Pre-surgical diagnosis of thyroid nodules based on DNA methylation profile

• Grant number: 21/09912-9
• Support Opportunities: Research Grants - Innovative Research in Small Business - PIPE
• Duration: June 01, 2022 - February 28, 2023
• Field of knowledge: Health Sciences - Medicine - Pathological Anatomy and Clinical Pathology
• Principal Investigator: Sandra Aparecida Drigo Linde
• Grantee: Sandra Aparecida Drigo Linde
• Host Company: Br4science Assessoria Técnica Científica Ltda
• CNAE: Atividades de serviços de complementação diagnóstica e terapêutica
• City: Botucatu
• Pesquisadores principais: Carlos Eduardo Frigério Domingues ; Catherine Elisabeth Marie David
• Associated researchers: Luiz Paulo Kowalski ; Silvia Regina Rogatto
• Associated scholarship(s): 22/08070-7 - Pre-surgical diagnosis of thyroid nodules based on DNA methylation profile, BP.PIPE

Abstract

Thyroid nodules are very common in the population and most are benign. Diagnosis by fine-needle aspiration puncture (FNAB) is challenging, especially with regard to distinguishing between malignant and benign lesions of follicular subtypes. With the increase in the indications for FNABs and the worldwide incidence of thyroid cancer, a large number of patients are still undergoing surgery with a diagnostic aim, which could be avoided with the use of diagnostic methods with greater specificity. Therefore, the development of molecular diagnostic methods for thyroid nodules is of great interest. In a previous study by our group, we identified potential malignancy markers based on DNA methylation analysis using the microarray technique. A predictive model combining few CpGs was designed and tested, demonstrating the ability to differentiate malignant from benign thyroid lesions. The objective of this proposal is to promote the translation of this method to the real clinical setting, and to establish a diagnostic service for thyroid nodules. To make testing more practical, faster and more cost-effective, we will develop a method based on sequencing driven by Oxford Nanopore technology. This method will allow direct analysis of (unmodified) DNA from target CpGs in multiple samples per run. To further optimize the classifier performance, we will incorporate analysis of virtually exclusive mutations from thyroid malignant lesions (BRAF and TERT genes). During the first phase of the proposal, we will carry out technical corroboration studies of our test (analytical sensitivity, specificity and reproducibility tests) on "gold standard" commercial samples (DNA 0 and 100% methylated, negative and positive for the studied mutations and of thyroid or non-thyroid origin). Thus, we intend to demonstrate the technical feasibility of the method (Phase I), for further analysis of diagnostic performance in FNAB samples (Phase II). We hope that the results obtained meet the needs not met in the current scenario, where the diagnostic limitation of thyroid nodules generates a great financial impact on the health system and on the quality of life of patients. Considering the small number of potential competitors in the national and international market, our proposal has a high potential to increase the development and competitiveness of our company. (AU)