Diagnostic performance of next-generation sequencing and genetic profiling in thyroid nodules from a single center in China

Abstract

Objective: The data regarding the mutation landscape in Chinese patients with thyroid cancer are limited. The diagnostic performance of thyroid nodules by fine-needle aspiration (FNA) cytology needs optimization, especially in indeterminate nodules. Methods: A total of 1039 FNA and surgical resection samples tested using the targeted multigene NGS panel were retrospectively collected. The features of gene alterations in different thyroid tumors were analyzed, and the diagnostic efficacy were evaluated. Results: Among 1039 samples, there were 822 FNA and 217 surgical FFPE samples. Among 207 malignant thyroid resections, a total of 181 out of 193 papillary thyroid carcinomas (PTCs) were NGS-positive (93.8%), with a high prevalence of BRAF mutations (81.9%, 158/193) and a low prevalence of RAS (1.0%, 2/193) and TERT promoter mutations (3.6%, 7/193). Gene fusions, involving the RET and NTRK3 genes, were present in 20 PTCs (10.4%) and mutually exclusive with other driver mutations. Two of 3 follicular thyroid carcinomas harbored multiple mutations. RET gene point mutations were common in medullary thyroid carcinoma (8/11, 72.7%). The combination of cytology and DNA-RNA based NGS analysis demonstrated superior diagnostic value (98.0%) in FNA samples. For indeterminate thyroid nodules, the diagnostic sensitivity and specificity of NGS testing were 79.2% (38/48) and 80.0% (8/10), respectively. Two mutation-positive benign cases harbored NRAS and TSHR mutations, respectively. Conclusions: Our study revealed the distinct molecular profile of thyroid tumors in Chinese population. The combination of NGS testing and FNA cytology could facilitate the accurate diagnosis of thyroid nodules, especially for indeterminate nodules.

Landscape of gene mutation in Chinese thyroid cancer patients: Construction and validation of lymph node metastasis prediction model based on clinical features and gene mutation marker

“…Furthermore, we also observed that RET fusion is the independent predictor for LNM, but not the missense mutation. Another clinical study from east China reported 10.4% RET fusions in 193 PTC patients, 31 7.08% RET fusion reported in a study from 14 tertiary hospitals of China 32 . Ullmann et al 33 also reported that RET‐driven tumors are more likely to have extrathyroidal extension, multifocal disease and distant metastases in American.…”

Performance of multigene testing in cytologically indeterminate thyroid nodules and molecular risk stratification

“…The BRAF V 600E and mutated RAS were considered to be two mutually exclusive drivers of PTC, possibly suggesting similar or redundant downstream effects, and causing different signaling effects followed by profound phenotypic differences ( Cancer Genome Atlas Research, 2014 ; Ren et al, 2022 ) However, less attention had been paid to concurrent molecular alterations, conveying a significant adverse prognosis and suggesting treatment via a total thyroidectomy of the thyroid nodules ( Bose, Sacks & Walts, 2019 ; Ren et al, 2022 ; Poller & Glaysher, 2017 ). In our study, some drivers in the PI3K pathway and tumor suppressor genes manifested a tendency to be concurrent with others, such as BRAF rearrangements and deletions, PTEN deletions, TERT Q302R , and mutations of AKT1 , EIF1AX , TP53, and PIK3CA.…”

“…These may result in repeat FNA, diagnostic lobectomy, and even unnecessary total thyroidectomy procedures. Thus, molecular pathogenesis has become a promising approach to supplement cytologic examination for preoperative diagnosis and treatment options ( Ren et al, 2022 ; Lee et al, 2022 ).…”

“…For instance, ThyroSeq, ThyGenX and ThyraMIR tests have both high PPV and NPV and can be used to determine malignancy, while Afirma GSC tests show high NPV and relatively low PPV and might be useful to rule-out the presence of malignancy for indeterminate thyroid lesions ( Bose, Sacks & Walts, 2019 ; Lee et al, 2022 ; Rossi et al, 2022 ). There is limited research applying these tests in the Chinese population and few verified self-designed multigene panels are available on the market ( Ren et al, 2022 ; Song et al, 2020 ). Here, we designed a multigene NGS panel to detect targeted DNA alterations and RNA fusions.…”

Molecular testing raises thyroid nodule fine needle aspiration diagnostic value

“…Therefore, a thyroid cancer 18-gene detection kit was independently developed by us and is based on the method of multiplex amplification combined with high-throughput sequencing to detect single nucleotide variants (SNVs), insertions/deletions (Indels), and fusion genes in DNA and RNA. The product was confirmed by internal performance and can achieve 99.3% (SNVs/indels) and 100% (fusion genes) detection accuracy ( 25 ). Under the input of a 5-ng library construction, the limit of detection (LoD) of (DNA) BRAF p.V600E was variant allele frequency (VAF)-1.0%, the LoD of TERT C228T was VAF-2.0%, and the LoD of (RNA) CCDC6 (E1)-RET(E12) fusion detection was 20 ng at a concentration of 20 copies/ng.…”