Clinical Protocol SeCore, uTYPE and 3500 Dx System: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Clinical Protocol SeCore, uTYPE and 3500 Dx System (NCT01285427), a registered phase not stated study. The primary outcome is All SeCore® Kits,Primary Analysis of Concordance Rate (Clopper-Pearson CI).

2. Clinical Question

3. Trial Design

The registry identifies this study as “Clinical Protocol SeCore, uTYPE and 3500 Dx System.” Its official title describes clinical performance testing of the SeCore Sequencing Kit and 3500xl Dx Genetic Analyzer against SSP UniTray. The listed condition is Human Leukocyte Antigens (HLA), and the listed sponsor is Life Technologies Corporation. The registry lists enrollment as 300 and the status as completed.

The recorded study start is 2011-01, and primary completion is recorded as 2011-06. The primary outcome timeframe is 10 weeks. The record does not explain how that timeframe relates to the start and completion dates, or give further details about the schedule of testing or data collection.

The arm description refers to DNA loci and the SeCore versus SSP UniTray platforms, but does not provide further arm-level details. The registry explicitly indicates that this was not a randomized comparison, that allocation is not stated, and that the arms are not a like-for-like control comparison. Consequently, the record does not establish a randomized allocation process or describe an equivalent control design. Further details about how specimens, alleles, or testing runs were assigned to platforms are not reported in the registry record.

The record lists nine outcome measures and no statistical analysis records. It does not report a protocol rationale for the enrollment, a sample-size justification, or details of masking, handling of repeats, or planned analysis populations. Those omissions mean the registry alone does not give a full account of the design and analysis decisions behind the clinical performance comparison.

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

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 All SeCore® Kits,Primary Analysis of Concordance Rate (Clopper-Pearson CI), measured over 10 weeks.

The primary outcome is the percentage of concordant alleles across all SeCore kits. Concordance describes agreement between results being compared: an allele counted as concordant is one for which the compared determinations agree according to the study’s definition. The specific operational definition of agreement, including how ambiguous or repeated determinations were handled, is not reported in the registry record.

A concordance percentage is used to describe how often compared results agree, rather than to measure a patient health outcome. In this study, the stated comparator is SSP UniTray with UniMatch interpretation software, while the SeCore system is paired with uTYPE interpretation software. The endpoint therefore addresses agreement between platform results in the clinical performance testing described by the record. It does not by itself establish why any disagreements occurred or which result should be considered correct.

The primary outcome description specifies an exact two-sided 90% confidence interval using the Clopper-Pearson method, and the timeframe is 10 weeks. A confidence interval communicates uncertainty around an estimated concordance rate. The registry states a study purpose of showing 95% concordance with 90% confidence, but does not report the observed percentage, its interval limits, or the denominator used for the calculation. Without those results and the endpoint’s detailed counting rules, the precision and numerical performance cannot be independently assessed from the registry record.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

The registry describes a percentage outcome and an exact confidence interval. These methods answer related but distinct questions: the percentage summarizes observed agreement, while the interval conveys uncertainty around that summary. The record names the Clopper-Pearson method for the interval, but does not provide the underlying counts needed to reproduce it.

What does a concordance percentage represent?

In general, a concordance percentage is formed by identifying the comparison units that meet a defined agreement rule and relating that count to the units eligible for assessment. The result is a descriptive rate. Its meaning depends on what counts as a unit, how agreement is defined, and what results enter the denominator. In this trial, the outcome is described as a percentage of concordant alleles across all SeCore kits. The registry record does not give the precise counting rules, numerator, denominator, or treatment of ambiguous and repeated results.

A concordance measure is not interchangeable with accuracy unless an appropriate reference standard and its role are clearly specified. Agreement can be high even when both methods share the same error, and disagreement alone does not identify which method is correct. The registry names SSP UniTray with UniMatch as the comparator, but the detailed adjudication or reference procedure is not reported. Accordingly, the endpoint should be read as a comparison of agreement, not as a complete account of correctness.

What does the Clopper-Pearson interval add?

In general, the Clopper-Pearson approach is an exact method for constructing an interval for a binomial proportion. It uses the observed count and denominator to produce confidence limits, rather than relying on a simple normal approximation. “Exact” describes the interval procedure’s coverage property under its binomial model; it does not mean the study’s measurements are free from error or that the interval captures every source of uncertainty.

