Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of ISIS-APO(a)Rx in Participants With High Lipoprotein(a): Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of ISIS-APO(a)Rx in Participants With High Lipoprotein(a) (NCT02160899), a randomized phase 2 study. The primary outcome is Percent Change From Baseline in Lipoprotein Lp(a) Plasma Concentration at Day 85/Day 99.

2. Clinical Question

This is a question about a measured laboratory outcome during the trial’s treatment period, not about clinical events or long-term outcomes. The record identifies safety, tolerability, pharmacokinetics, and pharmacodynamics as the study’s purposes. The posted primary result concerns pharmacodynamics: the change in plasma Lp(a) concentration. It does not by itself address whether a difference in that measure leads to a difference in health outcomes.

3. Trial Design

The registry describes a randomized, double-blind, placebo-controlled, parallel-group Phase 2 study. The trial was marked completed, with an enrollment of 64. The record lists the study start as 2014-06 and primary completion as 2015-11. The intervention was ISIS-APO(a)Rx, compared with placebo, in participants with elevated lipoprotein(a).

Dose titration was built into the recorded treatment schedules. In both cohorts, the ISIS-APO(a)Rx schedules listed 100 mg on Days 1, 8, 15, and 22, 200 mg on Days 29, 36, 43, and 50, and 300 mg on Days 57, 64, 71, and 78, with down-titration possible. Placebo was listed on Days 1, 8, 15, 22, 29, 36, 43, 50, 57, 64, 71, and 78. The record gives these schedules separately for Cohort A and Cohort B.

Posted primary-outcome results are split across six groups: placebo and two dose categories in each cohort. The outcome description says results are for evaluable participants and defines the Per-Protocol Set by receipt of at least 9 doses during the 12-week treatment period and the absence of significant protocol deviations expected to affect efficacy assessments. The record does not report the reason for the cohort structure or the allocation procedure used to assign participants among the groups.

The original sample-size justification, the trial’s prespecified statistical analysis plan, and any planned interim analyses are not reported in the registry record. The planning figures accompanying the recalculated comparison are separate illustrations based on the observed effect; they do not establish the assumptions used to design or conduct the trial.

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: A total of 86 participants were screened for the study and 64 participants were randomized into Cohort A and Cohort B and received study treatment. Two participants in Cohort B did not complete the study treatment but completed the post-treatment follow-up.

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: The Per-Protocol Set included the subset of the Full Analysis Set who received at least 9 doses of Study Drug within the 12-week treatment period and who had no significant protocol deviations that would have been expected to affect efficacy assessments. Day 85/Day 99 result is defined as the result at Day 85 or Day 99.

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 Set included all randomized participants who received at least one dose of study drug.

Only the first 6 of 7 groups are shown.

6. Primary Endpoint

The registry lists the primary outcome as Percent Change From Baseline in Lipoprotein Lp(a) Plasma Concentration at Day 85/Day 99, measured over Day 85/Day 99.

The primary endpoint is percent change from baseline in plasma Lp(a) concentration at Day 85/Day 99. It is a continuous measure: each participant’s result reflects a change in a laboratory concentration, and the posted group summaries report the mean and standard deviation. The endpoint description says that the results are for evaluable participants in the Per-Protocol Set.

Percent change puts the observed movement in concentration on a relative scale rather than reporting only an absolute concentration difference. In general, continuous outcomes can retain information about the magnitude of individual measurements and allow group means and their variability to be summarized. That makes the outcome suitable for describing the average change over the trial’s treatment period.

The registry record does not fully state how the Day 85/Day 99 result was constructed: its description ends after saying that the result is defined as the result. Details such as which visit was used when both measurements were available, how missing measurements were handled, or the exact calculation of percent change are not reported in the registry record. The endpoint is a biomarker measure; clinical outcomes and longer-term follow-up are not part of the posted primary result.

7. Results Posted in the Registry

• Cohort A: ISIS-APO(a)Rx >= 2000 mg: mean -70.00 versus -3.70 on control; difference -66.30 (95% CI -76.20 to -56.40), standardized effect d = -4.00; z-test p = <0.001.

