Webinar: Wet-lab processes for pathogen whole genome sequencing

Part one: Tuesday 16 May 2023 13:00 - 15:30 (AEST)

Part two: Thursday 18 May 2023 13:00 - 17:00 (AEST)

Overview

Are you a clinical scientist, medical microbiologist or infectious diseases physician wanting to gain expertise in whole genome sequencing?

At this two-part webinar co-hosted by the Communicable Diseases Genomics Network (CDGN) and the Australian Pathogen Genomics Program, learn from leading experts and gain skills in Illumina and Nanopore (ONT) sequencing for bacterial and viral pathogens, nucleic acid extraction considerations and validation.

Learning outcomes

Key learning outcomes of the first webinar in the Introduction to Pathogen Genomics for Public Health Webinar Series include:

• Knowledge of technical performance and considerations associated with sequencing techniques
• Overview of genomic DNA/RNA extraction methods
• Understanding of the role of positive, negative controls and reference strains
• Introduction to the characteristics of key pathogens that impact on sequencing approaches

Webinar facilitators

• Dr Susan Ballard, Principal Scientist, Microbiological Diagnostic Unit Public Health Laboratory
• Dr Michelle Sait, Project Lead, Development Group, Microbiological Diagnostic Unit Public Health Laboratory
• Dr Irani Rathnayake, Senior Scientist, Forensic and Scientific Services, Queensland Health
• Dr Louise Judd, Senior Research Genomics Scientist, Centre for Pathogen Genomics
• Dr Bethany Horsburgh, Research Associate, The Kirby Institute at UNSW Sydney
• Dr Penelope Adamson, Medical Scientist, SA Pathology
• Ms Jean Moselen, Senior Medical Scientist, Victorian Infectious Diseases Reference Laboratory

Registration

Please register via the link here.

Program

Part one: Tuesday 16 May 2023 13:00 - 15:30 (AEST)

Pre-analytical considerations for whole genome sequencing - Dr Michelle Sait

• Understanding of the appropriate extraction method fit for purpose of sequencing (short and long read).
• Understanding of best practice in measuring the quantity of nucleic acid and the impact of inhibitors.
• Understanding the requirements for different species (ie bacterial, viral, parasite,   fungi).
• Understanding the role of positive and negative controls.

Sequencing  101: The Illumina platform - Dr Irani Rathnayake

• An understanding of the technical performance, limitations and quality issues associated with sequencing library preparations and instruments.
• How to  manage batched sequencing of different species to ensure even sequence coverage across a variety of different genome sizes.
• An understanding  of sequencing capacity and how to choose the appropriate sequencing flow cell and instrument.
• Understanding the role of spike-in, positive and negative controls.

Sequencing 102: The Oxford Nanopore platform - Dr Louise Judd

• An understanding of the technical performance, limitations and quality issues with ONT sequencing.
• An understanding of sequencing capacity and real-time data capture.
• Understanding the role of spike-in, positive and negative controls.

Part two: Thursday 18 May 2023 13:00 - 17:00 (AEST)

Sequencing 201: Viral genomics - Dr Bethany Horsburgh

• An understanding of different library preparation and sequencing technologies   applied to viral genomes and their limitations.

Sequencing Challenging Organisms - Dr Penelope Adamson

• An understanding of targeted sequencing approaches and their advantages/limitations.
• Fungal pathogens

Implementation and validation of sequencing platforms - Dr Susan Ballard

• An understanding of the performance measures required for platform validation and how they may be determined
• Overview of implementation requirements for sequencing e.g. choice of platform, physical infrastructure requirements

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