With the advent of high-throughput technologies such as Illumina platforms and next generation sequencing, genetic and epigenetic data are becoming more available for both research and commercial purpose. These data show promise to revolutionise current knowledge of complex diseases and phenotypes in which genetic predisposition, epigenetic factors, and environmental factors are expected to interact with each other. The value of these data comes from the execution of the so-called genetic and epigenetic association studies with the objective of identifying regions of the genome whose genetic or epigenetic variations (e.g., single nucleotide polymorphism [SNP] and CpG methylation sites, respectively) are associated with a given disease or phenotype via systematic statistical testing. This workshop intends to explore the basics of these studies with special emphasis on genome-wide association studies (GWAS) using SNP data and epigenome-wide association studies (EWAS) for CpG methylation data. The workshop will be very practical with hands-on real-world data using both PLINK (GWAS) and the R software via package minfi (EWAS). The attendees will learn how to perform basic data quality controls, how to adjust to multiple testing, to construct genetic models, to present the respective results, and to retrieve important genetic information from existing public database such as ensembl or NCBI SNP database.  

Date: March 13 and 14, 2025, 10:00 a.m. – 3:00 p.m. (2-days online workshop).

Time: 10 hours (5 hours each day with a coffee break).

Location: online.

Group: for a group larger than 3 persons.

Teacher: Nuno Sepúlveda, Ph.D.

Price: 445 EUR (plus VAT if applicable).

Methods of payment: wire transfer.

Topics:

• Introduction to SNP and methylation data
• Quality controls for genetic data (Hardy-Weinberg Equilibrium Test, Heterozygosity, Minor allele frequency)
• Genetic models (additive, recessive/dominant, general, heterosis)
• Quality controls for methylation data (genetic variation)
• M values versus beta values for methylation data
• False discovery rate (Benjamini-Hochberg, Benjamini-Yekutelni and Benjamini-Kruger-Yekutelni procedures)
• Manhattan Plots

Learning Outcomes

After the workshop, participants will:

1. Understand the fundamentals of genetic and epigenetic association studies, with a focus on genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS).
2. Be able to independently perform key steps of GWAS using SNP data and EWAS using CpG methylation data, leveraging tools like PLINK and the R package minfi.
3. Gain practical skills in conducting data quality control, adjusting for multiple testing, constructing genetic models, and presenting findings effectively.
4. Learn to retrieve and interpret genetic information from public databases such as Ensembl and the NCBI SNP database.
5. Develop the ability to analyze and interpret genetic and epigenetic findings in the context of complex diseases and phenotypes.

Nuno Sepúlveda, Ph.D.

Assistant Professor from the Faculty of Mathematics & Information Science at the Warsaw University of Technology where he teaches biostatistics and other courses. Previously, he worked as a research fellow in statistical genetics and genetic epidemiology of Malaria and then as an Assistant Professor of Epidemiology and Biostatistics in the Department of Infection and Immunology (now the Department of Infection Biology), Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine. Nuno has more than 20 years of experience in the field of applied statistics and has more than 150 peer-reviewed publications in journals, such as Nature Genetics, PLoS Genetics, Lancet Infectious Diseases, Lancet Hematology, and Science Translational Medicine. His current research interest is the application of statistical and machine learning techniques to investigate the pathogenesis of Chronic Fatigue Syndrome/Myalgic Encephalomyelitis and long COVID with the special emphasis on genetic, epigenetic and serological data. Currently, he holds a Horizon Europe Widera Grant in a EU-funded project (PvSTATEM) aiming to perform two clinical trials on malaria control in Ethiopia and Madagascar. He is also Associate Editor of Frontiers in Medicine (Infectious Diseases: Pathogenesis and Therapy) and Frontiers in Public Health (Infectious Diseases: Epidemiology and Prevention).