8. Statistical Interpretation

9. Statistical Methods Explained

The primary measure is continuous, so its group summaries are means and standard deviations. A mean describes the group’s average percent change; a standard deviation describes how spread out participant results are around that average. Neither quantity alone expresses the uncertainty in the difference between two group means. The recalculated comparison therefore reports a mean difference and an interval, alongside a p-value.

What does the mean difference represent?

The recalculated contrast compares Cohort A ISIS-APO(a)Rx at or above 2000 mg with Cohort A placebo. The posted means are -70.0 and -3.7, respectively, and the recalculated mean difference is -66.3. The negative direction follows the order used for the comparison: the active group mean is lower than the placebo group mean on the percent-change scale. This is an unadjusted comparison based on the posted summary statistics. It does not control for covariates or other possible differences between participants.

The reported pooled standard deviation for this contrast is 16.58, and the standardized difference is -3.998. A standardized difference expresses the contrast relative to the within-group variability, which can help describe effect magnitude on a scale that is not tied to the endpoint’s units. It is not a clinical threshold, and its meaning depends on the population, measurement, and variability in this study. The reported standard errors for the two group means are 2.687 and 4.277. A standard error describes uncertainty in an estimated mean; it is distinct from the standard deviation, which describes participant-to-participant spread.

How should the p-values be read?

A p-value describes how compatible the observed data are with a statistical null model, under the assumptions of the chosen test. It does not give the probability that the null hypothesis is true, and it does not measure the size or clinical importance of an effect. The recalculated p-value for the Cohort A higher-dose comparison is < 0.001. The registry reports p <.001 for each of its two Cohort A ANOVA comparisons and p = 0.044 for its Cohort B Exact Wilcoxon Rank Sum Test comparison.

ANOVA is a method for comparing group means under its assumptions. The Exact Wilcoxon Rank Sum Test is a rank-based method that compares the distributions of observations rather than directly estimating a difference in means. The registry’s use of different named methods for the listed comparisons matters when interpreting their p-values: the Cohort B p-value does not represent the same type of mean-difference calculation as the recalculated Cohort A estimate.

Why does variability matter?

Variation among individual measurements affects how precisely a group mean and a between-group contrast can be estimated. Over-dispersion, in general, means that observed variability is greater than a model expects. If it is not accounted for, uncertainty can be understated. The registry record does not report an over-dispersion assessment or explain whether any variance adjustment was used in the sponsor’s analyses. The reported standard deviations indicate variability in the posted outcome groups, but they are not enough to reconstruct all details of those analyses.

The recalculation is explicitly unadjusted and uses the posted summary statistics for the two selected groups. It does not reproduce the full analysis dataset, account for any stratification, or resolve how the Per-Protocol Set was formed. The record’s description of that set includes receipt of at least 9 doses and no significant protocol deviations expected to affect efficacy assessments. Selection into a per-protocol population can affect which participants contribute to an outcome summary; the registry record does not provide enough detail to assess that process fully.

The posted analyses cover three pairwise comparisons, but the record does not report whether the analysis plan specified a hierarchy or a correction for multiple comparisons. When several statistical tests are conducted, the chance of at least one small p-value can increase in general. Whether that issue was addressed in the trial’s analysis is not reported in the registry record. The listed p-values should therefore be read as the values reported for those individual comparisons, without assuming an unreported multiplicity procedure.

10. Confidence Intervals and Precision

The recalculated Cohort A comparison gives a mean difference of -66.3, with an interval from -76.2 to -56.4. An interval conveys a range of values compatible with the estimate under the calculation’s assumptions; it is more informative about precision than the point estimate alone. The interval is fairly far from zero in the direction of the negative difference, but the range also shows that the exact size of the contrast is uncertain. The confidence level for this interval is not reported in the registry record.

Precision depends on both the spread of participant outcomes and the number of observations contributing to the estimate. For the recalculated contrast, the posted outcome group sizes are 26 for Cohort A placebo and 21 for Cohort A at or above 2000 mg. The pooled standard deviation is 16.58. These details help explain the uncertainty in the contrast, but they do not remove limitations arising from the trial’s design, population, or analysis procedures.

