CP-690-550 Ointment For Chronic Plaque Psoriasis: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for CP-690-550 Ointment For Chronic Plaque Psoriasis (NCT01246583), a randomized phase 2 study. The primary outcome is Percent Change From Baseline in Target Plaque Severity Score (TPSS) at Week 4.

2. Clinical Question

3. Trial Design

This was a phase 2a, multi-site, randomized, double-blind, placebo-controlled, parallel-group study. The registry lists 71 participants enrolled and the study status as completed. Its recorded start date is 2011-02-16, and its primary completion date is 2011-11-29. The listed condition is psoriasis.

Four groups are named: 2% CP-690,550 Ointment 1, Vehicle 1, 2% CP-690,550 Ointment 2, and Vehicle 2. Randomization and double masking are recorded, but the registry does not report the allocation ratio, the method used to generate the random sequence, or the details of how masking was maintained. The arm descriptions are empty, and the duration and schedule of treatment are not reported in the registry record.

The primary outcome was percent change from baseline in target plaque severity score at Week 4. The registry identifies the full analysis set as randomized participants who received at least one dose of investigational drug; for this outcome, the count refers to participants evaluable for the measure. The posted outcome counts differ across groups, and the reasons for those counts are not reported in the registry record.

The record lists 20 outcome measures in total and 19 posted secondary outcomes. These include target plaque severity and area measures at several visits, treatment-area psoriasis severity responses, itch severity, and patient satisfaction with study medication. The registry does not report the original sample-size justification, the intended allocation across the four groups, or the trial's planned statistical analysis details. Those details should not be inferred from the posted outcome counts or the recalculated comparisons.

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

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: Full analysis set (FAS) included all participants who were randomized to study and received at least 1 dose of investigational drug (CP-690,550 or vehicle). Here Overall Number of Participants Analyzed signifies those participants who were evaluable for this measure.

5. Baseline Characteristics

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

6. Primary Endpoint

The registry lists the primary outcome as Percent Change From Baseline in Target Plaque Severity Score (TPSS) at Week 4, measured over Baseline, Week 4.

The primary endpoint is percent change from baseline in target plaque severity score at Week 4. Target plaque was assessed for induration, scaling, and erythema. Each sign was rated on a severity scale from 0 to 4, with higher ratings indicating more severe signs. The three sign scores were summed to form the target plaque severity score, which ranged from 1 to 12; higher total scores represent greater psoriasis severity.

A change score focuses on how the measured target plaque severity at follow-up compares with baseline for each participant. Expressing that change as a percentage relates the change to the participant's baseline score. The group result is reported as a mean, with a standard deviation describing variation among participants. These summaries provide different information: the mean describes the group's average percent change, while the standard deviation describes how spread out the participant-level values were.

The endpoint is one way to quantify change in a selected plaque over the study period. It does not by itself summarize every aspect of psoriasis or represent all outcomes that may matter to participants. The record also lists measures of treatment-area severity, plaque area, itch, and satisfaction, but the primary result discussed in the comparisons is the Week 4 target plaque severity measure.

7. Results Posted in the Registry

• 2% CP-690,550 Ointment 1: mean -53.97 versus -41.01 on control; difference -12.96 (95% CI -29.64 to 3.72), standardized effect d = -0.48; z-test p = 0.128.
• 2% CP-690,550 Ointment 2: mean -24.26 versus -41.01 on control; difference 16.75 (95% CI -0.81 to 34.31), standardized effect d = 0.57; z-test p = 0.062.

8. Statistical Interpretation

9. Statistical Methods Explained

The primary outcome is continuous: it is a numeric percent change, and the registry reports a mean and standard deviation for each group. A mean is the arithmetic average of the measured values. The standard deviation describes their dispersion around that average. It is not the same as the standard error, which describes the precision of an estimated mean, nor is it a confidence interval, which expresses uncertainty around an estimate.

What does the mean difference represent?

Each posted comparison subtracts the Vehicle 1 mean from the mean in one active group. For Ointment 1, the reported difference is -12.96; for Ointment 2, it is 16.75. These are differences in mean percent change, in percentage points of the reported outcome scale. The sign depends on the order of the groups in the subtraction. Since percent change is negative for all four reported group means, a more negative value represents a larger decrease from baseline in the measured score; that description is about the scale, not a clinical judgment about the treatment.

