Laatste update: 12-12-2022

Variant effect prediction

Course Date: course 2023 to be announced 

This course is organised in collaboration with Dr. J.T. den Dunnen, Human Genetics & Clinical Genetics, LUMC, Leiden.

Aim of the course:
DNA sequencing, incl. NGS, is a standard technology used in most modern laboratories. When the focus is on the identification of variants in the sequence, the next challenge is to evaluate these variants and their potential consequences. The "Variant Effect Prediction" course has been developed to show what one can do to predict the consequences on DNA, RNA and protein level, i.e. to classify the variants.


This course has been developed for technicians and PhD students working in a DNA laboratory (e.g. research and clinical diagnostic laboratories) who are involved in DNA sequencing data analysis. Participants are expected to bring their own laptop: (PC or Mac) as this will be needed for the course. Participants can bring their data/from an article for some of the practical sessions.

Course structure:  

We offer a 4-day course consisting of a series of lectures on variants and variant effect prediction on both the DNA, RNA and protein level. Furthermore, we will show how these variants can be viewed in genome browsers, and give an overview of variant effect prediction softwareand including "hands-on" data analysis practicals. All participants will receive a course manual.

Topics included in the course:

Day 1
Variants: The basics

Variants in the genome, position and possible consequences Calling DNA variants (SNV, SV and CNV) and limitations from sequencing technologies
HGVS nomenclature - describing variants
DNA variants - the big databases

Day 2
Variants: Gathering information

Gene variant databases and the importance of sharing information
Human Phenotype Ontology (HPO)
Potential consequences on RNA level
Viewing data using a genome browser

Computer Practicals (parallel sessions):
Genome browser (Ensembl, UCSC)
Gene variant databases: adding and retrieving data

Day 3
Predicting consequences and variant classification

Potential consequences on protein level and protein prediction tools
Variant classification using ACMG recommendations
Variant annotation using VEP

Computer practical (parallel sessions):
ACMG classification
VEP Ensembl Outreach team, EMBL-EBI

Day 4
Functional testing and reporting

VEP: what may go wrong in Practice
Functional testing; animal models and lab testing
Quality standards, reporting results and future developments.

Course program 2019

Avans Hogeschool reserves the right to substitute speakers, and change the theoretical and practical program, in order to cover most current and future new sequening technologies applications.

Course staff:

Course leaders:
Dr. M.C.M. Verschuren, Avans Hogeschool, Research group Analysis Techniques in Lifes Science, Breda, NL
Course co-ordinator:
Prof.dr. J.T. den Dunnen, Human genetics & clinical genetics, LUMC, Leiden.

All participants will receive a certificate of attendance

General Information:
Code: 2542 (4-day course)
Registration fee: € 975,- The fee includes course materials and lunch
Language: English
Location:   Avans Hogeschool, Lovensdijkstraat 63, Breda, The Netherlands.

Registration form