The primary outcome description specifies a two-sided 90% interval. In general, a confidence interval is a method that, under its assumptions and repeated use, covers the underlying quantity at the stated rate. It is not a probability statement that the fixed true concordance value lies within a particular calculated interval. A narrower interval indicates greater statistical precision, while a wider one indicates less precision. The actual interval cannot be interpreted because its limits are not reported in the registry record.

For a binomial interval to be meaningful, the relevant observations need to correspond to the units being counted and the modeling assumptions need to be appropriate. If multiple alleles come from the same specimen or another form of clustering exists, those observations may not be statistically independent. Dependence can make a calculation that treats every allele as independent appear more precise than warranted. This is a general consideration, not a claim that such dependence was present or ignored in this study: the registry does not report the data structure or any adjustment for clustering.

How should the stated objective be read?

The brief summary describes an intention to show 95% concordance with 90% confidence. The primary outcome separately identifies a 90% confidence interval. These statements set out the intended performance question, but the registry does not provide a decision rule explaining exactly how the interval was to be judged against the objective. It also does not provide the interval limits or an analysis conclusion. No conclusion about whether the objective was achieved can be drawn from the stated aim alone.

The record lists no statistical analysis records. It does identify the interval method, but does not report additional details such as a prespecified hypothesis, treatment of multiple outcomes, subgroup analyses, or adjustment for the comparison structure. These omissions make it impossible to distinguish a complete prespecified analysis plan from the limited method description attached to the primary outcome.

What do planning illustrations mean?

Any sample-size illustrations associated with this record should be understood as planning calculations, not as observed power. The stated illustration assumptions use the observed effect, a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation; the effect to detect is expressed as a fraction of the observed effect. These are assumptions for a planning exercise, not evidence about the design choices made by the sponsor. The registry record does not report a sample-size justification or enough numerical outcome information to assess the illustrations as a reconstruction of the trial’s design.

In general, power is a property of a specified design and analysis under assumed effects and variability. It does not describe how likely a completed study’s result is to be true. A planning calculation based on an observed effect is especially different from a prospective design justification, because the observed effect is known only after data have been collected. The listed assumptions therefore do not establish that the trial was planned around those assumptions or that its analysis followed them.

10. Multiplicity, Missing Data and Analysis Populations

The registry lists nine outcome measures, while it identifies one primary outcome as the concordance rate across all SeCore kits. It does not report how the other outcomes relate to the primary question, whether they were confirmatory or exploratory, or whether any multiplicity procedure was planned. When several outcomes are examined, the chance of at least one apparently notable result can increase if each is assessed separately. In general, a prespecified hierarchy or adjustment can address that issue, but no such approach is reported in the registry record.

The record lists no statistical analysis records. Beyond the primary Clopper-Pearson interval description, it does not report a full statistical analysis plan, decision threshold, subgroup strategy, or the handling of comparisons across kits or loci. The number and structure of such comparisons are not detailed. It is therefore not possible to determine how selective reporting or multiple assessments were addressed.

Missing-data handling is also not reported. The registry does not say how unavailable, invalid, ambiguous, or repeated allele determinations were treated, nor whether any exclusions occurred. These details matter for a concordance percentage because the denominator and the inclusion rule determine what the estimate describes. Enrollment of 300 does not reveal how many allele results contributed to the primary outcome.

The analysis population is not described. The record does not specify whether every assessed unit was included, whether any units were excluded under predefined rules, or how incomplete platform pairs were handled. These are open reporting gaps rather than evidence that any particular procedure was or was not used. Without a stated population and missing-data approach, readers cannot establish whether the posted endpoint would represent all eligible assessments or only a subset.

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

The registry record establishes that the study set out to compare SeCore sequencing with uTYPE interpretation against SSP UniTray with UniMatch interpretation, using concordance as the primary measure. It gives the stated objective of 95% concordance with 90% confidence and names an exact two-sided confidence interval method. These details describe the question and a statistical approach; they do not constitute the numerical result.

The registry does not report the observed concordance percentage, the confidence limits, or the count of concordant alleles and denominator. As a result, the magnitude of agreement and its precision cannot be described from this record. It is also not possible to determine whether the stated objective was met. A completed status indicates the recorded study status, not that a particular outcome threshold was reached.

Even with a reported concordance rate, the interpretation would depend on the agreement definition, the comparison units, the handling of missing or repeated results, and the relevance of the comparator. The record does not provide those details. It also states that the comparison was not randomized, allocation is not stated, and the arms are not a like-for-like control comparison. The result should therefore not be given a stronger causal interpretation than the design supports.

