Safety Study of an Adeno-associated Virus Vector for Gene Therapy of Leber's Hereditary Optic Neuropathy: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Safety Study of an Adeno-associated Virus Vector for Gene Therapy of Leber's Hereditary Optic Neuropathy (NCT02161380), a non-randomized phase 1 study. The primary outcome is Number of Treatment Related Adverse Events.

2. Clinical Question

This is principally a safety-focused, early-phase dose-escalation question. The relevant descriptive information is how many participants in each dose group were counted as affected by serious and other adverse events, alongside the duration and completeness of follow-up. Those counts can characterize events recorded during the study, but they cannot by themselves establish that an event was caused by treatment or identify what would have happened to comparable patients without treatment. The registry record does not report a randomized contrast, an adjusted comparison, or a formal treatment-effect estimate.

3. Trial Design

This was a phase 1, open-label, non-randomized, parallel-group dose-escalation study of scAAV2-P1ND4v2 for Leber's hereditary optic neuropathy. It is listed as completed. The registry gives a start date of 2014-07-14 and a primary completion date of 2023-03-31. The planned enrollment was 28. Byron Lam is listed as the sponsor.

The four dose groups were low-dose (1.18x10e9 vg), medium dose (5.81x10e9 vg), high dose (2.40x10e10 vg), and higher dose (1x10e11vg). The arm descriptions specify 200 µL for the low- and medium-dose groups and 100 µL for the high- and higher-dose groups. The registry also describes participants by vision-loss history and severity in the arm descriptions. It does not provide a complete account of how those clinical categories were distributed across all groups.

Open-label means masking was absent: treatment assignment was not concealed from participants or investigators according to the registry. Non-randomized allocation means assignment was not based on random allocation as recorded. These design features matter when interpreting safety observations and any apparent differences across dose groups. Without random allocation and a concurrent control group, group-level differences may reflect characteristics other than dose, and investigators’ judgments about whether events are treatment-related may be influenced by knowledge of treatment.

The record identifies the study model as parallel and states that dose escalation was the study approach. Further operational details, including the rules for moving between dose levels, are not reported in the registry record. The registry’s brief summary states that the objective was to evaluate safety of mitochondrially targeted ND4 gene therapy with the adeno-associated viral vector in appropriate patients. It does not report a protocol-based rationale for the number enrolled, the dose-escalation decision criteria, or a statistical analysis plan.

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 28 participants with G11778A Leber Hereditary Optic Neuropathy (LHON) were enrolled in the study. They were distributed in the following groups: chronic bilateral visual loss \> 12 months (group 1, n=11), acute bilateral visual loss \< 12 months (group 2, n=9), or unilateral visual loss (group 3, n=8). Each participant received a unilateral intravitreal injection. Group 1 was treated with low, medium, high and higher dose, group 2 and 3 were treated with low, medium, or higher dose.

Overall Study

Reasons for not completing this period:

Analysis population for the primary outcome, as defined in the registry: One subject for medium dose was a loss to follow up after month 06. One subject for low dose missed visits for month 12, month 24 and month 36

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 Number of Treatment Related Adverse Events, measured over 3 years.

The primary endpoint is the number of participants with treatment-related adverse events. The registry says an investigator assessed each event’s relationship to the investigational product, and gives a timeframe of 3 years. This is a participant-count endpoint: it concerns whether participants were affected, rather than the total number of separate event episodes. The posted serious and other adverse-event summaries are presented by dose group.

Safety endpoints of this kind are used in early-phase studies to describe adverse events observed during exposure and to inform ongoing evaluation of an intervention. Recording investigator-assessed relatedness adds a judgment about whether an event is considered connected to the investigational product; it is not, by itself, proof of causation. The endpoint title refers to treatment-related events, while the adverse-event summary separately reports serious and other affected-participant counts. These are related safety descriptions, but they should not be treated as interchangeable measures.

