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Alban Ramette

Applications of nanopore sequencing technologies to whole genome sequencing of human viruses in the clinical setting

About Alban Ramette

Alban Ramette received a PhD degree in Natural sciences from the Swiss Federal Institute of Technology (ETHZ) Zurich Switzerland in 2002. His work mostly focused on environmental microbiology and biostatistical analyses of complex datasets (Michigan State University 2002- 2005; Max-Planck Institute Bremen, Germany, 2005-2014). From 2014-2016, he worked on the epidemiology of child asthma and respiratory diseases at the Institute for Social and Preventive Medicine, Bern, Switzerland. In September 2016, he started the Bioinformatics/Biostatistics group at the Institute for Infectious Diseases, University of Bern, Switzerland. Since then, his group has focused on high-throughput sequencing solutions for clinical applications with strong emphasis on products from Oxford Nanopore Technologies. He brings expertise in NGS analysis and statistical analysis of large datasets from clinical and environmental microbiology. Tuesday, 31 October 17 33 Website: http://www.ifik.unibe.ch/

Abstract

PCR-based detection is still the most commonly used method for routine identification of viruses of clinical importance, and this approach is often complemented by Sanger sequencing for further genotype determination. Yet, point mutations and recombination events that occur frequently in the genomes of human viruses can potentially lead to false negative results when PCR-based techniques are uniquely used. Here, we developed a set of assays based on Oxford nanopore technologies to obtain whole genomes of enteroviruses (RNA viruses) from clinical samples. We will present our conclusions about direct RNA sequencing vs. indirect sequencing of RNA (via cDNA synthesis and sequencing), in terms of costs, turnaround time, accuracy, and types of foreseen applications in the clinical setting

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