Comprehensive genomic profiling of infiltrative follicular variant of papillary thyroid carcinoma

Abstract Background Infiltrative follicular variant of papillary thyroid carcinoma (IFVPTC) exhibits nuclear characteristics typical of papillary thyroid carcinoma (PTC) but demonstrates a follicular growth pattern. The diagnosis of IFVPTC presenting with atypical nuclear features of PTC poses challenges for both preoperative cytopathology and postoperative histopathology. In such cases, molecular markers are needed to serve as diagnostic aids. Given the limited knowledge of IFVPTC's genomic features, this study aimed to characterize its genetic alterations and identify clinically relevant molecular markers. Methods Whole‐exome sequencing of 50 IFVPTC tumor–normal pairs identified single‐nucleotide variants, somatic copy number alterations (sCNAs), and subclonal architecture. Key mutations were verified via polymerase chain reaction and Sanger sequencing, whereas valuable biomarkers were validated via immunohistochemistry (IHC). Results This study found that endogenous processes rather than exogenous mutagens dominated the shaping of the genome of IFVPTC during tumorigenesis. BRAF V600E was the only common trunk mutation and significantly mutated gene in IFVPTC. Subcloning analysis found that most IFVPTC samples harbored two or more coexisting clones. sCNA analysis revealed that human leukocyte antigen C (HLA‐C) and HLA‐A were significantly amplified. Subsequent IHC investigations indicated that HLA‐C shows promise in averting the misclassification of challenging‐to‐interpret IFVPTC and invasive encapsulated follicular variant of PTC (I‐EFVPTC) as noninvasive follicular thyroid neoplasm with papillary‐like nuclear features (NIFTP). Although there were several similarities between classic PTC and IFVPTC, they differed significantly in their sCNA patterns. Conclusions This study provides valuable insights into IFVPTC's genetic alterations and highlights the potential of HLA‐C IHC to distinguish challenging‐to‐interpret IFVPTC and I‐EFVPTC from NIFTP, which will enhance the understanding of its molecular features for improved diagnosis and management.