Performance of Nucleic Acid Amplification Tests for the Detection of NG and CT: Complete Statistical Analysis

1. Trial at a Glance

This page covers the registry results for Performance of Nucleic Acid Amplification Tests for the Detection of NG and CT (NCT02870101), a na na study. The primary outcome is Number of Participants With Nucleic Acid Amplification Test (NAAT) 1 Index Test Results Relative to Anatomic Site Infection Status (ASIS) Reference Results for Neisseria Gonorrhoeae (NG) in Pharynx.

2. Clinical Question

3. Trial Design

This completed study evaluated diagnostic test platforms rather than comparing assigned medical treatments. The registry describes one group and lists allocation as not applicable. It also lists masking as none. These features mean the record does not describe a randomized, masked, treatment-control design. The study sponsor was Duke University.

The study title and record concern the performance of nucleic acid amplification tests for detecting NG and CT in extragenital sites. The arm description says swabs were collected from the pharynx and rectum, and the three tests were evaluated using participant samples. The primary outcome focuses on NAAT 1 results for NG in the pharynx, compared with ASIS reference results derived from NAAT 2 and NAAT 3.

The registry lists enrollment of 2767. In the participant-flow information cited by the primary outcome description, 2598 participants completed the overall study. Eight participants with incomplete test results were excluded from that outcome. The record gives a timeframe of one day for the primary outcome. Study start is listed as 2017-04-10, primary completion as 2018-03-12, and overall status as completed.

Design details beyond these registry fields are not reported in the registry record. In particular, the record does not state a randomized allocation scheme, a masking procedure, or a treatment-control comparison. The intervention labels identify three diagnostic tests, but the arm description available in the record is truncated after naming them. It therefore does not support further detail about test procedures or how samples were processed.

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: Of the 2598 participants who completed the overall study per the Participant Flow module, 8 participants had incomplete test results and were excluded from this outcome.

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: Participants who completed the study.

6. Primary Endpoint

The registry lists the primary outcome as Number of Participants With Nucleic Acid Amplification Test (NAAT) 1 Index Test Results Relative to Anatomic Site Infection Status (ASIS) Reference Results for Neisseria Gonorrhoeae (NG) in Pharynx, measured over One day.

The primary outcome counts participants according to NAAT 1 index-test results relative to anatomic site infection status (ASIS) reference results for NG in the pharynx. NAAT 1 categories include negative, positive, and no result. ASIS categories include negative, positive, indeterminate, and invalid. The reference classification is defined as the combination of NAAT 2 and NAAT 3 index-test results.

This kind of endpoint is used to describe how an index test classifies samples compared with a specified reference classification. In general, comparing positive and negative classifications can help characterize agreement and identify discordant results. The inclusion of no-result, indeterminate, and invalid categories is also important: these outcomes do not simply represent a positive or negative test classification and can affect how a diagnostic comparison is interpreted.

The registry names the measure as a number of participants, but the numerical counts for the result categories are not reported in the registry record. Sensitivity, specificity, predictive values, agreement measures, or confidence intervals for this primary endpoint are also not reported in the registry record. The endpoint description alone therefore establishes what was to be counted and compared, but does not show the observed distribution or quantify diagnostic performance.

7. Why No Re-analysis Is Shown

8. Statistical Interpretation

9. Statistical Methods Explained

The registry describes an outcome based on participant counts, with binary or categorical test-result information. The primary outcome is not a single numerical measurement such as a laboratory concentration. It classifies participants by the relationship between an index test and a reference result. The index test is NAAT 1 for NG in the pharynx; the reference is ASIS, based on the combination of NAAT 2 and NAAT 3 results.

What a diagnostic comparison counts

General explanation: when a diagnostic test is compared with a reference classification, results can be arranged by the index-test category and reference category. For example, positive index results can be considered alongside positive and negative reference results, and the same can be done for negative index results. The pattern of these counts helps describe agreement and disagreement. In this study, the categories are not limited to positive and negative: NAAT 1 also has a no-result category, while ASIS includes indeterminate and invalid categories. Those categories should be retained and interpreted explicitly rather than silently treated as ordinary negative results.

The registry record does not report the actual category counts for the primary outcome. It therefore does not support reconstructing a diagnostic accuracy measure. General explanation: sensitivity and specificity require counts defined against a reference classification, while predictive values depend on the distribution of reference-positive and reference-negative results in the analyzed sample. Agreement measures also depend on the observed cross-classification. Without the underlying counts or reported estimates, these measures cannot be assessed from the registry record.

Reference classification and interpretation

The reference result is described as the combination of NAAT 2 and NAAT 3 results. The record does not provide the full rule for combining those results, beyond identifying the combination as ASIS. It also does not describe an external confirmation procedure. General explanation: conclusions from an index-versus-reference comparison are conditional on how the reference is defined. If the reference itself consists of other tests, the interpretation concerns relative classification against that test-based reference, rather than an absolute determination of infection status independent of the tests.