The comparison estimate is a group-level contrast. It does not reveal whether most participants had values close to the mean, whether a small number of participants strongly influenced it, or how responses varied within subgroups. Participant-level data are not reported in the registry record. The group standard deviations provide a broad summary of variability but cannot answer those detailed questions.

How should the confidence interval be read?

A confidence interval gives a range of values compatible with the observed data under the statistical method's assumptions. It communicates uncertainty about the estimated mean difference rather than the spread of individual outcomes. For the Ointment 1 comparison, the interval is -29.64 to 3.715. For the Ointment 2 comparison, it is -0.809 to 34.31. Both ranges include zero, the value corresponding to no difference in group means. The interval endpoints also show that the estimates are not highly precise: each range includes materially different possible mean differences.

These intervals are recalculated, simple unadjusted comparisons based on the posted summary statistics. They do not incorporate any adjustment for multiple comparisons or other model terms. The registry record does not report whether the sponsor's original analysis used a different model, covariate adjustment, or method for handling missing outcomes. Those original analysis details are not reported in the registry record, so the recalculated statistics should not be taken as evidence that the original analysis followed the same method.

What does an unadjusted p-value tell the reader?

The posted p-values are 0.128 for Ointment 1 versus Vehicle 1 and 0.062 for Ointment 2 versus Vehicle 1. In general, a p-value measures how unusual results at least as far from the null as those observed would be if the null model and test assumptions were correct. It does not quantify the probability that a treatment effect exists, and it does not indicate the probability that the results will be reproduced. A p-value also does not describe the size or practical importance of an estimated difference.

Because the p-values are unadjusted, they do not account for the possibility of increased false-positive error from considering multiple outcomes or comparisons. The record includes multiple outcome measures, but the multiplicity strategy for the primary and secondary analyses is not reported in the registry record. A reader should not assume either that an adjustment was or was not used in the trial's original analysis.

Why do group size and variability matter?

In general, the precision of a group comparison depends on the amount of information in each group and the variation in the outcome. Smaller groups and more variable measurements tend to produce less precise estimates, all else being equal. Here, the primary outcome counts range from 9 to 23 participants across the four groups, and the reported standard deviations vary across groups. The result is that uncertainty should be considered alongside each point estimate. No new calculation is needed to see this: the confidence intervals already show a broad range of compatible differences.

The total enrollment and the number evaluable for the primary outcome are distinct quantities. The registry identifies the full analysis set as randomized participants who received at least one dose, while the primary outcome count represents those evaluable for that measure. It does not report the number randomized in each group, the reasons for not being evaluable, or the method used to address missing measurements. It is therefore not possible to assess from the record whether the analysis preserved the benefits of randomization in the presence of missing outcomes.

What is the role of the sample-size illustrations?

In general, power is the probability that a study design will detect a specified effect under stated assumptions if that effect is present. The planning illustrations use the observed effect as a reference and vary the fraction of that effect to be detected. They are not the trial's original design calculations, and they are not evidence about the chance that the completed study detected an effect. The trial's own sample-size justification and planning assumptions are not reported in the registry record.

The posted comparisons are unadjusted, and the record does not report a multivariable model, an analysis of covariance, or a repeated-measures model for the primary outcome. Those methods should not be attributed to the study without documentation. The outcome was assessed over time, but the primary comparison presented is for Week 4. The analytical handling of the earlier visits and any correlation among repeated measurements are not reported in the registry record.

10. Confidence Intervals and Precision

The estimated mean difference for Ointment 1 versus Vehicle 1 is -12.96, with a 95% confidence interval from -29.64 to 3.715. For Ointment 2 versus Vehicle 1, the estimate is 16.75, with a 95% confidence interval from -0.809 to 34.31. Each interval includes zero, so the posted data do not isolate a direction of mean difference with high precision. The intervals also include a range of values that differ in magnitude, making the point estimates alone an incomplete description of the evidence.

A confidence interval is not a range containing 95% of individual participant outcomes. It is an uncertainty interval for the estimated group difference, interpreted under the method's assumptions. The standard deviations describe participant-level spread; the confidence intervals describe uncertainty in the estimated comparison. These are related but not interchangeable quantities.

