Vaccine Therapy in Treating Patients With Chronic Phase Chronic Myelogenous Leukemia: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Vaccine Therapy in Treating Patients With Chronic Phase Chronic Myelogenous Leukemia (NCT00428077), a na phase 2 study. The primary outcome is Number of Participants With One-log Decrease in Circulation Breakpoint Cluster Region-Abelson Murine Leukemia(BCR-ABL) Transcripts That Persists for at Least Three Months During the 1-year Treatment Period..

2. Clinical Question

This is therefore a question about a molecular response observed during vaccine treatment, not a randomized test of vaccine treatment against an alternative. The endpoint defines a change in a laboratory measure and a requirement that the decrease persist; it is not itself a direct measure of symptoms, survival, or quality of life. Although the trial title and summary describe studying vaccine therapy, the registry record does not report a primary endpoint result. The listed enrollment of 4 is the number enrolled, not necessarily the number who completed treatment, had all scheduled measurements, or qualified for the per-protocol analysis. Those counts are not reported in the registry record.

3. Trial Design

This was a phase II, single-group pilot trial sponsored by OHSU Knight Cancer Institute. The official title describes a multi-center study of a synthetic tumor-specific breakpoint peptide vaccine in patients with chronic myeloid leukemia and minimal residual disease. The registry lists the condition as leukemia, and the brief summary identifies chronic phase chronic myelogenous leukemia. Enrollment was 4. The study began in 2005-10, had a primary completion date of 2009-04, and is recorded as terminated.

Allocation was listed as not applicable, the model was single-group, and masking was none. These design features mean the registry does not describe a randomized or masked comparison. There is no concurrent control arm for separating changes during treatment from changes that might occur for other reasons. As a pilot phase II study, it is useful to read its stated purpose and endpoint as a clinical research question, while keeping the small recorded enrollment and lack of comparator central to any statistical interpretation.

The intervention list includes a BCR-ABL peptide vaccine and reverse transcriptase-polymerase chain reaction. The primary outcome concerns a persistent decrease in circulating BCR-ABL transcripts during a 1-year treatment period, with measurement described every 3 months. The registry also lists safety of a vaccine containing native and synthetic CML peptides over 1 year as a secondary outcome. It records 6 outcome measures overall, but does not report the full analysis plan or outcome findings for those measures. The reason the trial was terminated, the recruitment history, and the protocol’s operational details are not reported in the registry record.

Because the design has one group, observed changes cannot be interpreted as a randomized treatment effect relative to usual care, no treatment, or another therapy. The registry’s enrollment count alone also does not establish how many participants contributed to each outcome. Missingness, withdrawals, and the analysis population for the safety outcome are not described in sufficient detail to reconstruct those denominators beyond the adverse-event counts that are posted.

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

Analysis population for the primary outcome, as defined in the registry: Per protocol.

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 Participants With One-log Decrease in Circulation Breakpoint Cluster Region-Abelson Murine Leukemia(BCR-ABL) Transcripts That Persists for at Least Three Months During the 1-year Treatment Period., measured over Every 3 months for the duration of the 1-year treatment period. ..

The primary endpoint counts participants with a one-log decrease in circulating BCR-ABL transcripts that persists for at least three months during the 1-year treatment period. The registry says transcript levels were assessed by RT-PCR every 3 months. This endpoint combines a threshold change in a molecular marker with a duration requirement: a decrease must be observed and persist, rather than being a transient measurement alone. The registry labels the measure as a number of participants and specifies the per-protocol population.

As a general statistical point, a binary endpoint reduces each participant’s outcome to whether the stated criterion was met. That can make a response count straightforward to interpret, but it discards information about the amount and timing of changes that do not satisfy the rule. The registry does not give further detail about how transcript values were processed, how a one-log decrease was determined from measurements, or how missing scheduled tests were handled. Those endpoint implementation details are not reported in the registry record.

