Epigenomics and Sequencing in Behaviour and Health

Upon successful completion of the course, students are expected to be able to:

1. describe the epigenetic mechanisms employed in human cells and their role in development and cell identity
2. relate these mechanisms to the effects of DNA polymorphisms and social and environmental factors that elicit individual differences in behaviour and health
3. explain array-based and sequencing techniques to measure genome-wide DNA methylation and RNA
4. interpret and cite research described in key scientific publications in expert journals such as Genome Biology, Epigenetics, and Nature
5. perform quality control and normalization of genome-wide DNA methylation datasets
6. perform an epigenome-wide association study and interpret results
7. compare research designs and summarize challenges in epigenetics 

Though our genetic material (DNA sequence) may be relatively fixed, the epigenetic mechanisms that regulate the expression of our genes vary across cell types and are subject to changes during development and in response to external influences. Epigenomics is concerned with the study of epigenetic mechanisms on a genome-wide scale. Sequencing is a technique that is applied for typing DNA, RNA, or DNA methylation on a genome-wide scale at the maximum resolution. This course aims to provide students with the theoretical background and with the analytical skills required to analyse and interpret genome-wide epigenomic data in the context of human epigenetic epidemiology research. Students will understand how life circumstances may alter gene expression and lead to individual differences in behaviour and health. The theoretical part, covered by lectures and a textbook, provides an understanding of the various epigenetic mechanisms employed in human cells, our current understanding of their role in behaviour and health, the techniques to measure whole genome DNA methylation and RNA including array-based methods and sequencing, and the research designs, quality control of data, statistical analysis, and challenges in human epigenetic epidemiology. A significant part of this course will be devoted to hands-on computer practical work in which the student will analyse epigenomic data (mostly DNA methylation arrays) from the Netherlands Twin Register in combination with survey data (e.g. environmental indicators). These practical assignments are intended to familiarize students with all aspects of the analysis of epigenomic data: from the initial data quality control and normalization to performing an epigenome-wide association study. The course duration is 4 weeks. The first 3 weeks consist of lectures and practicals. The course will end with a final integrative data analysis assignment, and with a written exam in week 4.