The outcome counts for the primary endpoint were 22 and 13 in the Ointment 1 and Vehicle 1 groups, and 23 and 9 in the Ointment 2 and Vehicle 1 groups. The relatively small group counts and the observed variability help explain why estimates need to be read with their intervals rather than as exact values. The record does not provide the original sponsor confidence intervals or enough information to verify their analysis method. The intervals cited are simple unadjusted recalculations from the posted summary statistics.

The interval width does not indicate whether a difference is clinically important. The registry does not report a threshold for a clinically meaningful difference on this endpoint. It also does not report a prespecified interpretation rule for the confidence intervals. Thus, precision can be described statistically, but clinical importance cannot be determined from the posted primary endpoint results alone.

11. 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.

The planning illustrations give participants per arm, not total participants across a comparison. They use a two-sided significance level of 0.05, equal allocation between the two arms, and a normal approximation. The effect to detect is set as a stated fraction of the observed effect. These are planning assumptions for the illustrations; the trial's own original design assumptions and sample-size justification are not reported in the registry record.

The 80% power column describes the number of participants per arm that the illustration estimates would be needed to have an 80% chance of detecting the specified effect under those assumptions. The 90% power column gives the corresponding per-arm number for a higher chance of detection under the same assumptions. This is not observed power: the figures are prospective planning illustrations based on the observed effect, not a measure of what the completed trial achieved.

For the Ointment 1 comparison, planning for 100% of the observed effect gives 68 participants per arm for 80% power and 91 participants per arm for 90% power. Planning for 75% of the observed effect gives 120 and 161 participants per arm, respectively; planning for 50% gives 270 and 361. For Ointment 2, the corresponding values are 49 and 66 for 100% of the observed effect, 87 and 116 for 75%, and 195 and 261 for 50%.

The pattern illustrates a general principle: smaller effects are harder to distinguish from random variation, so planning to detect a smaller fraction of the observed effect requires more participants. The calculations do not establish that those enrollment targets would be sufficient under a different analysis plan, allocation scheme, outcome variability, or missing-data pattern. The trial's original power target and calculation method are not reported in the registry record.

12. 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 z_1−α/2 = 1.960) and the desired power (z_1−β = 0.842 for 80% and 1.282 for 90%).

Formula

n is the number of participants in each arm, Δ is the difference in means to detect and σ is the common standard deviation.

Worked calculation for this trial

1. Observed difference Δ = -12.960; pooled standard deviation σ = 26.828.
2. n = 2 × (1.96 + 0.842)² × 26.828² / -12.960² = 67.3, rounded up to 68 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
delta <- -12.96                      # observed difference in means
sigma <- 26.8283613500205                     # pooled standard deviation
n_per_arm <- function(power, frac = 1) {
  ceiling(round(2 * (z_a + qnorm(power))^2 * sigma^2 / (delta * frac)^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 (t-based, so very slightly larger)
cat("power.t.test:", round(power.t.test(delta = delta, sd = sigma, power = 0.80)$n, 1), "\n")

# Simulation: exact two-sample t-test using simulated means and variances
set.seed(1246583)
n    <- n_per_arm(0.80)
reps <- 20000
m_diff <- rnorm(reps, delta, sigma * sqrt(2 / n))             # difference in sample means
s2     <- sigma^2 * rchisq(reps, 2 * (n - 1)) / (2 * (n - 1))   # pooled sample variance
tstat  <- m_diff / sqrt(s2 * 2 / n)
cat(sprintf("Simulated power at n = %s per arm: %.3f (%d replicates)\n", format(n, big.mark = ","), mean(abs(tstat) > qt(0.975, 2 * (n - 1))), reps))

Output from running the code

100% of observed effect: n per arm = 68 (80% power), 91 (90% power)
 75% of observed effect: n per arm = 120 (80% power), 161 (90% power)
 50% of observed effect: n per arm = 270 (80% power), 361 (90% power)
power.t.test: 68.2 
Simulated power at n = 68 per arm: 0.796 (20000 replicates)

The simulation draws many sets of group means and variances at the planned sample size and counts how often the two-sample t-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.