A molecular endpoint may be used to describe biological response, but it should not be treated as interchangeable with a clinical outcome. The registry’s primary endpoint is specifically about BCR-ABL transcripts; it does not report whether a participant experienced a clinical benefit or how the result relates to another outcome. Most importantly, the registry does not report the number meeting the endpoint, so the posted information does not establish the observed response frequency.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

For a binary outcome, each participant is classified according to whether the defined event occurred. In this trial, the event was a one-log decrease in circulating BCR-ABL transcripts that persisted for at least three months during the 1-year treatment period. The registry identifies the result as a number of participants, rather than reporting a continuous transcript change as the primary endpoint. To interpret such an outcome, readers would ordinarily need both the event count and the number of participants analyzed. The registry does not report the primary event count or the per-protocol denominator.

What does a confidence interval mean?

In general, a confidence interval describes the statistical uncertainty around an estimate under the method used to construct it. A narrow interval indicates greater precision under that method, while a wide interval indicates less precision. It does not guarantee that the estimate is free of bias or that the study design supports a causal conclusion. No confidence interval for the primary endpoint is reported in the registry record, so its precision cannot be assessed from the posted primary results.

Why does the single-group design matter?

In general, a comparison group can help distinguish outcomes observed under an intervention from outcomes that might have occurred over the same period without it, subject to the quality of the design and analysis. This study is listed as single-group, with allocation not applicable and no masking. There is no randomized control arm in the registry record. A change from a participant’s earlier measurement, if one were available, would remain a within-person observation and would not by itself provide a randomized estimate of the vaccine’s effect. The primary result itself is not reported.

How should the per-protocol population be read?

In general, a per-protocol analysis concerns participants considered to have followed the study requirements relevant to the analysis. The exact criteria depend on the protocol. Here, the primary endpoint population is labeled per protocol, but the protocol criteria and the number analyzed are not reported in the registry record. Enrollment of 4 therefore cannot be assumed to equal the primary analysis population. If participants were excluded from that population, the reasons and their outcome data would be important to understanding possible selection effects, but those details are not posted.

What does the sample-size illustration tell readers?

In general, sample-size planning asks how many participants a future study might need for a specified statistical objective under stated assumptions. The planning illustration associated with this record assumes a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation; the target effect is described as a stated fraction of the observed effect. These are planning assumptions, not evidence that this single-group trial used a two-arm design. The record’s design is single-group, so those assumptions do not describe its allocation or a randomized comparison.

Such illustrations are not observed power. They do not measure the probability that the completed study has demonstrated an effect, and they do not replace a reported outcome estimate. The record does not report the primary endpoint result from which a reader could assess the observed effect. Sample-size illustrations tied to an observed effect should therefore be understood as planning exercises, not as trial findings or justification for the enrolled sample. The trial’s enrollment of 4 is the recorded enrollment, not a power calculation.

Why can over-dispersion matter?

In general, over-dispersion means that outcome variability is greater than a statistical model assumes. When it is present and not accounted for, estimated uncertainty may be too small, making results appear more precise than they are. This issue is especially relevant to count outcomes modeled with assumptions about variability. The primary outcome in this record is a participant count for a binary event, and the registry does not post a model-based analysis or dispersion estimate. Over-dispersion is a general concept, not a reported feature of this trial’s analysis.

What can the posted analysis support?

The record lists 6 outcome measures and 0 analyses. It does not report statistical methods for the primary outcome, a hypothesis test, an effect estimate, or an uncertainty interval. General statistical methods can describe what would be needed to interpret a binary endpoint, but they cannot fill these reporting gaps. The available information supports describing the design, stated endpoint, enrollment, and posted safety counts. It does not support reconstructing a primary result or estimating a treatment contrast.

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("Breakpoint Cluster Region-Abelson Murine Leukemia(")
n      <- c(4)
events <- c(4)
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  Breakpoint Cluster Region-Abelson Murine Leukemia(  4  4  100.0  39.8  100.0  51.0  100.0  47.8  99.5

11. Multiplicity, Missing Data and Analysis Populations

The registry lists 6 outcome measures, including the primary endpoint and a secondary safety outcome. When a study evaluates multiple outcomes or makes multiple statistical comparisons, the chance of at least one apparently notable result can increase if each is assessed separately. As a general statistical practice, researchers may specify a primary outcome in advance and define how secondary outcomes and repeated tests will be interpreted. The registry identifies a primary outcome but does not report a multiplicity strategy, a statistical analysis plan, or analyses for the listed outcomes. Those details are not reported in the registry record.

