 primary endpoint: the observed event percentage was lower in the filgotinib group, while the uncertainty interval included zero. Secondary outcomes can add context about the range of measured parameters and timing, but they do not remove the primary estimate’s uncertainty. The available secondary comparisons also include different treatment pathways at Week 26, so they should not automatically be read as direct replications of the Week 13 randomized comparison.

In general, testing many outcomes increases the chance that some results may appear unusual even when there is no underlying effect. Adjustment for multiple comparisons can address that concern, but whether an adjustment was planned or used is not reported in the registry record. The secondary results should therefore be treated as less conclusive than a prespecified primary analysis, particularly where analyses are unadjusted. The registry does not report a comprehensive multiplicity strategy or a hierarchy for interpreting the secondary endpoints.

The posted secondary estimates should be considered endpoint by endpoint in their stated groups and time frames, without selecting only results that appear supportive. Their role is exploratory or contextual unless the registry reports a prespecified inferential plan establishing otherwise; such a plan is not reported in the registry record.

Secondary outcomes registered for this trial, for reference (only those above were recalculated):

9. Statistical Interpretation

Clinical Biostats interpretation

At Week 13, the posted event percentages were 1.5% in the filgotinib group and 9.0% in the placebo group. These percentages describe participants meeting the endpoint’s 50% decrease threshold. They are not the percentage change in sperm concentration averaged across all participants. The primary endpoint group sizes were 66 and 67, respectively.

The unadjusted recalculation gives a risk difference of -0.074, with a 95% confidence interval from -0.149 to < 0.001 and an unadjusted p-value of 0.055. On the proportion scale used for that recalculation, the negative estimate indicates a lower observed event proportion in the filgotinib group. The interval includes zero, so the recalculated data are compatible with no group difference as well as with differences in either direction within the interval. The p-value is close to, but above, the conventional 0.05 threshold; it should not be treated as a definitive boundary between meaningful and meaningless evidence.

The registry’s reported analysis gives a difference in percentage of -7.8, with a 95% confidence interval from -16.3 to 0.7. That estimate is expressed in percentage units, whereas the recalculated risk difference is expressed as a proportion. Both intervals include zero. The estimates are not identical, and the registry does not report the method used for its analysis or a p-value for it. The registry record does not explain the difference between the reported and recalculated intervals.

The observed data therefore show a lower event percentage in the filgotinib group than in the placebo group, but the uncertainty around the estimated group difference is substantial relative to the estimate. The trial’s posted results do not establish that the underlying event proportions differ, nor do they establish that they are the same. The available comparison is also specific to this threshold-based Week 13 endpoint and its analysis population; it is not a summary of every semen measure or every treatment period.

The small event counts matter to interpretation: six placebo participants and one filgotinib participant were counted as meeting the primary endpoint in the recalculation. With few events, adding or reclassifying a small number of participants could noticeably affect the estimated proportions and the interval. The endpoint findings should consequently be read alongside the confidence interval, analysis-population definition, and registry reporting gaps rather than as a stand-alone conclusion.

10. Statistical Methods Explained

For a binary endpoint, an event proportion is the number of participants meeting the endpoint divided by the number evaluated in that group. Here, the event is a decrease of 50% or greater from baseline in sperm concentration at Week 13. The percentages in the two groups describe how often that event was observed in the respective analysis groups; they do not describe the average amount of change among all participants.

What does a risk difference express?

A risk difference subtracts one group’s event proportion from the other group’s event proportion. It is an absolute contrast, not a relative ratio. The recalculated risk difference is -0.074, with the comparison defined as filgotinib relative to placebo. Its negative sign corresponds to the lower observed event proportion in the filgotinib group. The registry’s reported difference is expressed as a percentage difference rather than as a proportion, so its numerical scale differs.

How should the confidence interval be read?

A confidence interval describes a range of values reasonably compatible with the observed data under the analysis method and its assumptions. It communicates estimation uncertainty, rather than the range in which individual participant outcomes fall. The recalculated 95% interval is -0.149 to < 0.001. Because this interval includes zero, the data do not rule out a zero difference under that calculation. The registry’s reported 95% interval, -16.3 to 0.7, also includes zero on its percentage scale. Neither interval establishes equality; both leave room for effects on either side of zero.

What does the p-value add?

