NGS 2016 Glasgow Data Analysis Workshop - Clinical Bioinformatics Workflows

The times are changing in clinical diagnostic laboratories.  Where technology is concerned, next generation sequencing (NGS) has already gained approval for use in some clinical diagnostic settings – our hopes for NGS are that it will ultimately reduce both cost and turnaround time (TAT).  However, there are numerous issues pertaining to its enrolment in such settings – between a research and clinical setting, there is a world of difference in terms of NGS.  For bioinformaticians, additionally, the mode of thinking must change when transitioning between research and clinical environments.

At this workshop, we will mix theory with practical exercises that cover the process needed for bringing NGS into clinical diagnostic use in the National Health Service (NHS).  We will also take the audience through a fully functional NGS pipeline that is currently in use in the live diagnostic setting at a NHS laboratory, including an explanation of the involved bioinformatics needed for processing raw sequence data.  A full module will also be devoted to quality control of NGS sequence data in the clinical setting.  In addition, the audience will have a chance to learn fundamental skills in a linux operating system (OS) environment, which is the primary OS of choice for NGS data analysis.

A full list of modules in this workshop follows:

1. Development of a genetic test – UK Genetic Testing Network (UKGTN)
What is the UKGTN?
What is a genetic test?
ACCE framework
Approval process for a new genetic test
The Gene Dossier
Clinical utility
Evaluation criteria
Facts and figures
Would you approve? (practical)

2. NGS in genetic testing
Role of NGS in genetic testing
Summary of ACGS guidelines
Validation of NGS tests:
     Reproducibility
     Sensitivity
     Quality aspects
     Targeting methodology
     Library preparation
     Data analysis
Content to include in NGS clinical diagnostic reports

3. Introduction to linux (practical)

4. Enrolling NGS in the NHS:  a case study

5. Clinical NGS workflow (part-practical)
The NGS data format:  FASTQ
Overview of approved analytical workflow
     Alignment to the reference genome
     Variant calling
     Report generation
Everything that a bioinformatician won’t tell you