Genome-Wide Associations Studies: Cancelled
Course has been cancelled
Due to new guidelines from the University we are unfortunately cancelling the GWAS course.
Information from the Faculty of Medicine: https://www.med.uio.no/english/about/news-and-events/news/2020/information-coronavirus-for-employees-at-med.html
About the course Four days intensive course consisting of a series of lectures and workshops.
Credits 3 ECTS (directly available for PhD students of the Medical Faculty at UiO, PhD students at other faculties and universities should ask about availability at their educational offices)
Course content The majority of human traits including common diseases are likely polygenic in nature, that is, they are affected by numerous genetic variants with small individual effects. During the past couple of decades thousands of genetic loci associated with various human traits have been discovered throughout the genome using Genome-Wide Association Studies (GWAS). Although GWAS proved to be an effective approach to investigate the genetic architecture of complex human traits, it has left several questions unanswered and room for more advanced research to be conducted on top of it. In the course we will cover: Basic aspects of genetics and statistics important for understanding the GWAS framework. Essential stages of the standard GWAS pipeline, including processing of raw genotypes, QC, imputation, association (meta-) analysis and interpretation of association results. Tools to conduct these steps (including practical training). Publicly available resources providing access to GWAS summary statistics, online analysis tools and other related data. Several strategies for advanced post-GWAS analysis, including polygenic load assessment and investigation of genetic overlap between different traits (including practical tasks). Projects conducted in Norway and specifically at NORMENT.
Day 1 [16.03]. Genome-wide association studies background and applications. 9:00 – 9:30 General introduction and overview of projects in NORMENT. [Ole Andreassen] 9:30 – 10:30 Genes, genomes and genetic variation. [Tim Hughes] 10:30 – 10:40 Break. 10:40 – 11:40 Brain imaging and genetics. [Thomas Wolfers] 11:40 – 12:20 Lunch break. 12:20 – 12:50 Gene expression patterns in the brain: Implications for physical and mental health. [Daniel Quintana] 12:50 – 14:00 Preparing software and data for workshops. [Alexey Shadrin]
Day 2 [17.03]. GWAS essentials. 9:00 – 9:30 Genotyping. Quality control (QC) with GenomeStudio. [Lavinia Andresen] 9:30 – 10:30 Pre-imputation QC and imputation + workshop (part 1). [Elizabeth Corfield] 10:40 – 11:40 Break. 10:40 – 11:40 Pre-imputation QC and imputation + workshop (part 2). [Elizabeth Corfield] 11:40 – 12:20 Lunch break. 12:20 – 13:30 Testing for association meta-analysis and interpretation of the results + workshop. [Kevin O`Connell]
Day 3 [18.03]. Post GWAS analysis. Available tools and data. 9:00 – 9:50 FUMA, pathway and network analysis + workshop. [Shahram Bahrami] 9:50 – 10:30 Survey of available genetics data sets and overview of TSD (services for sensitive data). [Oleksandr Frei] 10:30 – 10:40 Break. 10:40 – 11:40 UK Biobank. Available data and technical protocols. [Oleksandr Frei] 11:40 – 12:20 Lunch break. 12:20 – 13:30 Polygenic risk scores (PRS) + workshop. [Alexey Shadrin]
Day 4 [19.03]. Post GWAS analysis. Clinical implications. Statistics. 9:00 – 9:30 GWAS. Clinical implications. [Nils Eiel Steen] 9:30 – 10:30 LD-score regression. Genetic correlation and Partitioned heritability + workshop. [Oleksandr Frei] 10:30 – 10:40 Break. 10:40 – 11:40 Genetic architecture beyond heritability. MiXeR. CondFDR. [Alexey Shadrin] 11:40 – 12:20 Lunch break. 12:20 – 13:30 Concluding remarks, discussion and distribution of examination tasks.
Prerequisites Basic starting knowledge of genetics and statistics as well as some experience with UNIX command line would be beneficial. In order to follow the workshops, you will need to download example data and install several software tools (we will do it together at the end of the first course day).
Software required for workshops Plink: https://www.cog-genomics.org/plink2 PRSice: https://choishingwan.github.io/PRSice LDSC: https://github.com/bulik/ldsc (including python interpreter and required packages; you may want to use anaconda distribution which already contains all required packages: https://www.anaconda.com/distribution/#download-section)
Examination The exam will be in the form of reports that participants should prepare within 3 weeks after the course week. Topics for the reports will be discussed at the last day of the course. Reports will be evaluated and classified as “pass” or “fail” within two weeks after they are received. The participants will get reviewer’s comments on their report regardless of the outcome. Alternatively, the participants can opt for a short presentation. Similarly to reports, presentations should be prepared within 3 weeks after the course week and then presented and discussed with a course commission on an agreed day.
Other information If you have any questions, please contact Alexey Shadrin