Molecular analysis of residual ThinPrep material from thyroid FNAs increases diagnostic sensitivity

Background: Molecular testing for genetic alterations associated with malignancy is a potential triage approach for thyroid fine-needle aspiration (FNA) samples with indeterminate cytology. Because liquid-based FNA material allows for efficient RNA extraction, the authors analyzed residual material for common point mutations and rearrangements.

Methods: Thyroid FNAs were classified according to The Bethesda System for Reporting Thyroid Cytopathology after routine ThinPrep slide preparation. Residual samples from malignant and indeterminate cases were submitted for molecular analysis, along with a random cohort of nondiagnostic and benign aspirates. Blinded analysis of BRAF and RAS point mutations and RET/PTC and PAX8/PPARγ rearrangements was correlated with subsequent follow-up.

Results: Adequate results were obtained in 402 of 597 cases (67%). Mutations or rearrangements were detected in 24 of 117 cytologically indeterminate specimens (21%) (17 RAS rearrangements, 6 BRAF rearrangements, and 1 PAX8/PPARγ rearrangement). BRAF mutations were preferentially associated with malignant cytologic diagnoses (22 of 42 cases; 52%), with less frequent detection in the suspicious for malignancy category (4 of 27 cases; 15%) and very low detection in all other categories (1%-4%). Surgical follow-up confirmed malignancy in all 21 BRAF-mutated cases, 42% of RAS-mutated cases (10 of 24 cases), and 37% of cases with no detected mutation (39 of 105 cases).

Conclusions: Molecular analysis is feasible on residual ThinPrep material with the advantage of not requiring additional FNA procedures. The majority of BRAF mutations are identified in cases classified cytologically as malignant, and, to a lesser extent, as suspicious for malignancy. The usefulness of BRAF testing is limited by the low rate of BRAF-positive cases in other categories, thereby highlighting the need to identify other genetic drivers of clinically aggressive thyroid cancers.