Development of Vitamin D as a Therapy for Breast Cancer - Phase 2: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Development of Vitamin D as a Therapy for Breast Cancer - Phase 2 (NCT00656019), a non-randomized phase 2 study. The primary outcome is Correlation of Vitamin D Levels, Prognostic Factors, and Gene Expression Profile in Patients With Breast Cancer.

2. Clinical Question

3. Trial Design

This was a phase 2, parallel, non-randomized study sponsored by Stanford University. The registry record lists enrollment of 63 participants, a start date of 2008-04, primary completion in 2010-08, and a completed status. Masking was listed as none. These details describe the registered design and conduct, but do not supply the allocation process beyond identifying it as non-randomized.

The groups were named according to vitamin D levels: normal, low-normal, low, and very low. The normal-level group received no additional vitamin D. The low-normal group was assigned 2000 IU orally per day, the low group 4000 IU per day, and the very-low group 6000 IU per day. The registry record does not report the duration of dosing, the specific thresholds used to define the vitamin D categories, or how participants entered each group.

The study addressed two related aims in its brief description: whether vitamin D levels were associated with characteristics of breast cancer at diagnosis, and whether a short course of vitamin D in women with low levels changed gene expression. The registered primary outcome described an expression pattern in breast core biopsy specimens and specified a timeframe of 10 days to 4 weeks post diagnosis. The registry lists one outcome measure but no analysis records. A detailed statistical analysis plan, the number analyzed for the primary outcome, and numerical primary-outcome results are not reported in the registry record.

Non-randomized allocation matters when interpreting group comparisons. Differences between groups may reflect their starting vitamin D levels or other characteristics, as well as any effects associated with dosing. The registered parallel model indicates separate groups, but does not by itself establish that they were comparable at baseline.

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:

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 Correlation of Vitamin D Levels, Prognostic Factors, and Gene Expression Profile in Patients With Breast Cancer, measured over 10 days to 4 weeks post diagnosis..

The primary outcome was the percentage of participants with a discernible pattern for expression of the set of 40 evaluated genes. The registry description places this outcome within an assessment of serum vitamin D levels, classic prognostic and predictive factors for breast cancer, and gene expression in breast core biopsy specimens. Its stated timeframe was 10 days to 4 weeks post diagnosis.

A proportion is useful for describing how common a defined outcome is within a group. In this case, the endpoint’s interpretation depends on what counted as a discernible pattern and how the expression pattern was determined. Those operational details are not reported in the registry record. Nor does the record give the observed percentage, a confidence interval, or a statistical test for the primary outcome.

The endpoint is a measure of gene-expression pattern, not a direct measure of clinical benefit or long-term breast-cancer outcomes. The study description also refers to associations with prognostic and predictive factors. The registered outcome does not, by itself, establish that vitamin D caused a change in gene expression or that a gene-expression pattern predicts a later clinical outcome. The posted results do not include a numerical endpoint estimate with which to judge the size or precision of any association.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

What does a percentage endpoint describe?

In general, a percentage or proportion summarizes the share of participants who meet a defined outcome. It is interpretable only when the outcome definition and the denominator are clear. For this study, the registered outcome was the percentage with a discernible pattern for expression of the set of 40 evaluated genes. The registry record does not report the observed percentage, the number of participants contributing to that endpoint, or the operational rule for classifying a pattern as discernible.

A point estimate alone would not convey its precision. In general, a confidence interval gives a range of values compatible with the observed data under the statistical method used. A narrow interval indicates more precision than a wide one, while neither interval width nor an estimate can be evaluated because no primary-outcome estimate or interval is reported in the registry record.

What does the non-randomized design imply?

In general, random assignment helps balance measured and unmeasured baseline characteristics across study groups, on average. This study is listed as non-randomized, and its groups are described by vitamin D level. The comparison between levels may therefore be affected by differences that existed before dosing. In a non-randomized study, an association between group membership and an outcome does not by itself establish that the assigned dose caused the outcome.

Adjustment for measured characteristics can sometimes address some group differences, but it cannot guarantee removal of confounding, particularly when relevant characteristics are unmeasured or poorly recorded. Whether any adjustment was planned or performed is not reported in the registry record. No specific statistical model or set of adjustment variables is reported.

How should gene-expression findings be read?

The primary outcome concerns a discernible expression pattern across a set of 40 evaluated genes. In general, an analysis that evaluates many genes or multiple related outcomes raises questions about multiplicity: the more separate statistical claims considered, the greater the chance that some may appear notable by chance. The registry record does not explain whether the genes were analyzed individually, how the expression pattern was defined, or whether any multiplicity procedure was planned. It would therefore be inappropriate to assume either that multiple testing occurred or that it was addressed.

