| BackgroundPapillary thyroid carcinoma (PTC) is the most common malignancy of the thyroid gland. It is characterized by its high prevalence and excellent prognosis. Lymph nodes involvement at the neck region is commonly seen in PTC. The lymph node metastasis are often micro-metastasis and thus hard to be detected by pre-surgical ultrasonography or intra-surgical palpation. In order to reduce the potential risk of disease recurrence, numerous patients with no evidence of lymph node involvement undergo a procedure called prophylactic central node dissection. However, this procedure may increase the possibility of recurrent laryngeal nerve injury or parathyroid gland injury. Therefore, a new diagnostic tool that helps distinguishing whether the patient has lymph node metastasis or not will spare the patient from an unnecessary central node dissection, thus lowering the risk of surgical related morbidities. In recent years, genetic studies of PTC have revealed several important mutations that may be involved in the pathogenesis of the disease. However the mechanism and driving mutations of lymph node metastasis are yet to be elucidated. Whole exome sequencing is an effective technology that discovers huge amount of single nucleotide polymorphisms (SNPs) and possible mutations. Putting the metastatic lymph nodes through whole exome sequencing (WES) will not only help us understand the mechanism of metastasis, but also provide key information for the future development of new diagnostic tools. Hence, the objectives of this study are: (1) acquiring disease related SNPs and mutations from whole exome sequencing; and (2) revealing the driving mutation and underlying mechanism of PTC lymph node metastasis.MethodsThis study recruits patients with PTC and numerous metastatic lymph nodes that is confirmed by pre-surgical ultrasonography, intra-surgical palpation or post-surgical pathological diagnosis. Specimens are obtained from surgical operations of the thyroid tumor. DNA are acquired from each specimen and then purified, hybridized and captured for whole exome sequencing. The quality of the sequencing procedure is strictly controlled. Multiple filtering standards and programs are applied to the sequencing results before they are cross-matched with previously known database of PTC-related SNPs to reveal SNPs of interest in this study.ResultsA total of 9 specimens were acquired from 3 patients. The average depth of the whole exome sequencing was 122 X, with more than 40000 SNPs identified for each specimen. After filtering and cross matching, a total of 53 SNPs were selected for their high possibility of relation with metastasis. Further analysis narrowed the number to 14. The role of BRAF in metastasis was not supported by the data. However, CHEK2 was found to be possible driving cause of lymph node invasion. Furthermore, a number of SNPs from multiple genes were identified to have possible relation with metastasis, including PDE4DIP, SPTB and TBC1D32.ConclusionsBoth primary tumor and metastatic tumor of PTC contain huge amount of SNPs. More than 50 possible SNPs related to metastasis were identified. CHEK2 may play a crucial role in the development of metastasis. SNPs concerning TBC1D32, PDE4DIP and SPTB may also contribute to this process.
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