The record notes that one medium-dose subject was lost to follow-up after month 06. It also notes that one low-dose subject missed visits at month 12, month 24, and month 36. These observations are important when interpreting a follow-up endpoint because participants with incomplete follow-up may have less opportunity for events to be recorded. The registry record does not describe a method for handling missing endpoint information or specify whether these participants were included in each posted count.

Best-corrected visual acuity is listed as a secondary outcome. The registry record does not post an analysis of that outcome, so the primary safety endpoint should not be read as an efficacy measure.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

The registry record describes a phase 1 dose-escalation study, but it does not report a statistical analysis plan. The primary endpoint is a count of participants with treatment-related adverse events, assessed by the investigator over 3 years. The posted safety summaries distinguish serious adverse events from other adverse events and present affected-participant counts by dose group. No statistical analysis of the primary endpoint is posted; the record lists 0 analyses.

What a participant count captures

A participant count records whether a person experienced an event within the endpoint definition. It is different from an event count, which may count repeated episodes in one person separately. It is also different from a time-to-event analysis, which uses event timing and follow-up duration. The endpoint title specifies the number of participants, and the posted group summaries give counts of participants at risk and affected. The registry record does not report a separate count of all event episodes or an analysis of time to first event.

For a binary outcome, such as whether a participant was affected, a proportion can be used to describe the observed fraction in a group. Such a summary depends on both the event count and the number of participants included. These group summaries are small, particularly for the high-dose group, so an affected participant can noticeably change the descriptive fraction. No uncertainty interval is posted alongside these figures. A formal comparison would need to account for the study design and the limited information in the group counts; the registry does not report such a comparison.

Why dose-group comparisons are limited

Random allocation is one way to make treatment groups more comparable on average. This study is recorded as non-randomized, and its masking is listed as none. Thus, the dose groups should not be interpreted as randomized treatment and control groups. Differences in their observed counts could reflect dose, participant characteristics, clinical history, follow-up, or other factors. The registry record does not report an adjusted model that attempts to account for such factors.

In a dose-escalation study, increasing dose levels can be relevant to safety monitoring, but a numerical ordering of doses does not make the groups exchangeable. The record says the design was dose escalation and identifies four groups, but does not give the escalation rules or explain how participants were assigned to each level. It is therefore not possible to determine from the registry record whether observed group differences were anticipated, prespecified, or assessed using a formal trend analysis.

Investigator assessment and event classification

The primary endpoint includes investigator assessment of the event’s relationship to the investigational product. Relatedness is a clinical judgment and is distinct from simply recording that an event occurred after treatment. Because masking was absent, investigators knew the treatment context; that knowledge can potentially affect event assessment. This is a general methodological consideration, not evidence that any particular assessment in this study was biased. The registry record does not describe an independent adjudication process or the criteria used to assign relatedness.

Serious adverse events and other adverse events are separate categories in the posted safety summary. Seriousness is not the same as treatment relatedness: an event can be serious without being judged related, and an event judged related need not be serious. The registry’s group counts provide serious and other affected-participant counts, while the endpoint describes treatment-related adverse events. The record does not fully explain how these categories map onto one another in the posted results, so one should not assume that the summary counts are equivalent to the primary endpoint.

Follow-up and missing observations

Longitudinal safety monitoring depends on the opportunity to observe and record events over time. A participant who misses visits or is lost to follow-up may have less complete ascertainment than a participant followed throughout the stated timeframe. The record notes one medium-dose subject lost to follow-up after month 06 and one low-dose subject who missed visits at month 12, month 24, and month 36. It does not report whether events were collected outside those visits, how missing data were handled, or whether the affected participants remained in each analysis population.

General statistical explanation: missing outcomes can create bias when the chance that an observation is missing is related to the outcome or to participant characteristics. Different assumptions and methods can produce different estimates. No imputation method, missing-data sensitivity analysis, or other missing-data procedure is reported in the registry record. The posted counts should therefore be read with the follow-up information in mind rather than treated as a complete accounting of every participant’s experience across the full timeframe.