The endpoint also involves a classification step: expression data are described as having or not having a discernible pattern. In general, the reliability of a binary classification depends on the measurement process and the rule used to classify observations. The registry record does not report those details, so the reproducibility and measurement uncertainty of the endpoint cannot be assessed from the posted information.

What do the planning assumptions mean?

The registry’s sample-size assumptions describe a planning illustration based on an observed effect, with a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation. They also describe planning for a stated fraction of the observed effect. Such calculations are hypothetical planning exercises; they are not observed power and do not establish what the completed study found. The record does not report a trial-specific sample-size justification or numerical planning results in the registry record for this analysis.

In general, a significance level is a threshold used in a statistical decision procedure, while a two-sided procedure considers departures in either direction. A normal approximation is a simplifying method whose suitability depends on the data and design. Equal allocation is a planning assumption for the illustrated comparison, not a description of the actual distribution of participants among this study’s vitamin D groups. The registry record does not report a primary-outcome analysis that would permit assessment of these assumptions.

What can be inferred from the posted analysis information?

The registry lists one outcome measure and no analysis records. An outcome definition is not the same as an analysis result: without an estimate, uncertainty measure, or stated statistical method, readers cannot assess the direction or precision of the primary result. The registry record also does not report whether the primary endpoint was analyzed in all enrolled participants, in a subset, or under another analysis population definition.

For safety outcomes, the listed serious adverse-event counts are descriptive counts. In general, counts should be interpreted alongside the relevant at-risk denominator and the period over which events were collected. The registry record does not provide a detailed safety-analysis method or specify the adverse-event collection period in the registry record. The zero serious adverse-event entries should not be mistaken for a numerical result on the gene-expression endpoint.

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("Normal Vitamin D Levels", "Low-normal Vitamin D Levels", "Low Vitamin D Levels", "Very-low Vitamin D Levels")
n      <- c(15, 18, 11, 4)
events <- c(0, 0, 0, 0)
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  Normal Vitamin D Levels  15  0  0.0  0.0  21.8  0.0  20.4  0.2  20.6
ARM  Low-normal Vitamin D Levels  18  0  0.0  0.0  18.5  -0.0  17.6  0.1  17.6
ARM  Low Vitamin D Levels  11  0  0.0  0.0  28.5  -0.0  25.9  0.2  26.5
ARM  Very-low Vitamin D Levels  4  0  0.0  0.0  60.2  0.0  49.0  0.5  52.2

11. Multiplicity, Missing Data and Analysis Populations

The registry lists one primary outcome measure, but the study description also refers to associations between vitamin D levels, breast-cancer prognostic and predictive factors, and gene expression. It does not report a complete list of planned statistical comparisons, a hierarchy of outcomes, or a method for handling multiplicity. Since the primary endpoint concerns a set of 40 genes, it is relevant to know whether the analysis treated the set as a single pattern or included separate gene-level tests. That distinction and any adjustment for multiple testing are not reported in the registry record.

The record lists no analysis records and does not report the number of participants with primary-outcome data. It also does not explain whether observations were missing, how missing measurements were handled, or whether any sensitivity analyses were conducted. Absence of these details in the registry record does not establish that data were missing; it means the completeness and handling of endpoint data cannot be evaluated from the posted information.

Analysis populations are likewise not described. The record does not say whether the primary outcome was assessed among all enrolled participants, only participants who received vitamin D, or another defined group. Enrollment of 63 does not establish that all 63 contributed to the primary endpoint. Without a reported endpoint denominator and analysis population, the representativeness and precision of any unreported estimate cannot be judged.

These omissions matter because decisions about which outcomes, comparisons, and participants to include can affect interpretation. The registry record does not report a detailed statistical analysis plan, so it is not possible to distinguish prespecified analyses from other analyses or to assess whether missingness or multiple testing influenced the reported findings.

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 0% reporting threshold.

The registry lists serious adverse-event counts separately for the vitamin D level groups. It reports 0 affected among 29 at risk in Vitamin D Normal, 0 among 19 in Vitamin D Low-normal, 0 among 11 in Vitamin D Low, and 0 among 4 in Vitamin D Very Low. No top serious adverse-event terms are listed. Death counts are not reported in the registry record.

These are serious adverse-event entries, not a complete account of every possible adverse event. A zero in the affected count means that the registry reports no serious adverse-event cases for that group in this entry; it does not establish that no other adverse events occurred. The registry record does not describe the safety observation period or provide further detail about event ascertainment.

The at-risk counts are safety denominators and should not be assumed to be the numbers analyzed for the primary gene-expression endpoint. Nor do the safety entries answer whether vitamin D levels were associated with prognostic factors or gene expression. The non-randomized design and the small number at risk in the very-low group also mean that these counts alone cannot establish comparative safety across doses.

