Advanced Analysis of Genome-wide Association Studies [ESP74]

Course highlights

EC points


Start date


End date


Course days

Monday to Friday (5 full days)


Prof. Fernando Rivadeneira, Dr. Carolina Medina Gomez and others

Course fee

€ 1058


Erasmus MC, Rotterdam NL




Basic understanding of genetic epidemiology and statistics (regression analysis and maximum likelihood estimation).

See course description below for more information.


  • Genetic Epidemiology


Go to the ESP website

Detailed information about this course:


Faculty: Prof. Fernando Rivadeneira, MD PhD, Carolina Medina Gomez, PhD, Katerina Trajanoska, PhD and others

Genome-wide association studies (GWAS) constitute a powerful approach to investigate the genetic basis of complex traits and disorders. The course consists of lectures providing a conceptual framework on crucial aspects of quality control, genotype imputation, methods to detect and correct for stratification, meta-analysis and genomic annotation of GWAS signals. An overview of the most frequently used statistical tools will be accompanied by instructive hands-on computer exercises on the principles of analysis of quantitative traits and disease outcomes. State of the art procedures for running GWAS will be taught, including: Quality Control / QC (PLINK2); GWAS analysis correcting for structured data (SAIGE and REGENIE); GWAS Meta-analysis and QC (EasyQC; METAL). Post-GWAS functional follow-up procedures will include downstream analysis (Conditional analyses, FINEMAP and PRS). While theoretical background is provided on all topics, this is by definition a "hands-on" practical course, meaning you will spend most of the day performing genetic analyses. The course format will allow interactive break-out discussion sessions on theoretical and practical aspects of running GWAS, together with expert-advice procurement on diverse components of collaborative research within networks and consortia.

Participants of this course should be familiar running Linux commands and with running scripts and packages in R-programming language. These skills are taught in the NIHES courses: EL016 (GE14) "Linux for Scientists" and EL019 (GE03) "Genome-wide Association Studies"; and participants are encouraged to follow these courses in advance.


  • This course aims to train participants in the (advance) principles of GWAS, addressing aspects of study design, data analysis, extending to the interpretation and follow-up of results.
  • After completing the course, participants will be able to understand the principles of GWAS; perform genome-wide association analysis using state-of-the-art software tools; interpret GWAS results; and integrate them in a genomic context by means of web-based bioinformatics resources.

Participant profile

Clinical researchers, clinical epidemiologists, molecular biologists, bioinformaticians and biostatisticians aspiring to run analyses of genome-wide association studies.



Reduction on fees

PLEASE NOTE: This does not apply to the fee of the research master programmes (120 EC points)

No fees are charged for  Erasmus MC PhD candidates, provided they have an account in Hora Finita, the Erasmus University PhD registration system. When submitting the application, you can state that someone else pays your tuition fee.

In case of cancellation or no show, the cancellation policy applies based on the full course fee.


25% reduction for all (international) PhD candidates without formal appointment at Erasmus MC

Upon receipt of your application you will receive a request to upload proof of enrollment as a PhD candidate.