Effectiveness of Molecular Testing Techniques for Diagnosis of Indeterminate Thyroid Nodules: A Randomized Clinical Trial

Abstract

Importance: Approximately 20% of thyroid nodules display indeterminate cytology. Molecular testing can refine the risk of malignancy and reduce the need for diagnostic hemithyroidectomy.

Objective: To compare the diagnostic performance between an RNA test (Afirma genomic sequencing classifier) and DNA-RNA test (ThyroSeq v3 multigene genomic classifier).

Design, setting, and participants: This parallel randomized clinical trial of monthly block randomization included patients in the UCLA Health system who underwent thyroid biopsy from August 2017 to January 2020 with indeterminate cytology (Bethesda System for Reporting Thyroid Cytopathology category III or IV).

Interventions: Molecular testing with the RNA test or DNA-RNA test.

Main outcomes and measures: Diagnostic test performance of the RNA test compared with the DNA-RNA test. The secondary outcome was comparison of test performance with prior versions of the molecular tests.

Results: Of 2368 patients, 397 were eligible for inclusion based on indeterminate cytology, and 346 (median [interquartile range] age, 55 [44-67] years; 266 [76.9%] women) were randomized to 1 of the 2 tests. In the total cohort assessed for eligibility, 3140 thyroid nodules were assessed, and 427 (13.6%) nodules were cytologically indeterminate. The prevalence of malignancy was 20% among indeterminate nodules. The benign call rate was 53% (95% CI, 47%-61%) for the RNA test and 61% (95% CI, 53%-68%) for the DNA-RNA test. The specificities of the RNA test and DNA-RNA test were 80% (95% CI, 72%-86%) and 85% (95% CI, 77%-91%), respectively (P = .33); the positive predictive values (PPV) of the RNA test and DNA-RNA test were 53% (95% CI, 40%-67%) and 63% (95% CI, 48%-77%), respectively (P = .33). The RNA test exhibited a higher PPV compared with the prior test version (Afirma gene expression classifier) (54% [95% CI, 40%-67%] vs 38% [95% CI, 27%-48%]; P = .01). The DNA-RNA test had no statistically significant difference in PPV compared with its prior version (ThyroSeq v2 next-generation sequencing) (63% [95% CI, 48%-77%] vs 58% [95% CI, 43%-73%]; P = .75). Diagnostic thyroidectomy was avoided in 87 (51%) patients tested with the RNA test and 83 (49%) patients tested with the DNA-RNA test. Surveillance ultrasonography was available for 90 nodules, of which 85 (94%) remained stable over a median of 12 months follow-up.

Conclusions and relevance: Both the RNA test and DNA-RNA test displayed high specificity and allowed 49% of patients with indeterminate nodules to avoid diagnostic surgery. Although previous trials demonstrated that the prior version of the DNA-RNA test was more specific than the prior version of the RNA test, the current molecular test techniques have no statistically significant difference in performance.

Trial registration: ClinicalTrials.gov Identifier: NCT02681328.

Conflict of interest statement

Conflict of Interest Disclosures: Dr Rao reports receiving personal fees from AstraZeneca and other support from Oncogenesis, 3J Biotech, and Zhiwei. No other disclosures were reported.

Figures

Figure 1.. CONSORT Diagram

The group randomized to the RNA test underwent testing with the Afirma genomic sequencing classifier; the DNA-RNA group underwent testing with the ThyroSeq v3 multigene genomic classifier.

Figure 2.. Expected Positive Predictive Value Curves of Molecular Tests

Expected positive predictive value curves of first-generation and second-generation RNA molecular tests and DNA-RNA molecular tests based on observed specificities and sensitivities over the range of possible prevalence of cancer or noninvasive follicular thyroid neoplasm with papillarylike features (NIFTP). Given a prevalence of cancer or NIFTP of 19.6% observed in the present study cohort, the RNA test compared with its previous version demonstrated a significant improvement in positive predictive value (37.5% vs 53.5%). The dotted dark blue line indicates the DNA-RNA test (ThyroSeq v3 multigene genomic classifier); dotted orange line, the previous version of the DNA-RNA test (ThyroSeq v2 next-generation sequencing); solid dark blue line, the RNA test (Afirma genomic sequencing classifier); and solid orange line, the previous version of the RNA test (Afirma gene expression classifier).