The unadjusted p-value of 0.055 is a measure of how incompatible the observed data are with a null model of no group difference, assuming that model and the calculation’s assumptions. It is not the probability that the null hypothesis is true, nor the probability that the result occurred by chance. The p-value does not convey the size or precision of the estimate by itself. The registry’s posted analysis has no p-value reported, so the recalculated p-value should not be presented as the registry’s own test.

Why can sparse events affect inference?

Only six participants in the placebo group and one in the filgotinib group were counted as having the primary event in the recalculation. When event counts are small, estimates can be sensitive to a few observations, and approximate methods may behave differently from methods designed specifically for sparse binary data. The recalculation is an unadjusted re-analysis of the posted summary counts, not a substitute for the trial’s own analysis. The registry does not identify the method used for its reported estimate.

What is the role of the analysis population?

The primary endpoint population is described as randomized and treated participants who had two eligible semen samples at baseline and two at the Week 13 analysis visit. This means participants without the required samples are not represented in that defined population. How many randomized participants lacked usable samples, how missing measurements were handled, and whether any sensitivity analyses addressed missingness are not reported in the registry record. In general, analysis restricted to participants with evaluable measurements can be affected if availability of those measurements is related to treatment or outcome.

These methods answer different questions: the event percentages describe the observed groups, the risk difference estimates an absolute contrast, the confidence interval describes its precision, and the p-value summarizes compatibility with a null model under specified assumptions. None alone supplies information that the registry does not report about missing data, analysis choices, or the reason the trial ended.

11. Confidence Intervals and Precision

The primary event percentages are based on 66 filgotinib participants and 67 placebo participants. The recalculated risk difference is -0.074, and its 95% confidence interval runs from -0.149 to < 0.001. This interval is wide enough to include zero and values on either side of it. The estimate therefore has limited precision for distinguishing a group difference from no difference.

The registry’s reported difference in percentage is -7.8, with a 95% confidence interval from -16.3 to 0.7. It also spans zero. The registry does not state the analysis method for this estimate, and its interval is not identical to the recalculated interval. The record does not explain the method-related or other reason for that variation, so the two intervals should be reported as separate analyses rather than blended into one.

In general, confidence intervals are more informative than a binary description of statistical significance because they show both the direction and range of uncertainty in an estimate. An interval that includes zero does not prove that the groups are equivalent. It indicates that the posted data and method do not exclude zero at the stated confidence level. The interval also includes nonzero differences, so the results remain compatible with some degree of group separation.

Precision is limited in part by the small number of observed endpoint events. The interval should be interpreted for the defined Week 13 semen analysis population, not as a range for individual outcomes or as evidence about all the secondary measures. Missing-data handling and the number excluded from the analysis population are not reported in the registry record, which further limits assessment of how representative the analyzed participants were.

12. Planning a Similar Trial: Sample Size

This is a planning illustration, not a re-evaluation of the original trial. It asks: if a new study wanted to detect a difference like the one observed, or a smaller one, how large would it need to be? It is deliberately not “observed power” of the finished trial, which is not a meaningful quantity.

Effect to detectParticipants per arm, 80% powerParticipants per arm, 90% power
100% of the observed effect140187
75% of the observed effect291389
50% of the observed effect747999
Sample size needed versus the size of the effect to detect
Sample size needed versus size of effect to detect1002005001,0002,00040%60%80%100%80% power90% powersize of effect to detect, as % of the effect observed (log vertical scale: participants per arm)
Treat these figures cautiously. The observed difference is imprecise: its confidence interval includes no difference at all. A sample size built on a noisy estimate can be far too small or too large, so the smaller-effect rows are the more cautious guide.
Method and assumptions. Two-sided α = 0.05, 1:1 allocation, pooled-variance normal approximation for two proportions. Counts were reconstructed from the posted percentages and arm sizes, so small rounding differences are possible. Calculated for the comparison: Filgotinib.

The sample-size planning figures are participants per arm, not total events. They are illustrations based on the observed effect, with the planning effect set to 100%, 75%, or 50% of that observed effect. The stated assumptions are a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. The original trial’s sample-size assumptions and justification are not reported in the registry record.

The 80% power column gives the number of participants per arm that the planning calculation indicates would be needed to have an 80% chance of detecting the specified effect under those assumptions, if that effect were the true one. The 90% power column applies the same idea with a higher target chance of detection. These are planning quantities, not guarantees about a future study’s result. The listed sample sizes are not observed power for this trial.

The rows based on smaller fractions of the observed effect require more participants per arm. This follows from a general statistical principle: smaller group differences are harder to distinguish from random variation, all else being equal. The curve should be read as illustrating that relationship under the stated planning assumptions, not as evidence about the trial’s actual design or its probability of success. The trial’s own original design assumptions are not reported in the registry record.

