Endocrine Abstracts

Background: The molecular landscape of thyroid carcinoma (TC) is characterised by diverse somatic alterations, most prominently affecting the MAPK and PI3K-AKT pathways. This study applied whole-exome sequencing (WES) to characterise the spectrum of driver mutations in archival tumour tissue from a TC cohort and to explore inter-tumour heterogeneity across different histological subtypes.

Methods: Archival formalin-fixed paraffin-embedded (FFPE) tumour DNA from 23 patients with histologically confirmed TC (papillary= 12, follicular= 5, medullary= 3, anaplastic= 3) underwent WES. Somatic single-nucleotide variants (SNVs) and small insertions/deletions (INDELs) were identified using Mutect2, Strelka, and VarDict. Variants passing all high-confidence filters (depth ≥ 30, tumour allele depth ≥ 5, allele frequency ≥ 1 %) were annotated through the Cancer Genome Interpreter and cross-referenced with the COSMIC Cancer Gene Census (v99). Selected driver variants were validated using droplet digital PCR (ddPCR).

Results: Across the cohort, 4639 high-confidence somatic variants were detected, all of which were SNVs; no INDELs passed filtering thresholds. Of these, 116 variants were classified as putative driver mutations. The most frequently altered genes were BRAF, NRAS, HRAS, TP53, ARID1B, and KMT2A, implicating the MAPK and PI3K-AKT pathways as dominant oncogenic axes. BRAFV600E occurred in 41.7 % of papillary cases, lower than TCGA (59.7 %), whereas NRASQ61R appeared in 60 % of follicular cases, exceeding published averages (38 %). Only three variants, BRAFV600E, NRASQ61R, and HRASQ61R, were shared across 13 patients, reflecting pronounced molecular heterogeneity. ddPCR validation confirmed these alterations with strong correlation between WES-derived VAF and ddPCR FA (r = 0.76, P < 0.05).

Conclusion: WES of TC tumours revealed a heterogeneous mutational profile dominated by SNVs, with limited inter-tumoural overlap even within histological subtypes. The predominance of BRAF and RAS mutations supports their central role in TC, while extensive molecular diversity highlights the need for personalised, mutation-guided surveillance and therapeutic strategies in TC.