The record lists 0 analyses. It does not provide a primary endpoint event count, a participant-level analysis denominator, an estimate, or an uncertainty interval. No imputation or missing-data method is reported. The primary endpoint is defined for a per-protocol population, but the size and selection criteria for that population are absent. It is therefore not possible to determine whether all enrolled participants had outcome data, how incomplete RT-PCR measurements were handled, or whether the endpoint was assessed consistently at each scheduled measurement.

These reporting gaps matter because incomplete outcome data can affect both the denominator and the interpretation of an event count. In general, excluding participants with missing measurements may change the population represented by an estimate, while assumptions used to handle missing observations can affect uncertainty. The registry does not report withdrawals, completion, or reasons for missing measurements, so the direction or extent of any such influence cannot be assessed. The primary outcome result itself is not reported, and no statistical conclusion about the endpoint can be recovered from enrollment alone.

12. 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 5% reporting threshold.

Most frequent serious adverse event terms

Most frequent non-serious adverse event terms

Serious events with the highest arm-level rate: acute viral gastroenteritis (25.0%).

The registry lists 4 participants at risk and 1 affected participant for the serious adverse event grouping labeled Breakpoint Cluster Region-Abelson Murine Leukemia (BCR-ABL). It also identifies Acute Viral Gastroenteritis as a top serious adverse event term at 25.0%. These entries describe the posted counts and term frequency; they are not a comparison between treatment groups, because the trial was single-group.

A serious adverse event count is not, by itself, evidence that the intervention caused the event. Causal attribution requires context about timing, clinical assessment, and other possible explanations. The registry does not report enough detail to assess attribution or provide a comparative risk estimate. The figure is based on a very small recorded group, so each participant’s event status has considerable influence on the description. The posted percentage should not be read as a precise estimate for a wider population.

The registry does not report a death count; the death field is not populated. It also does not describe the complete event profile or provide further detail about event timing and duration. The secondary outcome refers to safety over 1 year of treatment, but the record does not state whether all participants completed that period. The serious adverse event figures are therefore best read as limited descriptive reporting for this trial, not as a definitive assessment of safety.

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

The trial’s stated purpose was to study vaccine therapy in patients with chronic phase chronic myelogenous leukemia. Its primary endpoint was a persistent decrease in circulating BCR-ABL transcripts during the 1-year treatment period. The registry provides the definition of that endpoint, the measurement schedule, the per-protocol population label, and an enrollment count of 4. It does not report how many participants met the endpoint. The posted record therefore does not establish the observed molecular response in this trial.

Even with a reported response count, this design would need careful interpretation. A single-group study does not supply a randomized control comparison, so it cannot by itself separate an observed change during treatment from changes that might have occurred for other reasons. The record also lists masking as none. The absence of a comparator and the small enrollment limit what could be learned about comparative effects and precision. These are design constraints, not evidence for or against an intervention.

The endpoint is a molecular measure, not a direct statement about symptoms, survival, or another clinical outcome. The registry does not report a link between the transcript endpoint and those outcomes. Nor does it provide the analysis methods, the number included in the per-protocol population, or the handling of incomplete measurements. Those missing details prevent assessment of the endpoint estimate, its uncertainty, and the representativeness of the analyzed participants.

The safety entries provide limited descriptive information: the registry reports 1 affected participant among 4 at risk for the listed adverse-event grouping, and records Acute Viral Gastroenteritis at 25.0% among top serious adverse event terms. These data do not establish whether an event was caused by treatment or how event occurrence compares with another group. The trial status is terminated, but the reason is not reported in the registry record.

Accordingly, the record documents a research question and a small pilot study design, but its posted results are insufficient to answer the primary question quantitatively. The interpretation should remain limited to what is actually recorded, without treating an absent primary outcome result as either a positive or a negative finding.