13. How the Sample Size Is Derived

Power is the probability that a study of a given size rejects the null hypothesis when a specific true effect exists. It depends on four things: the effect to detect, the variability of the outcome, the significance level (here a two-sided α of 0.05, so z1−α/2 = 1.960) and the desired power (z1−β = 0.842 for 80% and 1.282 for 90%).

Formula

n = [ z1−α/2 √(2p̄(1−p̄)) + z1−β √(p0(1−p0) + p1(1−p1)) ]2 / (p1 − p0)2

n is the number of participants in each arm, p0 and p1 are the control and treatment proportions, and p̄ is their average.

Worked calculation for this trial

  1. Control proportion p0 = 0.090; treatment proportion p1 = 0.015; average p̄ = 0.052.
  2. First term: z1−α/2 × √[2p̄(1−p̄)] = 1.96 × 0.3150 = 0.6174.
  3. Second term: z1−β × √[p0(1−p0) + p1(1−p1)] = 0.842 × 0.3106 = 0.2614.
  4. n = (0.6174 + 0.2614)2 / (-0.0744)2 = 139.5, rounded up to 140 participants per arm for 80% power.

The smaller-effect rows in the table above repeat the same calculation with the effect multiplied by 0.75 and 0.5 (for ratios, applied to the logarithm of the ratio).

R code

alpha <- 0.05
z_a   <- qnorm(1 - alpha / 2)          # two-sided
p0 <- 0.0895522388059701                          # control proportion
p1 <- 0.0151515151515152                          # treatment proportion
n_per_arm <- function(power, frac = 1) {
  q1 <- p0 + (p1 - p0) * frac               # smaller effect = fraction of the observed difference
  pbar <- (p0 + q1) / 2
  z_b <- qnorm(power)
  ceiling(round((z_a * sqrt(2 * pbar * (1 - pbar)) + z_b * sqrt(p0 * (1 - p0) + q1 * (1 - q1)))^2 / (q1 - p0)^2, 6))
}
for (f in c(1, 0.75, 0.5))
  cat(sprintf("%3.0f%% of observed effect: n per arm = %s (80%% power), %s (90%% power)\n", 100 * f,
              format(n_per_arm(0.80, f), big.mark = ","), format(n_per_arm(0.90, f), big.mark = ",")))

# Check against R's built-in function (unrounded n per arm)
cat("power.prop.test:", round(power.prop.test(p1 = p0, p2 = p1, power = 0.80)$n, 1), "\n")

# Simulation: how often does the z-test reject at the 80%-power sample size?
set.seed(3201445)
n    <- n_per_arm(0.80)
reps <- 20000
x0 <- rbinom(reps, n, p0); x1 <- rbinom(reps, n, p1)
ph <- (x0 + x1) / (2 * n)
z  <- ((x1 - x0) / n) / sqrt(ph * (1 - ph) * 2 / n)
cat(sprintf("Simulated power at n = %s per arm: %.3f (%d replicates)\n", format(n, big.mark = ","), mean(abs(z) > z_a, na.rm = TRUE), reps))

Output from running the code

100% of observed effect: n per arm = 140 (80% power), 187 (90% power)
 75% of observed effect: n per arm = 291 (80% power), 389 (90% power)
 50% of observed effect: n per arm = 747 (80% power), 999 (90% power)
power.prop.test: 139.5 
Simulated power at n = 140 per arm: 0.842 (20000 replicates)

The simulation draws many pairs of event counts at the planned sample size and counts how often the two-proportion z-test rejects the null. It should land close to the target power; at very small required sample sizes it can fall below it, because the normal approximation is rough there.

14. Analyses Reported by the Sponsor

MethodEstimate95% CIP-value
not statedDifference in Percentage -7.8-16.3 to 0.7not reported

The registry’s reported analysis gives a difference in percentage of -7.8, with a 95% confidence interval from -16.3 to 0.7. The method and a p-value for that analysis are not reported in the registry record. The interval includes zero.

The unadjusted recalculation from the posted group summaries gives a risk difference of -0.074, with a 95% confidence interval from -0.149 to < 0.001 and an unadjusted p-value of 0.055. This recalculation is expressed on the proportion scale; the registry’s reported estimate is expressed in percentage units. Both analyses point to a lower observed event proportion in the filgotinib group, and both intervals include zero, but their estimates and interval limits are not identical.

