Next Generation Sequencing Bioinformatics

Details

Title

Next Generation Sequencing Bioinformatics

Type

Stage One

Module code

HBI102

Requirement

Compulsory

Module objective

By the end of this module the Clinical Scientist in HSST will be able to analyse, synthesise and apply their expert knowledge and understanding of Next Generation Sequencing (NGS) Bioinformatics within a clinical setting. They will master how to manage IT infrastructure, design, validate and implement a bioinformatics workflow for the analysis of clinical NGS data.

In clinical practice, they will adhere to best practice guidelines for NGS analysis at all times as they interpret, report and lead the development of NGS as appropriate to the role. They will be expected to comply with ethical and data governance frameworks (including safeguarding personal data, confidentiality and privacy) for the reporting and storage of variants and data arising from whole-genome/exome sequencing. The Clinical Scientist in HSST will also be expected to consistently demonstrate the attitudes and behaviours necessary for the role of a CCS leading high-quality clinical bioinformatics services.

Knowledge and understanding

By the end of this module the Clinical Scientist in HSST will analyse, synthesise, evaluate and critically apply their specialist knowledge of NGS, including:

• The applications of NGS in the clinical setting, including whole-genome sequencing, whole- exome sequencing, targeted resequencing and profiling of bacterial pathogens, and differentiate the advantages and limitations of each approach.
• The principles underpinning algorithms and statistics of the main tools used in an NGS workflow.
• Ethical and governance frameworks and regulations relating to NGS data capture, storage and interpretation, and the clinical and research contexts within which NGS analysis is performed.
• Safeguarding personal data, confidentiality, privacy, risk of inadvertent disclosure.
• How samples are prepared for sequencing.
• Sample capture and library preparation.
• Chemistry of sequencing technologies.
• A range of algorithms and statistics underpinning, quality metrics, alignment, depth of coverage, annotation and filtering.
• Current policies and best practice guidelines in clinical NGS data analysis.
• The commercial market to support NGS analysis solutions.
• How to appraise in-silico tools for novel variant analysis.

Technical and clinical skills

By the end of this module Clinical Scientists in HSST will have a critical understanding of current evidence and its application to the performance and mastery of a range of technical skills and will:

• Appraise, assemble and validate the IT infrastructure and networks necessary to analyse, transfer and store NGS data.
• Develop and evaluate protocols to distinguish commercially available NGS workflows.
• Construct NGS workflows combining the appropriate tools.
• Use appropriate workflow management systems or software to combine the analysis tools.
• Write and evaluate a SOP for triage of variants from whole-exome/genome sequencing analysis.

By the end of this module Clinical Scientists in HSST will be expected to master a range of clinical and communication skills with respect to NGS analysis. They will communicate effectively with the public, patients, clinicians, academics and other healthcare professionals within the multi-professional team and will:

• Critically appraise and differentiate the main NGS platforms and the technologies that they use.
• Work within ethical and governance frameworks in the performance of NGS analysis and reporting of clinically significant variants.
• Master the technique of NGS analysis in a clinical setting.
• Interpret NGS data developing/identifying, applying and critically evaluating current best practice guidelines for NGS data interpretation.
• Produce accurate clinical reports applying and developing the emerging standards for variant interpretation, reporting and sharing.
• Communicate and discuss the results of NGS tests with clinical colleagues.
• Document and store reported/unreported data in local databases so that it may be accessed subsequently.
• Attend and actively contribute to MDT meetings.

In addition they will be aware of their own attitudes, values, professional capabilities and ethics, and critically reflect on: (i) their professional practice; and (ii) the challenges of applying research to practice in relation to these areas of practice, identifying opportunities to improve practice, building on a critique of available evidence.