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Background: Afirma Genomic Sequencing Classifier (GSC) testing has been utilized for further risk stratification of thyroid nodules categorized as atypia of undetermined significance (AUS). The 2023 Bethesda system subcategorizes AUS diagnosis into AUS with nuclear atypia (AUS-N) and other atypia (AUS-O). The current study aims to determine if performance of GSC testing differs between the two AUS subcategories and between single AUS cohort and repeat AUS cohort. Methods: This retrospective study analyzed consecutive thyroid nodule fine-needle aspiration with a single or a repeat AUS diagnosis and a diagnostic GSC testing result (benign vs. suspicious). All AUS nodules were divided into AUS-N or AUS-O subcategory and followed by either surgical intervention or at least 12 months of clinical and/or ultrasound monitoring. We then assessed performance of GSC testing in each subcategory and subsequently compared the individual performance in AUS-N or AUS-O subcategory between single AUS cohort and repeat AUS cohort. Results: The study identified a total of 365 thyroid nodules subcategorized as AUS-N (N = 106) and AUS-O (N = 259). Both cohorts showed a significantly lower GSC benign call rate (BCR) in AUS-N nodules compared with AUS-O nodules (43% vs. 71% in single AUS, p = 0.001; 58% vs. 74% in repeat AUS, p = 0.02). The proportion of histology-proven malignancies associated with a suspicious GSC result tended to be greater in AUS-N nodules than AUS-O nodules (28% vs. 10% in single AUS, p = 0.09; 38% vs. 27% in repeat AUS, p = 0.3). Compared with AUS-N nodules, AUS-O cohorts demonstrated significantly higher specificity in the single AUS group (73% vs. 51%, p = 0.01). In both subcategories, the repeat AUS cohort yielded greater specificity, positive predictive value, and diagnostic accuracy compared with the single AUS group. However, the differences did not reach statistical significance. Conclusions: GSC BCR and diagnostic performance of GSC testing may vary in AUS-N versus AUS-O subcategories. However, there were no statistically significant differences in GSC performance between single and repeat AUS cohorts. [ABSTRACT FROM AUTHOR]