The recalculation is a check based on posted summary counts, not a replacement for the registry’s analysis. The record does not identify why the methods or intervals differ, so no specific explanation should be inferred. The p-value of 0.055 belongs to the unadjusted recalculation, not to the reported registry analysis.

15. Multiplicity, Missing Data and Analysis Populations

The registry lists 12 outcome measures and 6 analyses, and 11 secondary outcomes are posted. It does not report whether the primary endpoint was tested within a formal hierarchy, whether secondary tests were adjusted for multiple comparisons, or how any family of outcomes was defined. Without that information, the nominal inferential results for secondary outcomes should not be treated as if they controlled the overall false-positive risk.

The primary analysis population is described as the Semen Analysis Set. It includes randomized and treated participants who had two semen samples eligible for mean calculation at baseline and at the Week 13 analysis visit. This definition makes the requirement for evaluable samples explicit, but the number of randomized participants who did not meet it is not reported in the registry record. The full population description is incomplete in the record.

The handling of missing baseline or Week 13 samples, missed visits, and other incomplete measurements is not reported in the registry record. It is also not reported whether imputation, sensitivity analyses, or other methods were used to evaluate the effect of missing data. In general, complete-case estimates can be biased if having evaluable measurements is related to treatment or outcome; whether that issue arose in this study cannot be determined from the reported information.

The statistical method for the registry’s reported difference is not identified. Interim analyses, stopping rules, and the reason for termination are not reported in the registry record. The trial’s own sample-size calculation and its assumptions are also not reported. These omissions limit a full evaluation of the analysis plan and of how the posted result was selected and interpreted.

16. Safety Results

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

ArmParticipants with serious adverse eventsParticipants at riskPercentage
Filgotinib3923.3%
Placebo2702.9%
Participants with at least one serious adverse event
Serious adverse events by armFilgotinib3.3%Placebo2.9%% of participants with at least one serious adverse event

Deaths

ArmDeaths (participants affected of at risk)
Filgotinib0 of 92
Placebo0 of 70

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
Filgotinib47 of 92
Placebo24 of 70

Most frequent serious adverse event terms

Event termOrgan systemFilgotinibPlacebo
Colitis ulcerativeGastrointestinal disorders1 of 921 of 70
Crohn's diseaseGastrointestinal disorders1 of 920 of 70
COVID-19Infections and infestations0 of 921 of 70
PneumoniaInfections and infestations1 of 920 of 70

Most frequent non-serious adverse event terms

Event termOrgan systemFilgotinibPlacebo
NasopharyngitisInfections and infestations17 of 923 of 70
Colitis ulcerativeGastrointestinal disorders14 of 923 of 70
COVID-19Infections and infestations9 of 923 of 70
Latent tuberculosisInfections and infestations5 of 925 of 70
PyrexiaGeneral disorders5 of 924 of 70
Abdominal painGastrointestinal disorders3 of 925 of 70
GastritisGastrointestinal disorders7 of 921 of 70
HeadacheNervous system disorders7 of 920 of 70
FuruncleInfections and infestations1 of 924 of 70

Serious events with the highest arm-level rate: colitis ulcerative (1.4%), covid-19 (1.4%), crohn's disease (1.1%), pneumonia (1.1%).

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.

For serious adverse events, the registry lists 3 affected participants among 92 at risk in the filgotinib group and 2 among 70 at risk in the placebo group. For other adverse events, it lists 47 among 92 at risk in the filgotinib group and 24 among 70 at risk in the placebo group. These are counts of participants with events and the corresponding group denominators, not the primary semen-analysis group sizes.

The registry lists no deaths in either group. The serious-event terms shown include Colitis ulcerative and COVID-19 at 1.4% each, and Crohn's disease and Pneumonia at 1.1% each. These terms and percentages describe reported serious events; they do not by themselves establish whether an event was caused by study treatment.

Safety counts should be read with their denominators and with the registry’s reporting limitations. The record does not provide enough detail to infer comparative risk, duration of exposure, or causality. These figures are separate from the Week 13 sperm-concentration endpoint and should not be used as a substitute for interpreting that endpoint.

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

The posted primary results show that 1.5% of the filgotinib group and 9.0% of the placebo group met the threshold of a 50% or greater decrease in sperm concentration by Week 13. The unadjusted recalculation estimates a lower event proportion in the filgotinib group, but its confidence interval includes zero. The registry’s own reported interval also includes zero. The data therefore leave uncertainty about the size and direction of the underlying group difference.

