The genomic landscape of papillary thyroid carcinoma on next-generation sequencing in patients undergoing total thyroidectomy

Background: Thyroidectomy is increasingly performed for suspected malignancy. This cohort study aimed to identify genetic markers associated with malignancy and determine the molecular landscape of papillary thyroid carcinoma (PTC) through next-generation sequencing (NGS) in patients undergoing total thyroidectomy.

Patients and methods: Among 116 surgical candidates, 103 patients (age = 42.9 ± 13.7 years; Male: Female = 14:89) with benign or malignant thyroid nodules were eligible. Live thyroid tissue samples harvested intraoperatively with adequate DNA and RNA yield were subjected to NGS on the Illumina NovaSeq 6000 platform for genomic and transcriptomic analysis, respectively.

Results: Histopathology comprised 20 malignant (19.4%) and 83 benign (80.6%) cases, including 16 PTC (15.5%) cases. On NGS, single nucleotide polymorphisms (SNPs) in NTRK1 at NC_000001.11:156879016 on chromosome 1 and ALK at NC_000002.12:29717663 on chromosome 2 were frequent in malignant lesions (p < 0.05). A SNP in ALK at NC_000002.12:29193706 was consistently a homozygous alternate allele across the cohort. DNA-sequencing of PTC lesions identified recurrent somatic mutations in BRAF (100%), ALK (56.3%), RET (18.8%), PIK3CA (12.5%), NTRK1 (12.5%), NTRK2 (87.5%), NTRK3 (12.5%), NRAS (6.3%), and PTCH1 (31.3%) genes. RNA sequencing revealed novel fusion genes, including MKRN1-BRAF, RN7SL1-CDH1, IRF2BPL-MED12, MED12-IRF2BPL, CPM-MDM2, and AC005895.3-PDGFRB. In receiver operative characteristics analysis, the AUCs of ALK mutation predicting recurrence and metastases were 0.818 and 0.783.

Conclusion: This Indian study identified novel somatic mutations and fusion genes in PTC, revealing a distinct genomic landscape with implications in precision diagnostics and personalized therapies. NGS with intraoperative live sampling shows promise in prognostication and therapeutic optimization of advanced/metastatic PTC cases.

Trial registration no: CTRI/2020/09/027607 dt 04/09/2020; REF/2020/08/036119.