Feasibility of nanopore sequencing for classification of pediatric germ cell tumors

• Grant number: 22/07041-3
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: July 01, 2022
• End date: May 31, 2026
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal Investigator: Mariana Tomazini Pinto
• Grantee: Ana Flávia Souza Péres
• Host Institution: Hospital do Câncer de Barretos. Fundação Pio XII (FP). Barretos , SP, Brazil
• Associated research grant: 19/07502-8 - Investigation of the transcription factors inducing Epithelial-Mesenchymal Transition (EMT) in germ cells tumors, AP.JP
• Associated scholarship(s): 23/15715-7 - Advancing pediatric germ cell tumor classification through Nanopore sequencing, BE.EP.DD

Abstract

Pediatric Germ Cell Tumors (GCTs) are considered a rare type of tumor, however, still very little is known about the genetics associated with its pathogenesis, since the studies around GCTs are usually developed in adult patients. Thus, the in-depth study of Molecular Biology related to GCTs in children could reveal predictive markers for diagnosis, prognosis, and precision treatment for these patients. The available technologies for analysis and study of genetic alterations have undergone great development since its emergence in the 70s, reaching the present day with different methodologies, in between them the Illumina and Nanopore platforms. Both are sequencing technologies that briefly distinguished by the size of the DNA fragment they are capable of sequence and the need or not of a previous amplification step. A project in development by our group at Hospital de Câncer de Barretos was capable of sequence the exome, through the Illumina platform, of pediatric GCTs, getting relevant results. Still, given the need for methods that help in the classification of pediatric tumors, our group stablished a partnership with a group of researchers from St Judes Children's Research Hospital with the purpose of classifying GCTs through nanopore sequencing. Thereby, the goal of this project is to analyze the feasibility of nanopore sequencing for GCTs classification, in addition to comparing the results with the exome results previously sequenced by our group. The development of methods that can classify pediatric GCTs patients will help in the early and assertive diagnosis, bringing benefits to the clinical management of the patients and increase the survival rate. (AU)