UiB Blogg            

Clinical analysis of NGS data


Dates: March 16-20, 2020

Location: Grand Hotel Terminus, Bergen

Lecturers: Kim Brügger

Recommended credits: 5 ECTS

Registration: HERE

Registration deadline: February 24th

 

Course description

Traditionally molecular diagnostic analysis has relied on microarrays, sequencing single genes with capillary sequencing or looking at chromosomes through a microscope. With the revolution of Next Generation Sequencing (NGS) it is now possible to replace many of the tests by sequencing a diagnostic gene panel, all the genes or even the whole genome of a patient in a single experiment. However though NGS analysis is well established in the academic setting, translating this into a clinical services is not a trivial task. This is due to the fact that a wrong diagnosis can lead to no or wrong treatment, or even to the termination of a life! As these consequences of a wrong diagnosis are so dire extra controls and legislation have been put in place to ensure the safety for the patients.

This course will introduce, explore and assess the tools, procedures and requirements needed for making the translation from academic to clinical software. This will be done through a series of lectures and group discussions culminating in a small group project.

 

Learning outcomes and competence

  • Understand the difference between academic and diagnostic software development and deployment
  • The accreditation procedure related to ISO 15189 with an emphasis on software development and deployment.
  • Be able to perform a validation of a pipeline to ensure it is suitable for diagnostic service
  • Generate a gene panel for a rare disease
  • Implement, deploy and run a clinical NGS pipeline

 

Prerequisites

Basic knowledge of bioinformatics.
Familiarity with Next Generation Sequencing, and especially DNA analysis pipelines. An knowledge about clinical environments is an advantage.

 

Tentative course program

Monday 16.03

Welcome
Clinical and diagnostic work

Tuesday 17.03
Development cycle
Pipeline validation
Software deployment
Secure computational environments

Wednesday 18.03
Standard operation procedures (SOP) Data management
and information tracking
Reporting
Gene panels

Thursday 19.03
Quality assurance GDPR and legislation Accreditation (ISO) Group project

Friday 20.03
Group project
Group project
Project presentation
Final discussion & goodbyes