Monika Stoll, Univ.-Prof. Dr.
Department Genetic Epidemiology, Institute of Human Genetics

 

Modul Evolutionäre Medizin

Projekt Genomics of Complex Diseases
April 18th, until May 13th, 2016

The course at the Department of Genetic Epidemiology at the IFHG will focus on Next Generation Sequencing (NGS) and genome-wide association studies (GWAS) including analysis strategies for genetic variants of complex diseases. The practical work will be split up into a lab and a computational part.

Students will get insight into current experimental sequencing methods for detecting genetic variation in models of cardiovascular diseases. Data will be analyzed using established software tools in addition to customized analysis scripts, where necessary.

Students will learn theoretical foundations of the methods used for NGS data analysis as well as software programs implementing those methods/algorithms. Further, popular visualization tools for sequencing data will be presented and students will have the opportunity to try out different analysis steps on a small NGS dataset.

Students will learn about design and analysis of genome-wide association studies (case-control and family-based). Publicly available statistical software programs like R and plink will be used to assess and characterize microarray-based genetic variants of a cardiovascular disease cohort. Their impact on disease susceptibility will be analyzed for statistical significance and will be validated in a replication cohort.

Additionally, high throughput lab facilities for genome-wide genotyping, gene expression experiments, automated sample processing and DNA concentration measurement will be demonstrated in the Illumina Core Facility.

Suggested reading:

Metzker, M. L. (2010). "Sequencing technologies - the next generation." Nat Rev Genet 11(1): 31-46.

Frazer, K. A., S. S. Murray, N. J. Schork and E. J. Topol (2009). "Human genetic variation and its contribution to complex traits." Nat Rev Genet 10(4): 241-251.

Manolio, T. A. (2010). "Genomewide Association Studies and Assessment of the Risk of Disease."
N Engl J Med 363(2): 166-176.
Pabinger S. et. al. (2014) „A survey of tools for variant analysis of next-generation genome sequencing data“, Brief. Bioinform. (2014) 15 (2): 256-278.
„Genome Analysis Toolkit“, https://www.broadinstitute.org/gatk/