Objective  We investigated the differences of gene alterations between thyroid cancer and benign thyroid nodules by next-generation sequencing and bioinformatics methods in order to distinguish benign and malignant thyroid nodules at molecular level.

  Methods  In this study, 187 thyroid nodule samples were collected from thyroid patients enrolled in Tianjin Cancer Hospital from December 2014 to May 2018, and these samples were divided into thyroid carcinomas and suspected benign nodules by B-ultrasonography and fine needle aspiration biopsy (FNA). Thyroid carcinomas were further confirmed by postoperative pathological examinations. DNA and RNA were all extracted from these 187 samples, meanwhile we also collected 81 paracancerous normal thyroid samples and extracted DNA and RNA from them. Gene alterations of all the samples mentioned above were detected by next-generation sequencing technology. And the results were analyzed by bioinformatics methods.

  Results  A total of 476 mutation sites were detected, and 40 mutated genes were involved, including driver oncogenes, DNA damage repair genes, immune-related genes, chromatin remodeling genes and hormone-related genes, etc. The types of mutations included missense mutations, frame shift mutations, insertion, deletion and nonsense mutations. Genetic alteration features of thyroid cancer were significantly different from those of suspected benign nodules. Among them, the mutation frequencies of BRAF, ZNF717, TERT, GGT1, CHEK2, OTUD4, RET protein kinase domain and the occurrence of gene fusions in cancer are significantly higher than those in suspected benign nodules, and RET protein kinase domain and GGT1 mutations were positively correlated with lymph node metastasis in thyroid cancer. Fourteen samples harboring gene fusions were detected in RNA samples, and fusion types were CCDC6-RET, NCOA4-RET, ETV6-NTRK3 and TPM3-NTRK1.

  Conclusions  The genetic alteration features of thyroid cancer are significantly different from those of suspected benign nodules. Although there is no significant difference in the mutation proportions of some genes between cancer and suspected benign nodules, the mutation proportions in BRAF, TERT, ZNF717, GGT1, CHEK2, OTUD4, RET PKD, PI3K/Akt and AMPK pathway related genes and gene fusions in cancer were significantly higher than those in suspected benign nodules. So these disparity in genetic alteration profiles can be used as potential biomarkers to effectively distinguish malignancies from benign thyroid nodules at molecular level.