An atlas of polygenic risk score associations to highlight putative causal relationships across the human phenome
5 March 2019
Tom G Richardson, Sean Harrison, Gibran Hemani, and George Davey Smith
eLife (2019) 8: e43657
An individual’s risk of developing many diseases, including heart disease and schizophrenia, is influenced by a complex combination of lifestyle factors and the genes they inherit at birth. The total number of genetic variants that an individual has that increases their risk of developing a particular disease can be measured as their ‘polygenic risk score’. These scores allow researchers to predict whether it is likely that someone will develop a disease during their lifetime.
Polygenic risk scores can also be used to link different conditions or traits to each other. For example, if high blood pressure can be caused by obesity, then genetic variants linked to obesity will also influence blood pressure. As a result, individuals with a high polygenic risk score for obesity will, on average, have a higher blood pressure than those with a low score. Comparing associations between polygenic risk scores and traits can therefore suggest whether one trait causes another.
Richardson et al. have developed an ‘atlas’ that uses data from the UK Biobank study – which contains genetic data from over 300,000 people – to investigate how shared characteristics and risk factors in individuals relate to their genetic likelihood of developing a disease. The data currently includes 162 different polygenic risk scores and 551 traits.
Richardson et al. used the atlas to evaluate which traits are most strongly linked to the polygenic risk score for schizophrenia. Analyses of these traits suggested that individuals with a high genetic risk of developing schizophrenia tend to perform worse in IQ and short-term memory tests, and that they are less likely to successfully quit smoking. These characteristics have previously been observed in studies of individuals with schizophrenia.
In the future, the atlas could be used to identify possible relationships between a wide range of individual traits and diseases. This could help to prioritise which relationships should be investigated further as part of studies to understand the causes and consequences of disease. In the long term, such studies should improve our ability to prevent and treat many different medical conditions.
The age of large-scale genome-wide association studies (GWAS) has provided us with an unprecedented opportunity to evaluate the genetic liability of complex disease using polygenic risk scores (PRS). In this study, we have analysed 162 PRS (p<5×10−05) derived from GWAS and 551 heritable traits from the UK Biobank study (N = 334,398). Findings can be investigated using a web application (http://mrcieu.mrsoftware.org/PRS_atlas/), which we envisage will help uncover both known and novel mechanisms which contribute towards disease susceptibility. To demonstrate this, we have investigated the results from a phenome-wide evaluation of schizophrenia genetic liability. Amongst findings were inverse associations with measures of cognitive function which extensive follow-up analyses using Mendelian randomization (MR) provided evidence of a causal relationship. We have also investigated the effect of multiple risk factors on disease using mediation and multivariable MR frameworks. Our atlas provides a resource for future endeavours seeking to unravel the causal determinants of complex disease.
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