Precision and inference

General statistical explanation: estimates based on a small number of participants are usually less precise than estimates based on more observations. Precision describes how much uncertainty surrounds an estimate, while statistical significance addresses compatibility with a specified null hypothesis under a model. Neither can be assessed from a count alone without an appropriate method and its assumptions. The registry record does not post confidence intervals, p-values, or hypothesis tests for the adverse-event data.

The sample-size assumptions listed with the record concern planning illustrations based on an observed effect, with equal allocation, a two-sided significance level of 0.05, and a normal approximation. Those illustrations are not the trial’s own design justification and are not observed power. The record does not report a protocol-based sample-size justification. Because no efficacy analysis or comparative estimate is posted, the planning illustrations should not be interpreted as evidence that the study had a particular ability to establish a treatment effect.

General statistical explanation: over-dispersion matters when variability in count data exceeds what a simple model assumes; ignoring it can make uncertainty estimates misleading. The registry record does not report a count model, dispersion estimate, or an analysis requiring such a model. This concept therefore does not establish anything about the study’s results; it illustrates why a statistical method must match both the outcome and the study design.

10. Exact Estimates for Each Arm

No two-arm comparison is shown for this trial, but each arm's result can still be summarized with exact interval estimates computed from the posted counts. The Clopper-Pearson interval is exact and conservative; the Wilson interval is a common closer-to-nominal alternative; the Bayesian credible interval uses a uniform Beta(1, 1) prior. For small groups the three can differ noticeably.

R code and output

arm    <- c("Low-dose (1.18x10e9 vg)", "Medium Dose (5.81x10e9 vg)", "High Dose (2.40x10e10 vg)", "Higher Dose (1x10e11vg)")
n      <- c(8, 8, 3, 7)
events <- c(1, 1, 1, 5)
for (i in seq_along(n)) {
  ci <- binom.test(events[i], n[i])$conf.int          # Clopper-Pearson exact interval
  cr <- qbeta(c(0.025, 0.975), 1 + events[i], 1 + n[i] - events[i])   # Bayesian, uniform Beta(1,1) prior
  wi <- (function(x, n) { p <- x / n; z <- qnorm(0.975); d <- 1 + z^2 / n
    c((p + z^2 / (2 * n) - z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d, (p + z^2 / (2 * n) + z * sqrt(p * (1 - p) / n + z^2 / (4 * n^2))) / d) })(events[i], n[i])
  cat(sprintf("ARM|%s|%d|%d|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f|%.1f\n", arm[i], n[i], events[i], 100 * events[i] / n[i],
              100 * ci[1], 100 * ci[2], 100 * wi[1], 100 * wi[2], 100 * cr[1], 100 * cr[2]))
}

ARM  Low-dose (1.18x10e9 vg)  8  1  12.5  0.3  52.7  2.2  47.1  2.8  48.2
ARM  Medium Dose (5.81x10e9 vg)  8  1  12.5  0.3  52.7  2.2  47.1  2.8  48.2
ARM  High Dose (2.40x10e10 vg)  3  1  33.3  0.8  90.6  6.1  79.2  6.8  80.6
ARM  Higher Dose (1x10e11vg)  7  5  71.4  29.0  96.3  35.9  91.8  34.9  91.5

11. Multiplicity, Missing Data and Analysis Populations

The registry record identifies best-corrected visual acuity as a secondary outcome and lists 2 outcome measures, but it does not provide analyses for those outcomes. It lists 0 analyses. The record does not report a multiplicity adjustment, a hierarchy of hypotheses, or a prespecified strategy for interpreting multiple outcomes or comparisons. Without those details, the statistical handling of multiple questions cannot be assessed.

Multiplicity is a general concern when multiple outcomes, groups, time points, or comparisons are tested. Examining many hypotheses can increase the chance of a seemingly notable result arising by chance. An analysis plan may address this by defining a primary question, ordering outcomes, or adjusting inference. These are general methods; the registry record does not state that any particular approach was used in this study. Since no hypothesis tests are posted, no multiplicity-adjusted or unadjusted efficacy conclusion is available.