13. Multiplicity, Missing Data and Analysis Populations

The registry lists one primary outcome and 19 posted secondary outcomes, with 20 outcome measures recorded in total. Secondary measures include plaque severity at multiple visits, treatment-area severity responses, target plaque area, itch severity, and patient satisfaction. Considering many outcomes or repeated time points can increase the chance of observing a nominally unusual result by chance. In general, multiplicity methods are used to control or otherwise account for this issue.

The registry record does not report whether the original analysis plan adjusted for multiple outcomes, comparisons, or time points. The posted p-values for the primary comparisons are unadjusted. This should be kept in mind when interpreting those values; it does not establish that the sponsor's analysis omitted adjustment. The original multiplicity strategy is not reported in the registry record.

The record describes the full analysis set as randomized participants who received at least one dose of investigational drug. For the primary measure, the number analyzed refers to participants evaluable for that outcome. It does not report the number of randomized participants in each arm, the reasons participants were not evaluable, or how missing outcome values were handled. It is also not reported whether the original analysis used imputation, a model-based approach, or another missing-data method. The effect of missingness on the estimates cannot be determined from the record.

These details matter because analysis population and missing-data decisions can affect the interpretation of a randomized comparison. Randomization is intended to make groups comparable at allocation, but exclusions or unavailable outcomes after allocation may alter the composition of the analyzed groups. The registry's definition and outcome counts do not establish that such bias occurred; they leave insufficient information to assess it.

Finally, the record does not report a protocol or statistical analysis plan, interim analyses, or the original sample-size justification. It is not possible to establish whether the posted outcome definitions and analyses match a prespecified plan. The absence of those details is a limitation in evaluating selective reporting and the analysis process, not evidence that selective reporting occurred.

14. Safety Results

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

Other (non-serious) adverse events

Participants with at least one non-serious event at or above the registry's 2% reporting threshold.

Most frequent non-serious adverse event terms

The serious adverse event figures report 0 affected participants in each group: 2% CP-690,550 Ointment 1, Vehicle 1, 2% CP-690,550 Ointment 2, and Vehicle 2. The corresponding numbers at risk were 23, 13, 25, and 10. These are counts of participants with at least one serious adverse event, not counts of all serious-event episodes. The registry lists no top serious-event terms.

For other adverse events, the record reports 10 affected participants among 23 at risk for Ointment 1, 3 among 13 for Vehicle 1, 9 among 25 for Ointment 2, and 3 among 10 for Vehicle 2. Those figures describe participants with other adverse events as recorded, not event rates per unit of time. The record does not provide further detail about severity, timing, relatedness, or event-specific counts in the registry record.

Deaths are not reported in the registry record; a blank death field should not be interpreted as a confirmed count of zero. Safety counts are descriptive and should be read in the context of the group sizes and the study's duration, which is not reported in the registry record. These figures alone do not establish comparative safety.

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

The results describe mean percent change in target plaque severity at Week 4 for the participants evaluable for that outcome. Ointment 1 had a mean of -53.97, while Vehicle 1 had a mean of -41.01; the unadjusted comparison estimate was -12.96. Ointment 2 had a mean of -24.26, while Vehicle 1 again had a mean of -41.01; the unadjusted comparison estimate was 16.75. The two comparisons point in different directions on the percent-change scale, and both confidence intervals include zero.

These figures do not establish whether either formulation has a clinically meaningful effect. The registry does not report a threshold for clinical importance, and the confidence intervals are compatible with a range of possible mean differences. The unadjusted p-values do not provide a probability that a treatment works or does not work. They are statistical summaries under a null model, not a verdict about clinical benefit.

The results also do not answer every question about the interventions. The posted primary comparisons use Vehicle 1 for both active groups; a direct comparison of the two ointments and a posted comparison of Ointment 2 with Vehicle 2 are not reported. The registry lists additional outcomes, but their results are not included in the registry record for interpretation. The effects on other psoriasis measures, itch, satisfaction, or longer-term outcomes cannot be inferred from the primary endpoint alone.

The study was randomized and double-blind, but the registry record does not report enough detail to assess allocation procedures, treatment duration, missing-data handling, or the full analysis plan. Nor does the record establish how well its participants represent people outside the study. The findings therefore characterize the posted Week 4 data and should not be extended to unreported outcomes, populations, or time periods.

