Copy number variations: A novel molecular marker for papillary thyroid cancer

Abstract

Background: We aimed to screen tumor-associated functional genes on a large scale through copy number variation (CNV) analysis of papillary thyroid cancer (PTC). Methods: We analyzed 74 tissue samples from 41 patients with thyroid nodules. The samples were subjected to whole-genome resequencing and then analyzed by the ‘WISECONDOR’ method. Potential chromosome CNV regions were identified between the different sample groups. Results: Of the 74 samples from 41 patients, 28 were PTC tissue samples, 29 were para-carcinoma tissue samples, 13 were benign tumor tissue samples and 4 were para-benign tumor tissue samples. According to our findings, PTC can be identified by CNVs at the corresponding positions on chromosomes 5, 7, 8, 10, and 17. For carcinoma tissue, the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy and area under the curve (AUC) of the test method were 100%, 66.7%, 87.5%, 100.0%, 90.0% and 0.83 (95% confidence interval [CI], 0.67–1.00) and for para-carcinoma tissue, these values were 96.6%, 75.0%, 96.6%, 75.0%, 93.9% and 0.86 (95% CI, 0.60–1.00). Conclusion: CNV analysis assays involving high-volume sequencing analysis can increase the identification of PTC, potentially avoiding errors caused by position deflection in sampling.

Keywords

• Copy number variations
• Papillary thyroid cancer
• Thyroid nodules
• Functional genes