That distinction does not establish a direction or size of any difference in performance. It identifies what the comparison means. The primary outcome description alone cannot establish whether NAAT 1 agreed more or less often with ASIS, or whether a particular category was frequent.

Uncertainty and statistical testing

General explanation: a confidence interval describes a range of values compatible with the observed data under a statistical model, and its width reflects precision. For categorical diagnostic results, intervals can be calculated for suitable proportions or accuracy measures when the required counts are available. A p-value addresses compatibility with a specified null hypothesis under a test procedure; it does not measure the size or clinical importance of an effect. Neither confidence intervals nor p-values for the primary comparison are reported in the registry record. The statistical model, test procedure, and any adjustment method are also not reported in the registry record.

Because the results are not numerically reported, no estimate can be evaluated for precision, and no claim about statistical significance can be drawn from this endpoint description. The record lists 12 outcome measures and 24 analyses, but does not describe a statistical analysis plan or how those analyses were organized.

Planning calculations

The sample-size material associated with the analysis is a planning illustration based on an observed effect; it is not the study’s original design calculation and must not be read as observed power. The stated assumptions are a two-sided significance level of 0.05, equal allocation between two arms, and a normal approximation, with the effect to detect expressed as a fraction of the observed effect. Those assumptions describe a hypothetical planning exercise. The registry lists a single-group diagnostic study with allocation not applicable, so the equal-allocation scenario is not a description of the trial’s design.

General explanation: sample-size planning asks how many observations a future study might need under specified assumptions. Its answer depends on the target effect, variability or event frequency, significance threshold, allocation, and analysis method. A planning calculation does not show that a completed study had a particular probability of detecting an effect, and it does not substitute for the observed estimate and its uncertainty. Numerical planning estimates and a protocol-based sample-size justification are not reported in the registry record.

What cannot be reconstructed

The registry record does not report the detailed analysis population for each outcome, the handling of invalid or indeterminate results in every analysis, the approach to multiple testing, or the prespecified statistical model. These omissions preclude reproducing the primary analysis from the endpoint description alone. The record also does not provide the information needed to evaluate whether results were adjusted for participant or specimen characteristics. Any such methods should be treated as not reported in the registry record, rather than inferred from common practice.

10. Multiplicity, Missing Data and Analysis Populations

The registry lists 12 outcome measures and 24 analyses. It does not describe how these measures and analyses were grouped into primary, secondary, or exploratory families for statistical testing, nor whether any correction for multiple comparisons was planned or used. A multiplicity adjustment is not reported in the registry record. Without that information, the number of analyses alone cannot establish which results were confirmatory or how the chance of false-positive findings was managed.

For the primary outcome, the registry states that 2598 participants completed the overall study and that eight participants with incomplete test results were excluded from this outcome. These are the only outcome-specific statements about incomplete results in the primary description. The registry does not provide the number of missing, invalid, or indeterminate results in each category, or explain whether those participants were handled differently in other analyses.

General explanation: missing or uninterpretable diagnostic results can affect the denominator and the meaning of a performance estimate. Excluding such results can lead to an analysis focused on participants with classifiable results, while counting them as a separate category answers a different question about overall test outcomes. The registry identifies no-result, indeterminate, and invalid categories, but does not report enough detail to assess how they were treated across all analyses.

The registry does not state whether all enrolled participants were eligible for every outcome, or provide analysis-population definitions beyond the primary outcome’s exclusion statement. Details of imputation, sensitivity analyses for missing data, and analysis populations are not reported in the registry record. The 2767 enrolled participants, the 2598 who completed the overall study, and the participants analyzed for a specific outcome should therefore not be assumed to represent the same denominator.

11. 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 0% reporting threshold.

The safety record lists 2598 participants at risk for serious adverse events and 0 affected. It also lists 2598 participants at risk for other adverse events and 0 affected, with 0 deaths. No serious adverse-event terms are listed. These entries describe what was recorded in the registry for the intervention group.

A zero in a registry adverse-event field is a recorded count, not a statistical demonstration that an event is impossible or that there is no safety risk. Interpretation depends on the event definitions, the period of observation, completeness of reporting, and the population included. The adverse-event fields do not specify detailed event definitions or observation procedures, so those details are not reported in the registry record.

The primary outcome has a one-day timeframe, but that timeframe should not be assumed to define the safety observation period: the registry does not state that relationship. These safety figures also do not answer the diagnostic-performance question. They are a separate part of the record and should be read independently from the comparison of NAAT 1 with ASIS.

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

The record establishes that the study evaluated three nucleic acid amplification tests using participant samples from extragenital sites, including the pharynx and rectum. Its primary endpoint focuses specifically on participant results for NAAT 1 for NG in the pharynx, compared with ASIS reference results based on NAAT 2 and NAAT 3. The endpoint description specifies the result categories and the reference approach.