For missing data, the registry notes one medium-dose subject lost to follow-up after month 06 and one low-dose subject who missed visits at month 12, month 24, and month 36. The primary endpoint timeframe is 3 years. The record does not state how the missing visits affected endpoint status, whether additional follow-up information was collected, or whether the participants were included in the safety summaries. It also does not report imputation, censoring rules, sensitivity analyses, or a missing-data assumption.

The analysis populations are not described in detail. In particular, the registry record does not specify a safety population, an intention-to-treat population, or an evaluable population, and it does not explain how participants with incomplete follow-up were handled. These omissions limit reproducibility and make it difficult to determine whether the posted group counts use consistent inclusion rules. No statistical plan, interim analysis method, or stopping rule is reported in the registry record.

12. 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: visual acuity loss (11.1%).

The serious adverse-event figures are affected-participant counts, not a measure of treatment-relatedness by themselves. The low-dose group lists 1 of 9 participants at risk with a serious adverse event; the medium-dose group lists 1 of 9; the high-dose group lists 0 of 3; and the higher-dose group lists 0 of 7. The registry lists 0 deaths in each group. Other adverse-event counts are listed separately: 3 of 9 in the low-dose group, 3 of 9 in the medium-dose group, 1 of 3 in the high-dose group, and 7 of 7 in the higher-dose group.

The record’s top serious adverse-event term is Visual Acuity Loss, listed at 11.1%. This term-level figure should be read as a separate summary, not as a dose-specific count. The record does not provide enough detail in this summary to connect that term to an individual group or to establish its investigator-assessed relationship to treatment.

These counts are not randomized comparisons. The groups differ in size, and the high-dose group includes 3 participants at risk. The registry does not provide uncertainty intervals or a formal between-group analysis. A zero count in a group means no affected participant was recorded in that group’s posted serious-event summary; it does not establish that the underlying risk is zero. Follow-up limitations also matter: the record notes missed visits and a loss to follow-up, but does not explain their effects on the safety counts.

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

The registry record documents safety observations in a completed, open-label, non-randomized phase 1 dose-escalation study. It reports serious and other adverse-event counts by dose group, with no deaths listed. The results are descriptive records of affected participants; they do not by themselves determine whether the investigational product caused an event. The primary endpoint involves investigator-assessed treatment relatedness, but the summary does not provide event-by-event detail or a formal analysis of that endpoint.

The findings do not establish a causal dose-response pattern. Participants were not randomly allocated, and the dose groups are not like-for-like controls. The groups also have different sizes, and follow-up was incomplete for the participants noted in the record. The registry does not report adjusted comparisons, confidence intervals, or hypothesis tests that would quantify uncertainty or account for design limitations.

The record identifies best-corrected visual acuity as a secondary outcome, but no efficacy analysis is posted. The safety counts therefore do not establish whether visual acuity changed, whether any change was related to the intervention, or how an outcome might compare with a control group. No such comparative conclusion is available from the registry record.

General statistical interpretation: an observed count is not the same as an estimate that applies to a broader population. The extent to which a study’s results generalize depends on how participants were selected, the completeness of outcome ascertainment, and the suitability of the analysis. The registry record does not provide all of those details. The appropriate conclusion is limited to describing the posted observations in the enrolled dose groups and recognizing the uncertainty created by the design and incomplete follow-up.

Likewise, the planning illustrations should not be read as evidence of observed power or as proof that the study could answer a clinical efficacy question. They are described as illustrations based on an observed effect and specified planning assumptions, rather than the trial’s own design justification. The record does not report the analysis needed to interpret an efficacy effect. These results should therefore be understood as a registry-based safety summary, not as a treatment recommendation or a definitive assessment of benefit.

14. Why This Trial Matters Statistically

This study is statistically informative as an example of how design shapes interpretation. A phase 1 dose-escalation study has a safety-oriented objective, and dose groups can describe what was observed at each level. However, non-randomized allocation and absent masking constrain comparisons. The group counts should not be treated as if dose were the only difference between participants or as if one dose group were a control for another.

