Application of next generation sequencing or Whole Genome Sequencing WGS in Clinical Management, Infection Control and Public Health

Details

Title

Application of next generation sequencing or Whole Genome Sequencing WGS in Clinical Management, Infection Control and Public Health

Type

Stage Two

Module code

HLS270

Requirement

Compulsory

Module objective

By the end of the training period trainees* will, in respect to developing skills and knowledge required for understanding the scientific basis of WGS, methods, current applications, its potential and have developed a capacity to keep abreast of developments in sequencing technology and software solutions for its application as WGS methods become integrated into mainstream practice, be able to:

• analyse, synthesise, evaluate and apply knowledge
• perform, adapt and master a range of technical and clinical skills and procedures and
• demonstrate the attitudes and behaviours necessary for professional practise as a Consultant Clinical Scientist dealing with the complexities, uncertainties and tensions of professional practise at this level

*The trainee will learn how to work in tandem with specialists in bioinformatics and information technology.

Knowledge and understanding

By the end of the training period the trainee will be able to demonstrate the ability to analyse, evaluate and synthesise relevant knowledge and its application to their professional practice in relation to:

• Knowledge of sequencing methods including:
  • Sanger sequencing
  • Next generation sequencing
  • High throughput machines
  • Bench top machines
  • Methods under development
• The rational basis for specimen selection according to context
• Laboratory protocols, including specimen preparation and archiving
• Sequence assembly software
• Interpretation of results, their display and communication to colleagues

(These aspects will involve learning to work closely with specialists in bioinformatics and IT.  The trainee will develop a capacity to track these aspects: as methods become increasingly semi-automated and user- friendly, the trainee will take on an increasingly independent role in managing sequencing assembly and data interpretation).

• Knowledge of applications for NGS, including:
  • species identification
  • detection of virulence genes
  • detection of genetic determinants of antimicrobial resistance
  • high resolution typing
• Understand the influence of NGS on service provision and laboratory management

Technical and clinical skills

By the end of the training period the trainee will be able to demonstrate a critical understanding of current relevant research, theory and knowledge and its application to the performance, adaptation and mastery of the following technical procedures and laboratory skills:

• sequencing protocols and use of bench top machines
• sequence assembly and data interpretation (in liaison with specialists in bioinformatics and IT).

By the end of the training period the trainee will be able to apply knowledge of the scientific basis of WGS, methods, current applications and its potential be able to perform, adapt and master the clinical skills necessary to:

• know the limitations and potential offered by NGS according to context and will be able to advise clinical colleagues on the use of NGS tests, be able to process specimens and interpret the results.