In conjunction with the Research Symposium, we will also host a UK Biobank Instruction Day on Tuesday February 6th, to demonstrate and teach aspects of data access and data analyses. The sessions aim to be informal, with opportunity to ask questions and interact with Instructors.
Workshop Requirements:
A laptop with R and R-studio installed for the instruction day will be useful (but not essential) for some of the workshop material.
The current program includes 4×1.5hr workshop sessions on:
1. Using summary statistics & running a PheWAS in the UK Biobank.
09:00 AM – 10:30 AM
This session will begin with a data-focused introduction in the UK Biobank and briefly define genome-wide association studies. Next, the session will detail downloading and using summary statistics, both from the UK Biobank and external studies. A workshop during the session will demonstrate the use of SBayesR for the prediction of polygenic scores (PGS) from UKB summary statistics. The final part of the session will begin with a more detailed introduction to disease-related phenotypes, and how to conduct a PheWAS (phenotype-wide association study) in the UK Biobank.
Instructors:
Dr Jian Zeng is a statistical geneticist and NHMRC Emerging Leadership Fellow at the Institute for Molecular Bioscience (IMB) at the University of Queensland (UQ). His research focuses on the development and application of innovative statistical methods for estimating the genetic architecture and evolutionary signals in complex traits, identifying genetic variants, genes and molecular intermediates associated with phenotype variation, and predicting trait phenotypes using genome sequence data. He received an IMB Impact Award for Enabling Technology & Method Development in 2021 and serves as the Director of Genetics and Genomics Winter School since 2022.
Isabelle McGrath is a final year PhD candidate in the Centre for Population and Disease Genomics working with Dr Sally Mortlock and Professor Grant Montgomery. She is passionate about improving endometriosis management and understanding, so in her PhD she is investigating the relationship between endometriosis and its comorbid disorders using the UK Biobank and large genomic datasets. Before commencing her PhD, she studied biomedical science and bioinformatics at the University of Queensland.
2. Navigating the UK Biobank Research Analysis Platform.
11:00 AM – 12:30 PM
We will guide you through the process of accessing and analyzing UKB data on the Research Analysis Platform (RAP). This includes setting up your RAP account, accessing the UKB data on the RAP, understanding the differences between cluster and cloud computing, as well as demonstrating how to submit and monitor a job using both the user interface and the command line interface.
Instructors:
Dr Huanwei Wang is a postdoctoral research fellow in the institute for molecular bioscience (IMB) supervised with Dr. Loic Yengo and Prof. Peter Visscher. Prior to this, he was a PhD student in IMB/UQ with Prof. Jian Yang and Dr. Allan Mcrae. His current research focus is to use whole exome/genome sequencing data on the RAP to estimate the contribution of ultra-rare variants to the heritability for human complex traits.
3. Mendelian Randomisation analyses using UK Biobank data.
01:30 PM – 03:00 PM
In this session we will learn about Mendelian randomization (MR), an epidemiological method which uses genetic data to investigate potential causal relationships between variables in observational studies. The first part of the session will introduce MR, show examples of how to calculate causal effect estimates, explore the limitations of MR and some sensitivity analysis. The second part of the session will begin with a general overview of the recently released UK Biobank Pharma Proteomics Project (UKB-PPP) dataset and then demonstrate the use of the UKB-PPP as exposures in a MR context.
Instructors:
Dr Gunn-Helen Moen was awarded her PhD on the “Genetic and environmental etiology of glucose metabolism and cardiometabolic traits during pregnancy and in later life” in 2019 from the Faculty of Medicine at the University of Oslo. After finishing her PhD she was awarded a Mobility/Marie Sklodowska-Curie Fellowship from the Research Council of Norway and as part of that fellowship spent two years as a visiting academic at the University of Queensland. She is currently an ARC DECRA fellow at IMB. Her research focus is on using Mendelian randomization to investigate intergenerational effects.
Emily Daubney is a final year PhD student in the Evans group at UQ IMB. Her research involves using ‘omics data (genetic, metabolite, and protein data) to gain insight into the aetiology of complex traits.
4. Using UK Biobank Imaging data.
03:30 PM – 05:00 PM
The UK Biobank is the world’s largest multi-modal imaging study. It began in 2014 with the aim of re-inviting 100,000 participants to undergo brain, cardiac and abdominal magnetic resonance imaging, dual-energy X-ray absorptiometry and carotid ultrasound. Performing imaging at this scale is unprecedented and allows researchers to identify associations between lifestyle and genetic factors and imaging-derived measures of body structure and function. The session will demonstrate the data available for research and demonstrate analysis applications.
Instructors:
Baptiste Couvy-Duchesne is a postdoctoral researcher at the University of Queensland, CJ Martin fellow, and INRIA researcher (French national research institute for digital science and technology). He works at the intersection of genetics and neuroimaging. In particular, he develops methods inspired by genetics to analyse large scale and high-dimensional neuroimaging data.
Elise Delzant is a second year PhD student at the Paris Brain Institute, under the supervision of Olivier Colliot and Baptiste Couvy-Duchesne. She is visiting the University of Queensland as part of a collaborative project with PCTG (Program for Complex Trait Genomics), funded by INRIA (French national research institute for digital science and technology). In her recent project, Elise has processed and compared several versions of the brain MRI collected by the UK Biobank.
Caio Seguin is a postdoctoral researcher at the University of Melbourne. His research combines neuroimaging data with mathematical and computational models to understand brain structure and function. In particular, he is interested in applying concepts from network science and graph theory to the human connectome, with the aim of understanding how organizational properties of brain networks facilitate large-scale neural communication.
Participation is free of charge, but registration is essential for catering purposes. We will provide lunch and coffee.
Inquiries and suggestions to Dr Kathryn Kemper (k.kemper@uq.edu.au).