14. Why This Trial Matters Statistically

This trial is statistically instructive because it makes the distinction between a well-defined outcome question and a reported outcome result especially clear. The registry specifies a binary molecular endpoint: participants are counted if a one-log decrease in circulating BCR-ABL transcripts persists for at least three months during the 1-year treatment period. It also identifies the measurement method and schedule. Yet the number meeting that definition is not reported. A detailed endpoint definition cannot substitute for the outcome data needed to estimate a response frequency.

The record also illustrates how design determines the kind of inference a study can support. This phase II pilot was single-group, had no masking, and enrolled 4 participants. Without a randomized comparator, the study cannot provide a like-for-like estimate of how outcomes differ under vaccine treatment and an alternative. This remains true even when a study measures a marker repeatedly: repeated measurement can describe a course over time, but it does not create a control group.

Small enrollment makes transparent reporting of denominators and individual outcome status particularly important. When each participant can substantially affect a count, readers need to know who was assessed, who contributed data, and how incomplete observations were handled. The registry does not report the primary per-protocol denominator, missing-data approach, or primary result. The safety counts offer an example of why denominators and context matter: the reported figures are descriptive, and they cannot be treated as comparative or precise population estimates.

Finally, planning calculations should be kept distinct from observed findings. Sample-size illustrations based on an assumed fraction of an observed effect are planning exercises, not observed power and not evidence of what happened in this trial. With no primary effect estimate posted in the registry record, those calculations cannot resolve the missing outcome result. The statistical value of this record lies in showing why design, outcome reporting, denominators, and uncertainty all matter when interpreting a clinical trial.

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.

The main trial-specific limitation is the absence of a reported primary endpoint result. Although the endpoint is clearly named and its timeframe and measurement schedule are stated, the number of participants meeting the criterion is not posted. The per-protocol population is identified, but its size is not reported. Consequently, neither the response frequency nor its statistical uncertainty can be assessed.

Enrollment was 4, and the study had a single-group design. The available record therefore offers no randomized comparator and cannot support a comparative treatment-effect estimate. Masking was listed as none. The record does not describe procedures that might reduce measurement or assessment bias, nor does it give enough information to evaluate how the intervention was administered across participants.

Important operational details are not reported in the registry record: the reason for termination, participant completion and withdrawal counts, missing RT-PCR measurements, the per-protocol criteria, and the handling of incomplete outcome data. The registry also does not report the statistical analysis plan, multiplicity approach, or analyses for the 6 listed outcome measures. These omissions limit assessment of prespecification and analysis choices.

The safety information is sparse and has no comparison group. Although the registry posts adverse-event counts and a serious adverse event term, it does not provide sufficient context to determine attribution, timing, or whether the 1-year safety period was completed by all participants. The record’s enrollment and posted counts describe this small trial; they do not establish precise event frequencies in a broader population. The registry does not report additional clinical outcomes that would connect the molecular endpoint to patient-centered outcomes.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Vaccine Therapy in Treating Patients With Chronic Phase Chronic Myelogenous Leukemia — NCT00428077.
• Registry record last updated 2011-09-02; status last verified 2011-08.
• Results first posted 2011-08-31.
• 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

This phase II pilot trial studied a BCR-ABL peptide vaccine in chronic phase chronic myelogenous leukemia, with RT-PCR listed for measuring circulating BCR-ABL transcripts. It was single-group, unmasked, and enrolled 4 participants. The primary endpoint was a one-log transcript decrease persisting for at least three months during the 1-year treatment period, assessed every 3 months in a per-protocol population.

The registry records the study as terminated, with a start date of 2005-10 and primary completion date of 2009-04. It lists 6 outcome measures and 0 analyses. The primary endpoint result, per-protocol denominator, and statistical analysis methods are not reported in the registry record. Safety entries include 1 affected participant among 4 at risk for the listed grouping and Acute Viral Gastroenteritis at 25.0% as a top serious adverse event term. The single-group design and limited posted results do not support a randomized treatment comparison.