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

The registry record establishes that this phase 2 study examined vitamin D levels in women diagnosed with breast cancer and described vitamin D dosing for participants in lower-level groups. It also defines a primary endpoint based on the percentage of participants with a discernible gene-expression pattern. These details clarify the scientific question and the way the outcome was framed.

The record does not report the numerical primary result or an analysis of it. It therefore does not show the estimated proportion with the expression pattern, the strength or direction of an association, or the precision of an estimate. The absence of a posted result is not evidence that the study found no association or no change. It means the registry record does not allow readers to evaluate that question quantitatively.

The design cannot establish a causal effect from a simple comparison of the groups. Allocation was non-randomized, and the groups were defined by vitamin D level. Differences in baseline characteristics could be related to both group membership and outcomes. The record does not report analyses that would quantify or address these potential differences.

The outcome is also limited in scope. A gene-expression pattern assessed 10 days to 4 weeks post diagnosis is not itself a measure of long-term clinical outcomes. The registry record does not report whether the gene-expression finding predicts later outcomes, nor does it provide evidence about that relationship. The listed serious adverse-event counts are a separate safety record and do not fill the gap in the primary endpoint results.

Accordingly, the posted information supports a careful account of the study’s design, groups, and endpoint definition, but not a judgment about the size, certainty, or clinical significance of a primary outcome effect. Any stronger interpretation would require results and methods not reported in the registry record.

14. Why This Trial Matters Statistically

This study illustrates why a registry entry can be useful even when it does not include enough information to judge an outcome result. It records a specific question about vitamin D levels, breast-cancer characteristics, and gene expression, alongside the intended endpoint and its timeframe. That context helps readers distinguish the study’s aims from conclusions that would require numerical results.

It also illustrates the interpretive importance of allocation. The groups were defined by vitamin D levels and the study was non-randomized. A statistical association across such groups can be informative as a description, but it does not alone separate the role of dosing from the role of differences between participants. A careful reading keeps those interpretations distinct.

The endpoint raises a further general issue: a gene-expression outcome based on a set of genes depends on how the pattern is defined and how multiple comparisons are handled. Those details affect how reproducible and precise the result would be. The registry record does not report the needed analysis details or a numerical primary result, so the scientific question cannot be resolved from this entry alone.

Finally, the safety entries show why outcomes need to be read separately. The posted serious adverse-event counts describe one aspect of safety, while the primary endpoint concerns gene expression. Neither outcome can stand in for the other. Taken together, the record is most useful as a description of the study’s design and reporting gaps, rather than as a basis for estimating an effect.

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 primary limitation for interpretation is that the registry record does not report a numerical result for the primary endpoint. It provides no group-specific percentages, uncertainty intervals, p-values, or analysis method. The number contributing to the endpoint is also not reported, so the total enrollment of 63 cannot be treated as the endpoint denominator.

The non-randomized allocation is an additional design limitation for causal interpretation. Vitamin D-level groups may differ in ways related to their outcome, and the registry record does not report a statistical adjustment strategy. The definitions of the vitamin D categories and the process by which participants entered each group are not reported in the registry record.

The endpoint description does not give the rule for identifying a discernible pattern across the set of 40 evaluated genes, the measurement details, or the approach to any gene-level comparisons. The registry record also does not report multiplicity procedures, missing-data handling, analysis populations, or a detailed statistical analysis plan. These omissions limit assessment of reproducibility, bias, and precision.

The stated timeframe is 10 days to 4 weeks post diagnosis, but the timing and completeness of measurements are not described. The dosing duration is also not reported in the registry record. The safety denominators differ across the listed groups, including 4 at risk in the very-low group; those safety counts do not establish the endpoint sample sizes. These limits constrain interpretation of both group comparisons and the scope of the posted safety information.

16. Related Tutorials

17. Related Statistical Calculators

18. Sources

• ClinicalTrials.gov: Development of Vitamin D as a Therapy for Breast Cancer - Phase 2 — NCT00656019.
• Registry record last updated 2017-12-02; status last verified 2017-10.
• Results first posted 2017-12-02.
• 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

NCT00656019 is a completed phase 2, parallel, non-randomized study sponsored by Stanford University. The registry lists enrollment of 63, no masking, a start date of 2008-04, and primary completion in 2010-08. The study concerned vitamin D levels and breast-cancer characteristics in women diagnosed with breast cancer.

The primary outcome was the percentage of participants with a discernible expression pattern for a set of 40 evaluated genes, with a stated timeframe of 10 days to 4 weeks post diagnosis. Vitamin D doses were listed for the low-normal, low, and very-low groups; the normal-level group received no additional vitamin D. The registry record does not report a numerical primary-outcome result or analysis records. Serious adverse-event counts were listed as 0 for each group, with group-specific at-risk counts of 29, 19, 11, and 4. Death counts are not reported in the registry record.