16. Why This Trial Matters Statistically

This trial provides a useful example of why a point estimate should be interpreted together with its uncertainty. The mean differences are -12.96 for Ointment 1 versus Vehicle 1 and 16.75 for Ointment 2 versus Vehicle 1. Their confidence intervals cross zero and span a range of possible values. A reader who focuses only on the signs or magnitudes of the estimates would miss how uncertain those comparisons are.

It also illustrates that multiple active formulations and several vehicle groups do not automatically translate into a single, simple comparison. The primary results use Vehicle 1 as the comparator for both active formulations, while the registry does not report a direct active-versus-active result or the Ointment 2 versus Vehicle 2 result. Clear identification of the comparison is essential for interpreting the estimate.

The registry includes multiple outcome measures and repeated assessment times. Without a reported multiplicity strategy, unadjusted p-values should be understood as applying to individual comparisons rather than as a complete account of error across all outcomes. Missing-data methods and the original analysis plan are also not reported, limiting evaluation of how the reported results were produced.

Finally, the planning illustrations demonstrate how sample-size requirements depend on the effect size selected for planning. They use the observed effects as references, and smaller target effects require more participants per arm. Those illustrations are not the trial's design record and cannot replace a prespecified justification. Together, these points show the importance of separating observed summaries, uncertainty, analysis assumptions, and planning scenarios when reading a clinical trial registry.

17. Limitations

• The posted summary statistics are the only data these results rest on; patient-level data, full protocols and statistical analysis plans are not available.
• Recalculated results are simple, unadjusted calculations from posted summaries. They do not replace the sponsor's prespecified analysis.

The registry record contains limited detail about conduct and analysis. Although it identifies the study as randomized, double-blind, multi-site, and parallel-group, it does not report the randomization method, allocation ratio, masking procedures, treatment schedule, or treatment duration. The arm descriptions are blank, and further formulation details are not reported in the registry record.

The primary endpoint results are available as group summaries and recalculated unadjusted comparisons. The sponsor's original statistical analysis details, including any covariate adjustment, handling of repeated measurements, and missing-data method, are not reported in the registry record. The original multiplicity strategy and sample-size justification are also not reported. This limits the ability to assess whether the posted comparisons reflect the prespecified analysis.

The analysis counts for the primary endpoint are 22, 13, 23, and 9 across the four groups, while enrollment was 71. The record defines who belongs to the full analysis set but does not explain the outcome-specific counts, provide reasons for missing or unevaluable measurements, or describe the participants not represented in each analysis. The potential effect of missingness therefore cannot be assessed.

There are four named groups, but the posted primary contrasts compare both active ointments with Vehicle 1. The reason for this comparator choice is not reported, and results for the other possible group contrasts are not included. The record also lists 19 secondary outcomes but the outcome results and multiplicity handling for those measures are not available in the registry record. No conclusion about them should be inferred from the primary result.

Finally, the record does not provide a clinical-importance threshold for the endpoint or enough information to judge how representative the study population was. These limitations restrict interpretation of the posted Week 4 estimates; they do not, by themselves, demonstrate bias or invalidate the observed data.

18. Related Tutorials

19. Related Statistical Calculators

20. Sources

• ClinicalTrials.gov: CP-690-550 Ointment For Chronic Plaque Psoriasis — NCT01246583.
• Registry record last updated 2021-01-11; status last verified 2020-12.
• Results first posted 2021-01-11.
• Data retrieved from ClinicalTrials.gov on 2026-11-09.
• Group sizes, means, event counts and sponsor-reported p-values are reproduced as posted. Effect estimates, confidence intervals and p-values not attributed to the sponsor are independently calculated from the posted summary statistics.

21. Record Summary

NCT01246583 is a completed phase 2a, multi-site, randomized, double-blind, placebo-controlled, parallel-group study of two CP-690,550 ointment formulations in adults with mild to moderate chronic plaque psoriasis. The registry lists 71 participants enrolled and four groups: 2% CP-690,550 Ointment 1, Vehicle 1, 2% CP-690,550 Ointment 2, and Vehicle 2.

The primary outcome was percent change from baseline in target plaque severity score at Week 4. The two posted unadjusted comparisons against Vehicle 1 have estimates of -12.96 and 16.75, and both confidence intervals include zero. The record lists 20 outcome measures, including 19 posted secondary outcomes. Details of the original sample-size justification, multiplicity strategy, and missing-data methods are not reported in the registry record.