Introduction to Pathogen Genomics for Public Health Webinar Series
Webinar: Bioinformatic analysis of pathogens for clinical and public health
Part one: Tuesday 20 September 2022 13:00 - 16:15 (AEST)
Part two: Wednesday 28 September 2022 13:00 - 16:45 (AEST)
Overview
Are you a clinical scientist, medical microbiologist or infectious diseases physician wanting to gain an understanding of the application of bioinformatics for pathogen genomics in public health?
Following on from the wet-lab webinar held in July, this is the second of a three-part webinar series co-hosted by the Communicable Diseases Genomics Network (CDGN) and the Australian Pathogen Genomics Program.
Learning outcomes
Key learning outcomes of the second webinar in the Introduction to Pathogen Genomics for Public Health Webinar Series include:
Overview of bioinformatics processes for pathogen genomics
Understanding the implication of data quality for downstream analyses
Knowledge of the limitations associated with different bioinformatics processes
Webinar facilitators
Dr Lex Leong, Pathogen Genomics Lead, South Australia Pathology
Dr Joep de Ligt, Senior Science Lead Bioinformatics & Genomics, Institute of Environmental Science and Research
Dr Kristy Horan, Bioinformatics Section Leader, Microbiological Diagnostic Unit Public Health Laboratory
Dr Elena Martinez, Bioinformatician, Institute of Clinical Pathology and Medical Research
Dr Stanley Pang, Senior Bioinformatician, PathWest
Dr Mitchell Sullivan, Bioinformatics Analyst, Forensic and Scientific Services, Queensland Health
Ms Patricia Wolf, Bioinformatician, Forensic and Scientific Services, Queensland Health
Ms Cara Minney-Smith, Acting Medicial Scientist in Charge, Pathwest
Registration
Registrations have now closed.
Program
Part one: Tuesday 20 September 2022 13:00 - 16:15 (AEST)
Assessment of sequence quality and filtering - Dr Lex Leong
Recognise the differences between raw sequence outputs
Understand the differences between long and short read sequence data
Be able to explain the QC metrics required to pass a run/sample.
Understand the trimming process (when or if trimming required)
Methods of whole genome sequencing assembly - Dr Stanley Pang
Understand the differences between assembly methods
Recognise the differences between tools used in de novo assembly, mapping and hybrid
Species identification and subtyping - Dr Kristy Horan
Understand the differences between kmer, alignment, and profile-based identification
Understand the concepts of MLST, cgMLST, and SNP distances, and their different levels of resolution
Awareness that genomic and traditional serotyping/laboratory methods may be discordant
Analysis and reporting example: Salmonella example - Ms Cara Minney-Smith
Understand the process required to determine serovars in Salmonella
Recall differences obtained through different serotyping tools
Interpreting clusters of Salmonella outbreaks with the help of epi data.
Use of Nullabor pipeline for salmonella
Part two: Wednesday 28 September 2022 13:00 - 16:45 (AEST)
Whole genome sequencing approach for antimicrobial resistance - Dr Elena Martinez
Understanding different methods & tools
Comparing both gene detection vs mutational resistance detection
Database & nomenclature challenges
Be mindful of the challenges present in in-silico AMR determination
Introduction to phylogenetics and cluster analysis - Ms Patricia Wolf
Recognise the common phylogenetic models used and other variables
Understand that different organisms have different cluster thresholds
Overview of shotgun metagenomic sequencing of clinical specimens - Dr Mitchell Sullivan
Understand different types of metagenomics analysis and what each can tell us, eg. Species ID, AMR, typing
Understand different tools for analysis, including tools for targeted panels vs shotgun metagenomics
Understand the importance of controls and how to use them for interpreting results
Data reproducibility and version control of bioinformatic tools - Dr Joep de Ligt
Understanding challenges of classification of bacteria using WGS
Defining acceptance/rejection criteria for organism identification
Understanding taxonomic classification and continuous monitoring for updates to international standards
Validation, including when it has to be in-silico (no wetlab data to use)
AMR detection