The other group summaries have much smaller sample sizes: the below-2000-mg Cohort A group has 3 evaluable participants and the Cohort B placebo group has 2. The Cohort B at-or-above-2000-mg group has 8. A mean based on a small group can be sensitive to individual observations, and the posted record does not give confidence intervals for each group mean. No primary-outcome mean or standard deviation is available for the Cohort B below-2000-mg group because its evaluable sample size is 0.

The interval and p-value address sampling uncertainty under statistical assumptions; they do not capture every source of uncertainty, such as missing analysis details or limits to generalizability. The sponsor’s reported analyses do not include posted effect estimates or intervals, so their precision cannot be evaluated from the reported p-values 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 display relates hypothetical group sizes to fractions of the observed Cohort A mean difference for ISIS-APO(a)Rx at or above 2000 mg versus placebo. It is a planning illustration based on the observed effect, not the sample-size justification used to design this trial. The trial’s original design assumptions are not reported in the registry record.

The figures are participants per arm, not total participants across both arms and not total events. The stated assumptions are a two-sided significance level of 0.05, equal allocation between the two arms, and a normal approximation. The effect to detect is set to the stated fraction of the observed effect. For 100% of the observed effect, the display lists 1 participant per arm for 80% power and 2 participants per arm for 90% power. For 75% of the observed effect, it lists 2 participants per arm for 80% power and 3 participants per arm for 90% power. For 50% of the observed effect, it lists 4 participants per arm for 80% power and 6 participants per arm for 90% power.

The 80% power column describes the hypothetical group size at which the planning calculation would have an 80% chance of detecting the specified effect if its assumptions held. The 90% column describes the corresponding calculation for a 90% chance. Smaller effects need more participants because they are harder to distinguish from random variation. The displayed figures are not observed power: they do not measure the probability that the completed trial detected an effect, nor do they establish that the original trial was adequately sized.

The record’s planning assumptions apply to this particular recalculated continuous-outcome comparison. They should not be generalized to other dose groups or outcomes, and the unusually large observed effect used as the starting point can produce small illustrative group sizes.

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 = -66.300; pooled standard deviation σ = 16.583.
2. n = 2 × (1.96 + 0.842)² × 16.583² / -66.300² = 1.0, rounded up to 1 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 <- -66.3                      # observed difference in means
sigma <- 16.5834254603806                     # 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(2160899)
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 = 1 (80% power), 2 (90% power)
 75% of observed effect: n per arm = 2 (80% power), 3 (90% power)
 50% of observed effect: n per arm = 4 (80% power), 6 (90% power)
power.t.test: 2.4 
Simulated power at n = 1 per arm: NA (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. Analyses Reported by the Sponsor

The registry reports three sponsor analyses: ANOVA for Cohort A placebo versus ISIS-APO(a)Rx below 2000 mg, ANOVA for Cohort A placebo versus ISIS-APO(a)Rx at or above 2000 mg, and an Exact Wilcoxon Rank Sum Test for Cohort B placebo versus ISIS-APO(a)Rx at or above 2000 mg. The corresponding reported p-values are <.001, <.001, and 0.044. The analyses are labeled as superiority comparisons in the record.

The recalculated Cohort A higher-dose comparison is a simple, unadjusted mean-difference calculation from the posted summary statistics. It gives a mean difference of -66.3, an interval from -76.2 to -56.4, and p < 0.001. The registry’s own ANOVA result for that comparison also reports p <.001. The recalculation provides an effect estimate and interval that are not posted for the sponsor analysis; it does not replace the sponsor’s analysis or reproduce its model. Where a recalculated result and the sponsor’s own analysis differ, the sponsor’s analysis takes precedence. No discrepancy is flagged for this comparison.

The Cohort B sponsor analysis uses a rank-sum test, whereas the recalculation concerns Cohort A means. These results therefore answer different statistical comparisons and should not be treated as interchangeable. Details such as covariate adjustment, multiplicity handling, and the full sponsor analysis plan are not reported in the registry record.