The endpoint also illustrates the distinction between an event count, an affected-participant count, and an investigator judgment about relatedness. These answer different questions. The registry’s primary endpoint concerns participants with treatment-related adverse events, while the posted safety summary separates serious and other affected-participant counts. Clear definitions and analysis populations are important for understanding how such summaries relate to each other; further detail is not reported in the registry record.

Small groups make uncertainty especially relevant. A count can describe the observed experience, but without an uncertainty measure it cannot show how precisely that experience estimates a broader risk. The registry does not provide confidence intervals or a formal comparison. The follow-up notes also emphasize that safety ascertainment depends on continued observation and that missing visits may complicate interpretation.

Finally, the study record separates a safety objective from the listed secondary visual-acuity outcome, but does not post an efficacy analysis. This distinction prevents a safety summary from being mistaken for evidence about efficacy. Statistically, the key lesson is to match the conclusion to the design, endpoint, observed data, and analysis actually recorded. Here, the posted evidence supports descriptive statements about safety counts, with substantial limits on causal and comparative interpretation.

15. 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.

Several trial-specific limitations restrict interpretation. The study was open-label and non-randomized, with no like-for-like control comparison. Dose groups therefore cannot be assumed to be comparable, and differences in counts cannot be attributed to dose alone. The registry record does not describe a method for adjusting for participant or clinical-history differences.

The sizes of the posted groups vary: 9 participants were at risk in each of the low- and medium-dose groups, 3 in the high-dose group, and 7 in the higher-dose group. These counts are small, particularly for the high-dose group, and the record does not report uncertainty intervals for the safety summaries. It also does not provide a formal analysis comparing dose groups.

The record notes one medium-dose subject lost to follow-up after month 06 and one low-dose subject who missed visits at month 12, month 24, and month 36. It does not explain how these observations affected endpoint ascertainment or analysis populations. The endpoint timeframe is 3 years, but the record does not report a missing-data method or sensitivity analysis.

The registry gives limited detail about event classification. It does not report the criteria for investigator-assessed relatedness, whether serious events were independently adjudicated, or how serious and other event categories map to the treatment-related primary endpoint. The top serious term, Visual Acuity Loss, is listed at 11.1%, without further dose-specific detail in that summary.

Finally, no statistical analysis plan, sample-size justification, interim analysis method, or efficacy analysis is reported in the registry record. Best-corrected visual acuity is listed as a secondary outcome, but no results analysis is posted. These gaps limit assessment of prespecification, statistical precision, and the scope of conclusions that can be drawn.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Safety Study of an Adeno-associated Virus Vector for Gene Therapy of Leber's Hereditary Optic Neuropathy — NCT02161380.
• Registry record last updated 2025-06-05; status last verified 2025-05.
• Results first posted 2024-08-07.
• 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.

19. Record Summary

The registry describes NCT02161380 as a completed phase 1, open-label, non-randomized, parallel dose-escalation study of scAAV2-P1ND4v2 for Leber's hereditary optic neuropathy caused by the G11778A mutation in mitochondrial DNA. Enrollment was 28. Byron Lam is listed as sponsor. The study objective was to evaluate safety.

The primary endpoint was the number of participants with treatment-related adverse events over 3 years, assessed by the investigator. The safety summary reports affected-participant counts for serious and other adverse events across low-, medium-, high-, and higher-dose groups, and lists 0 deaths in each group. Best-corrected visual acuity is a secondary outcome, but the registry record lists 0 analyses.

The registry notes a medium-dose loss to follow-up after month 06 and missed low-dose visits at month 12, month 24, and month 36. It does not report a statistical analysis plan, formal dose-group comparisons, confidence intervals, or an efficacy analysis. The posted safety counts are descriptive and should be interpreted in light of the non-randomized design, group sizes, and incomplete follow-up.