This finding concerns one threshold-based semen measure at one time point in a defined analysis population. It does not describe the average change in sperm concentration for every participant, and it does not by itself summarize all semen parameters, later measurements, or all aspects of testicular safety. The registry lists further outcomes, but their interpretation depends on their specific measures, populations, and time points.

The result should not be read as proof that the groups are the same, nor as proof that they differ. A confidence interval including zero is not evidence of equivalence. Demonstrating equivalence would require a prespecified margin and an analysis designed for that question; such details are not reported in the registry record.

The endpoint is based on semen samples, and participants had to meet the stated sample requirements to enter the primary analysis set. The registry does not report the number excluded for missing or ineligible samples or how missing measurements were handled. That information would help readers assess the reach of the result beyond participants with evaluable samples.

In general, a clinical trial result is best understood as an estimate with uncertainty, tied to a particular population, comparison, endpoint, and analysis. Here, the numerical contrast is informative as a description of the posted groups, but the uncertainty and reporting gaps constrain broader conclusions.

18. Why This Trial Matters Statistically

This trial illustrates why a safety question can require attention to both an endpoint’s definition and its analysis population. The primary outcome is not simply a mean change: it counts participants who crossed a specified sperm-concentration decrease threshold. That makes the event proportion accessible to interpret, while leaving the magnitude of changes below the threshold outside the primary endpoint.

It also illustrates the difference between an observed group contrast and a precise estimate of an underlying effect. The posted percentages differ, but the confidence intervals include zero, and only a small number of participants met the primary event definition. A point estimate alone would conceal that uncertainty. The interval and event counts are essential to a balanced statistical reading.

The registry’s reported analysis and the unadjusted recalculation use different numerical scales and have nonidentical intervals. Reporting both, and keeping the recalculated p-value distinct from the registry analysis, helps avoid treating a secondary calculation as though it were the trial’s own reported test. The lack of a reported analysis method also demonstrates why transparent methods are needed to assess how estimates were obtained.

Finally, the record leaves important questions about multiplicity, missing data, the original sample-size plan, and termination unanswered. Those omissions do not negate the posted observations, but they limit the strength of conclusions that can be drawn from them. This is a useful example of interpreting a clinical result through its design, estimand, precision, and reporting completeness together.

19. Limitations

The trial is listed as terminated, but the reason for termination is not reported in the registry record. The registry also does not report the original sample-size justification or design assumptions, so the relationship between the planned enrollment and the eventual analysis cannot be fully assessed from the record.

The primary analysis requires two eligible semen samples at baseline and two at Week 13. The number of randomized participants who met that requirement, the number who did not, and the handling of missing measurements are not reported. This limits assessment of possible selection related to sample availability.

The registry’s reported estimate does not identify its statistical method, and the reported interval is not identical to the unadjusted recalculation. The record does not explain the difference. The registry also does not report whether multiplicity was addressed, whether interim analyses occurred, or how secondary outcomes were prioritized.

The arm descriptions are incomplete, particularly regarding treatment changes after Week 13. This matters for understanding Week 26 comparisons, which include responder and nonresponder pathways and should not be assumed to preserve the original randomized comparison. Standard of Care is listed as an intervention but is not represented in the posted primary comparison.

Finally, the primary finding is based on a threshold outcome and a limited number of observed events. It does not capture the full distribution of sperm-concentration changes. The listed safety counts use different denominators from the primary endpoint analysis, and the registry does not provide enough information in these results to establish causality or compare safety risk comprehensively.

20. Related Tutorials

21. Related Statistical Calculators

22. Sources

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23. Record Summary

NCT03201445 is a randomized, double-blind, placebo-controlled phase 2 study of filgotinib in adult males with moderately to severely active IBD. The registry lists 139 participants enrolled and the status as terminated. The primary endpoint was the percentage with a 50% or greater decrease in sperm concentration from baseline to Week 13.

The posted primary percentages were 1.5% for filgotinib and 9.0% for placebo. The recalculated risk difference was -0.074, with a 95% confidence interval from -0.149 to < 0.001 and an unadjusted p-value of 0.055. The registry’s reported difference was -7.8, with a 95% confidence interval from -16.3 to 0.7. Both intervals include zero.

The results describe the defined Week 13 analysis population and do not settle the underlying group difference. Important details about missing data, multiplicity, the original sample-size plan, the analysis method, and the reason for termination are not reported in the registry record.

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