Concordance is an agreement outcome, not a patient health outcome. It cannot by itself establish clinical benefit, identify the source of disagreement, or demonstrate that either platform is correct in every instance. The registry record does not report a reference-standard analysis or enough method detail to assess those questions. Nor does it report a complete safety analysis that would support a broader clinical assessment.

The defensible conclusion is narrow: the record describes a clinical performance comparison with a concordance endpoint and a specified interval method, but leaves the primary numerical result unreported. Any conclusion about the actual level of agreement or the success of the stated objective would require result information that is not reported in the registry record.

12. Why This Trial Matters Statistically

This study is statistically notable for using concordance as its central performance measure. Agreement rates are common summaries when two methods or platforms are compared, but their interpretation depends on the definition of a match and on the units contributing to the rate. The record identifies the outcome as a percentage of concordant alleles and names the systems being compared, while leaving the operational counting details unreported.

The specified Clopper-Pearson interval makes uncertainty part of the stated primary analysis rather than relying only on a point estimate. That is useful in principle: a rate without an interval can conceal substantial uncertainty. Here, however, the registry does not report either the observed rate or the interval limits. The statistical method is described more fully than the numerical result, so readers can identify the intended approach but cannot judge its outcome or precision.

The record also highlights why study structure matters alongside an endpoint. The comparison is explicitly not randomized, allocation is not stated, and the arms are not a like-for-like control comparison. Statistical descriptions of agreement do not remove these design limitations. Readers need to distinguish a measured degree of concordance from evidence that would require a different comparison structure.

Finally, the record illustrates the limits of registration information for understanding a completed analysis. It lists nine outcomes and no analysis records, and it does not describe multiplicity, missing-data handling, or analysis populations. Those are not minor technical details when the primary estimate depends on what observations are counted. The record supplies a useful outline of the statistical question, but not enough information to evaluate the numerical finding or all choices affecting it.

13. 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 most consequential limitation for interpreting the primary endpoint is the absence of the numerical concordance result. The registry record does not report the percentage, confidence-interval limits, numerator, or denominator. Although it names an exact two-sided 90% Clopper-Pearson interval, that method description cannot replace the result or establish whether the objective was achieved.

The record gives limited detail about the comparison. It states that the study was not randomized, that allocation is not stated, and that the arms are not a like-for-like control comparison. The arm description refers to DNA loci and the SeCore versus SSP UniTray platforms, but does not explain how assessments were organized or paired. The comparator is identified, but the record does not explain how discordant findings were resolved or whether an independent reference was used.

The endpoint’s counting rules are not reported. The record does not specify how concordance was defined, how repeated or ambiguous calls were handled, or what constituted an evaluable allele. It also does not explain whether observations were clustered within specimens or whether the analysis accounted for any dependence. These are relevant because they affect both the interpretation of the rate and the precision of its interval.

Further limitations include the absence of a stated analysis population, missing-data rules, multiplicity plan, and detailed statistical analysis plan. The enrollment entry of 300 does not identify the number of allele results analyzed. Although the registry lists nine outcome measures, it gives no analysis records. These reporting gaps do not prove that procedures were absent from the trial, but they prevent readers from assessing them using the registry record alone.

14. Related Tutorials

15. Related Statistical Calculators

16. Sources

• ClinicalTrials.gov: Clinical Protocol SeCore, uTYPE and 3500 Dx System — NCT01285427.
• Registry record last updated 2014-04-17; status last verified 2014-04.
• Results first posted 2014-04-17.
• 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.

17. Record Summary

The registry record describes a completed clinical performance study titled “Clinical Protocol SeCore, uTYPE and 3500 Dx System.” Its official title identifies testing of the SeCore Sequencing Kit and 3500xl Dx Genetic Analyzer against SSP UniTray. The listed condition is Human Leukocyte Antigens (HLA), the sponsor is Life Technologies Corporation, and enrollment is listed as 300.

The record gives a study start of 2011-01 and primary completion of 2011-06. Its primary outcome is the percentage of concordant alleles across all SeCore kits, with a 10 weeks timeframe and an exact two-sided 90% Clopper-Pearson confidence interval. The stated study aim is 95% concordance with 90% confidence.

The comparison is identified as nonrandomized, allocation is not stated, and the arms are not described as a like-for-like control comparison. Although nine outcome measures are listed, no statistical analysis records are listed. The numerical primary result and its interval are not reported in the registry record.