14. Multiplicity, Missing Data and Analysis Populations

The registry lists three analyses of the primary outcome. Two compare Cohort A placebo with separate ISIS-APO(a)Rx dose categories using ANOVA; the third compares Cohort B placebo with the at-or-above-2000-mg group using an Exact Wilcoxon Rank Sum Test. The record reports p-values for these comparisons but does not report whether they were prespecified as a family of tests, placed in a testing hierarchy, or adjusted for multiplicity. It is therefore not possible to determine from the registry record whether the reported p-values were intended to control a family-wise error rate or another multiplicity criterion.

The primary outcome description identifies the Per-Protocol Set as the analysis population. It includes participants in the Full Analysis Set who received at least 9 doses during the 12-week treatment period and had no significant protocol deviations expected to affect efficacy assessments. The record does not report the membership of the Full Analysis Set, the number excluded from the Per-Protocol Set, or the reasons for individual exclusions. It also does not report a separate intention-to-treat analysis of the primary outcome.

The primary outcome description says that the Day 85/Day 99 result is defined as the result, but the definition is incomplete in the registry record. Specific rules for choosing or combining visits, handling missing measurements, and analyzing incomplete participant data are not reported. There are no posted secondary outcomes in the record. Thus, the available primary-outcome results provide group summaries and named comparison methods, but not a complete account of the analysis population and missing-data procedures.

In general, prespecification and transparent reporting of multiplicity and missing-data methods help readers distinguish planned confirmatory tests from exploratory comparisons and understand how incomplete observations may affect estimates. The registry record does not provide enough information to assess those features for this trial.

15. Safety Results

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

Deaths

Other (non-serious) adverse events

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

Most frequent serious adverse event terms

Most frequent non-serious adverse event terms

Serious events with the highest arm-level rate: myocardial infarction (33.3%), angina pectoris (25.0%).

The serious adverse event figures are reported separately by cohort and treatment group. In Cohort A, the serious-event count is 0 among 26 participants at risk in placebo, 2 among 4 at risk in the ISIS-APO(a)Rx group below 2000 mg, and 0 among 21 at risk in the group at or above 2000 mg. In Cohort B, the corresponding figures are 1 among 3 at risk for placebo, 0 among 2 at risk below 2000 mg, and 0 among 8 at risk at or above 2000 mg. The record reports 0 deaths in every listed group.

These are descriptive counts, not adjusted comparisons of safety risk. The group sizes are small, particularly for the Cohort A below-2000-mg group and both Cohort B groups. A zero count in a group does not show that an event is impossible or rule out uncommon events. The registry also lists myocardial infarction at 33.3% and angina pectoris at 25.0% among the top serious adverse event terms, but does not identify those percentages by treatment group in the information.

The number at risk for safety reporting is not always the same as the evaluable outcome sample size. For example, Cohort A placebo has 26 participants at risk for safety and 26 in the primary outcome results, while Cohort B placebo has 3 at risk for safety and 2 in the primary outcome results. The record does not explain the differences in analysis populations.

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

The posted primary outcome is a measure of change in plasma Lp(a) concentration at Day 85/Day 99. Its group summaries describe mean percent changes during the study period, and the recalculated Cohort A comparison estimates a difference between the at-or-above-2000-mg group and placebo. These results are evidence about the measured biomarker in the participants included in the reported outcome analysis.

The outcome is not a clinical event endpoint. The record does not report whether changes in Lp(a) were associated with changes in symptoms, cardiovascular events, survival, or other health outcomes. It also does not provide long-term follow-up results. The trial’s stated purposes include safety, tolerability, pharmacokinetics, and pharmacodynamics, but the primary result cannot answer every one of those questions.

A large estimated difference and a small p-value do not establish clinical importance. The interpretation of a biomarker change as clinically meaningful requires evidence beyond the statistical comparison, and that evidence is not reported in the registry record. Nor can these results be used to make a treatment recommendation. They describe what was observed in this trial’s specific groups and outcome population.

The group sizes, especially for the lower-dose categories and Cohort B placebo, are limited. The endpoint is described as per-protocol, and details about missing measurements, multiplicity, the full statistical plan, and the complete endpoint calculation are not reported. Those limitations matter when judging how stable or broadly applicable the observed estimates may be. The results are best read as a short-term, trial-specific description rather than a definitive account of effects on clinical outcomes or effects in populations not represented by these participants.