What the record does not establish is the observed distribution of those results. Numerical primary-outcome counts are not reported in the registry record, and neither are diagnostic accuracy estimates, confidence intervals, or p-values for the comparison. Consequently, the record does not show the degree of agreement between NAAT 1 and ASIS or the precision of any performance estimate. It also does not establish how the tests compare for CT or at the rectal site through the primary endpoint; those are broader topics in the study title and description, but their numerical outcome results are not reported in the registry record.

General explanation: diagnostic performance is always interpreted relative to a target condition, reference classification, specimen type, and study population. Here the primary reference is a combination of two other tests. Any performance estimate would therefore describe agreement with that particular reference, not an unrestricted statement about test performance in every setting.

The record also does not establish treatment effects or changes in health outcomes. This is a diagnostic platform evaluation, not a randomized trial of care. Its listed serious and other adverse-event counts are a separate registry record of safety events, not evidence about diagnostic accuracy. The most defensible conclusion is that the registry documents the intended diagnostic comparison and some participant-flow information, while leaving the primary numerical findings unavailable in the registry record.

13. Why This Trial Matters Statistically

Diagnostic studies require careful attention to what counts as a positive, negative, indeterminate, invalid, or unavailable result. This record makes those categories visible in the primary endpoint description: NAAT 1 has positive, negative, and no-result categories, while the ASIS reference has positive, negative, indeterminate, and invalid categories. Keeping these categories distinct matters because collapsing them can change both the denominator and the interpretation of a comparison.

The reference definition is also statistically important. ASIS is formed from the combined results of NAAT 2 and NAAT 3. This makes clear that the primary analysis is not simply a comparison against an independently described clinical standard. General explanation: an index test’s apparent agreement depends on the reference classification used, so specifying how the reference is formed is central to interpreting an accuracy analysis.

Participant flow provides another key piece of context. The registry lists 2767 enrolled participants, 2598 participants who completed the overall study, and eight participants with incomplete test results excluded from the primary outcome. Those figures indicate that the overall enrollment and the primary outcome population are not interchangeable, while the detailed disposition of results remains incomplete in the record.

Finally, the record illustrates why a diagnostic study should not be read like a randomized treatment comparison. Allocation is listed as not applicable and the design is single-group. The central statistical questions concern classification, agreement, missing or uninterpretable results, and uncertainty—not differences between assigned treatment arms. Because the primary numerical outcomes and analysis methods are not reported in the registry record, the study description supports understanding the comparison’s structure but not judging the magnitude or precision of its findings.

14. 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 limitation for interpretation is that the primary outcome’s numerical results are not reported in the registry record. The endpoint is described in detail enough to identify the index test, reference classification, site, pathogen, and result categories, but not to determine the observed counts or estimate accuracy. The record also does not report confidence intervals or a statistical test for this comparison.

The reference classification is based on the combination of NAAT 2 and NAAT 3 results. The registry does not describe an independent reference procedure or the full rule used to combine results. Therefore, any interpretation of the primary endpoint would be relative to this stated reference definition. General methodological consideration: when an index test and reference classification are both test-based, their relationship may differ from the relationship with another standard; the record does not provide enough information to quantify that issue.

The outcome-specific population is not fully characterized. The registry reports 2598 overall study completers and exclusion of eight participants with incomplete results for this outcome, but does not give a full participant disposition by result category. It also does not explain how no-result, indeterminate, or invalid outcomes were handled across all analyses. Eligibility criteria and analysis-population definitions are not reported in the registry record.

The primary endpoint is specific to NG in the pharynx, even though the study concerns NG and CT at pharyngeal and rectal sites. Numerical findings for those broader site and pathogen combinations are not reported in the registry record. The record lists 12 outcomes and 24 analyses but does not describe multiplicity procedures or a complete statistical analysis plan. These limits mean the registry supports a description of the study question and design, but not a comprehensive assessment of diagnostic performance or robustness.

15. Related Tutorials

16. Related Statistical Calculators

17. Sources

• ClinicalTrials.gov: Performance of Nucleic Acid Amplification Tests for the Detection of NG and CT — NCT02870101.
• Registry record last updated 2019-05-15; status last verified 2019-05.
• Results first posted 2019-04-26.
• 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.

18. Record Summary

NCT02870101 is a completed, single-group diagnostic study sponsored by Duke University. It evaluated three nucleic acid amplification test platforms for NG and CT using participant samples from pharyngeal and rectal swabs. Enrollment was 2767; 2598 participants completed the overall study.

The primary endpoint counts NAAT 1 results for NG in the pharynx relative to ASIS reference results formed from NAAT 2 and NAAT 3. Eight participants with incomplete test results were excluded from that outcome. Numerical primary results and detailed statistical methods are not reported in the registry record.

The registry lists 12 outcome measures and 24 analyses. It records 0 serious adverse events, 0 other adverse events, and 0 deaths among 2598 participants at risk in the corresponding fields. Those safety entries are distinct from the diagnostic endpoint.