Introduction: Afima ® Expression atlas (XA) assesses mRNA expression of gene variants and fusions in indeterminate and malignant thyroid nodules. It was expanded in March 2020 from its the original version created in 2018. It is designed to risk stratify Afirma Gene Sequencing Classifier (GSC) suspicious nodules and provide prognostic information in Bethesda V and VI nodules that do not undergo Afirma GSC testing. Afirma® XA measures 905 DNA variants and 235 RNA fusions in over 593 genes. We wanted to study the performance of Afirma XA test as a prognosticator in suspicious and malignant nodules in our practice.
Setting: Dedicated thyroid ultrasound fine needle biopsy clinic in a large community practice.
Methods: Retrospective review was performed on data collected on all thyroid nodules that underwent ultrasound-guided fine-needle biopsy between 6/27/18 to 8/30/21. Cytopathology reports utilized The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). Afirma® XA was obtained for all the TBSRTC grade 3 and 4 nodules that were suspicious on Afirma® Gene Sequencing Classifier (GSC) and on all TBSRTC category 5 and 6 nodules.
Results: A total of 1168 nodules underwent US guided FNA. There were 171 (14.6%) Indeterminate (ITN) nodules - 129 TBSRTC category 3 and 42 TBSRTC category 4. Adequate RNA material was available for GSC testing in 165/171 ITN nodules. Sixty-five out of 162 nodules were suspicious on Afirma® GSC testing. There were 27 (2.6%) TBSRTC category 5 and 6 nodules. Afirma® XA was run on these 93 nodules. Afirma-XA detected genomic alterations in 50/93 nodules (54%). TBSRTC category 6 had the highest percentage (81%) of positive XA results, compared to 67% in TBSRTC category 5, and 45% in TBSRTC category 3 and 4 (Indeterminate nodules) that were GSC suspicious. The most common genomic alteration in TBSRTC -3 and TBSRTC -4 GSC suspicious was NRAS:p.Q61R. TBSRTC -5 and B-6 were enriched with BRAFV600E variants and RET/PTC1 and RET/PTC3 fusions. Afirma XA also detected unique gene fusions such as BRAF_MKRN1 and EML4_NTRK3. Samples were then studied and found to have positive correlation with final histopathological grade and incidence of lymph node metastasis.
Conclusions: Afirma® XA is a relatively new tool which in addition to other mutational markers holds great promise in prognostication of suspicious and malignant nodules, and thereby help with surgical planning and adjuvant treatment