17. Why This Trial Matters Statistically

This trial is statistically informative because it illustrates how a continuous biomarker outcome can be reported as a group mean, standard deviation, and between-group contrast. The recalculated Cohort A higher-dose comparison includes both an estimate and an interval, making the magnitude and uncertainty of the difference more visible than a p-value alone. The registry’s own analyses show that the record also reports comparisons using more than one statistical method.

At the same time, the differing group sizes make clear why an overall enrollment figure does not describe the precision of every group estimate. The outcome summaries include 3 participants in the Cohort A lower-dose category, 2 in Cohort B placebo, and no evaluable participants in the Cohort B lower-dose category. Such unevenness limits the strength of conclusions that can be drawn for some comparisons, even when a test result is reported.

The record also highlights the value of complete reporting. A clear endpoint definition, analysis population accounting, missing-data rules, and multiplicity plan would help readers understand how the estimates were produced and how to interpret several comparisons together. The registry record does not report those details fully. In general, statistical interpretation depends not only on the numerical result but also on the population analyzed, the design, the assumptions, and the scope of the outcome.

Finally, the sample-size illustrations show how planning calculations depend on the assumed effect size and chosen power target. Because these illustrations use the observed effect, they should not be mistaken for the trial’s original design rationale or a measure of observed power. Separating such planning examples from the actual trial design is important for sound statistical reading.

18. 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 primary outcome definition in the registry record is incomplete. Although it names percent change from baseline in plasma Lp(a) concentration at Day 85/Day 99 and identifies an evaluable Per-Protocol Set, it does not fully explain how the visit result was selected or calculated. Missing-data rules and the handling of participants without an evaluable measurement are not reported.

The outcome group sizes are uneven, with very small numbers in some groups and no evaluable participants in the Cohort B group below 2000 mg. These groups cannot support equally stable estimates, and their summaries should not be compared as if they had equal precision. The primary outcome population is per-protocol, but the registry does not report enough information to assess exclusions from the Full Analysis Set or the effect of protocol deviations on the analysis.

The record does not report the original sample-size justification, the prespecified analysis plan, interim analyses, multiplicity procedures, or whether the sponsor’s analyses used covariate adjustment. The reported comparison methods and p-values do not supply all the detail needed to reproduce the sponsor analyses. The confidence level for the recalculated interval is also not reported in the registry record.

Follow-up for the primary endpoint is at Day 85/Day 99, and no secondary outcomes are posted. The result therefore does not address longer-term changes or clinical outcomes. Safety figures are descriptive and based on small group sizes; the registry does not provide comparative safety estimates adjusted for exposure or other factors. These limitations restrict the conclusions to the specific posted measurements and analyses.

19. Related Tutorials

20. Related Statistical Calculators

21. Sources

• ClinicalTrials.gov: Safety, Tolerability, Pharmacokinetics, and Pharmacodynamics of ISIS-APO(a)Rx in Participants With High Lipoprotein(a) — NCT02160899.
• Registry record last updated 2019-12-20; status last verified 2019-12.
• Results first posted 2019-12-20.
• 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.

22. Record Summary

The registry describes a completed, randomized, double-blind, placebo-controlled, parallel-group Phase 2 study of ISIS-APO(a)Rx in participants with elevated lipoprotein(a). Enrollment was 64. The posted primary outcome is percent change from baseline in plasma Lp(a) concentration at Day 85/Day 99 in an evaluable Per-Protocol Set.

For Cohort A, the mean change was -3.7 with placebo, -44.5 with ISIS-APO(a)Rx below 2000 mg, and -70.0 with ISIS-APO(a)Rx at or above 2000 mg. The recalculated unadjusted mean difference for the higher-dose group versus placebo was -66.3, with an interval from -76.2 to -56.4 and p < 0.001. The registry also reports two ANOVA comparisons in Cohort A and an Exact Wilcoxon Rank Sum Test comparison in Cohort B.

Several group sizes are small, and the Cohort B lower-dose group has no evaluable primary-outcome participants. Details of the complete analysis plan, missing-data methods, multiplicity handling, and the original sample-size justification are not reported in the registry record. The posted results concern a short-term biomarker outcome and do not establish clinical outcomes.