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Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank

Nature Genetics volume 49, pages 1311–1318 (2017)Cite this article

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Abstract

Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform understanding of the human phenome and accelerate progress toward precision medicine. However, a critical question when analyzing high-dimensional and heterogeneous data is how best to interrogate increasingly specific subphenotypes while retaining statistical power to detect genetic associations. Here we develop and employ a new Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyze genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies new associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying the approach to genetic risk scores (GRSs), we show the extent of genetic sharing among IMDs and expose differences in disease perception or diagnosis with potential clinical implications.

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Figure 1: Schematic of a diagnosis classification tree and genetic coefficient transition scenarios tested.
Figure 2: Evidence of HLA-B*27:05 allele association with risk for clinical diagnoses in the HES data set.
Figure 3: Sensitivity and specificity analysis of TreeWAS on simulated data.
Figure 4: Genetic analysis of HLA allelic variation in the risk of clinical phenotypes from the UK Biobank SR diagnosis and HES data sets.
Figure 5: Association analysis of genetic risk for multiple IMDs derived from clinical phenotypes in the UK Biobank SR diagnosis and HES data sets.

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Acknowledgements

This research has been conducted using the UK Biobank Resource (application number 10625). The research has been supported by the Wellcome Trust (095552/Z/11/Z to P.D., 100308/Z/12/Z to L.F., 100956/Z/13/Z to G.M., and 090532/Z/09/Z and 203141/Z/16/Z to the Wellcome Trust Centre for Human Genetics), the Danish National Research Foundation (grant number 126 to L.F.), the Wellcome Trust/Royal Society (204290/Z/16/Z to C.A.D.), Takeda, Ltd. (L.F. and C.A.D.), the Medical Research Council (grant number MC_UU_12010/3 to L.F.), and the Oak Foundation (OCAY-15-520 to L.F.). This work was supported by the Australian National Health and Medical Research Council (NHMRC), Career Development Fellowship 1053756 (S.L.), and by Victorian Life Sciences Computation Initiative (VLSCI) grant VR0240 on its Peak Computing Facility at the University of Melbourne, an initiative of the Victorian government in Australia (S.L.). Research at the Murdoch Children's Research Institute was supported by the Victorian government's Operational Infrastructure Support Program.

Author information

Author notes

  1. Adrian Cortes and Calliope A Dendrou: These authors contributed equally to this work.

  2. Lars Fugger and Gil McVean: These authors jointly directed this work.

Authors and Affiliations

  1. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK

    Adrian Cortes, Calliope A Dendrou, Luke Jostins, Alexander Dilthey, Peter Donnelly & Gil McVean

  2. Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, Oxford Centre for Neuroinflammation, John Radcliffe Hospital, University of Oxford, Oxford, UK

    Adrian Cortes, Calliope A Dendrou & Lars Fugger

  3. MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK

    Calliope A Dendrou & Lars Fugger

  4. Centre for Systems Genomics, Schools of Mathematics and Statistics and of BioSciences, University of Melbourne, Parkville, Victoria, Australia

    Allan Motyer, Damjan Vukcevic & Stephen Leslie

  5. Murdoch Children's Research Institute, Parkville, Victoria, Australia

    Damjan Vukcevic & Stephen Leslie

  6. Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, US National Institutes of Health, Bethesda, Maryland, USA

    Alexander Dilthey

  7. Department of Statistics, University of Oxford, Oxford, UK

    Peter Donnelly

  8. Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark

    Lars Fugger

  9. Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK

    Gil McVean

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Contributions

A.C. and G.M. performed the analyses with contributions from C.A.D. A.C., C.A.D., L.J., P.D., L.F. and G.M. conceived the study. A.M., D.V., A.D. and S.L. performed HLA imputation. A.C., C.A.D. and G.M. wrote the manuscript, and all other authors reviewed the manuscript.

Corresponding author

Correspondence to Gil McVean.

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Competing interests

G.M. is a cofounder of, holder of shares in, and consultant to Genomics, PLC. P.D. is a cofounder of, holder of shares in, and director and executive officer of Genomics, PLC. A.D., G.M., P.D. and S.L. are partners in Peptide Groove, LLP. Peptide Groove has licensed HLA typing technology to Affymetrix, Ltd. The other authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 BFtree statistic and the number of non-zero nodes at a threshold of PP = 0.75 over the parameter space of θ and π1 for HLA-B*27:05 allele association with risk for clinical diagnoses in the HES data set.

Supplementary Figure 2 Comparison of rate of active node identification in TreeWAS and PheWAS analyses with simulated data.

Rate of active node identification at increasing posterior probability (PP) thresholds and different simulated allele frequencies of the causal genetic variant, for the TreeWAS method (θ = 1/3 and π1 = 0.001) and assuming a model with complete independence among phenotypes (θ → ∞ and π1 = 0.001), which is equivalent to PheWAS. We simulated data for 500 replicates where the genetic variant affects clinical annotations found distributed in the tree. The rate of active node identification was calculated for the five affected clinical annotations (circles) and for the rest of the annotations is the tree with zero genetic coefficients (diamonds).

Supplementary Figure 3 Sensitivity analysis for clustered active nodes.

Sensitivity analysis in the detection of genetic association at the tree level as measured by the BFtree statistic. We simulated data where the causal variant affected clustered nodes in the tree and fitted the TreeWAS method (blue) and the PheWAS models where we assume complete independence among phenotypes (orange) and where we assume complete independence among phenotypes and all nodes to be active (yellow).

Supplementary Figure 4 Sensitivity analysis for distributed active nodes.

Sensitivity analysis in the detection of genetic association at the tree level as measured by the BFtree statistic. We simulated data where the causal variant affected distributed nodes in the tree and fitted the TreeWAS method (blue) and the PheWAS models where we assume complete independence among phenotypes (orange) and where we assume complete independence among phenotypes and all nodes to be active (yellow).

Supplementary Figure 5 Linkage disequilibrium between identified HLA associations.

Linkage disequilibrium between independent HLA associations found in the analyses for the SR and HES data sets. Each allele shown was found in at least one of the analyses, seven of which were found in both. With the exception of the HLA-DRB1*15:01 and HLA-DQB1*06:02 alleles, all identified associations were not in linkage disequilibrium (r2 < 0.02). The HLA-DRB1*15:01 and HLA-DQB1*06:02 alleles were identified in the SR and HES analyses, respectively, and both are in high linkage disequilibrium (ρ = 0.98) and were fine-mapped to the same phenotypes.

Supplementary Figure 6 Effects of T1D on T2D diagnosis misclassification in TreeWAS summary statistics.

Individuals with a type 1 diabetes (T1D) diagnosis were misclassified as having type 2 diabetes (T2D) at different misclassification rates, ranging from 0.5 to 10% of the cohort with a T2D diagnosis. TreeWAS analysis was performed with both T1D and T2D GRSs in the SR and HES data sets. 100 simulations were generated for each misclassification rate. (a,b) Evidence of association at the tree level (BFtree) in the SR (a) and HES (b) data sets for the T1D and T2D GRSs. (c,d) Distribution of estimated posterior probabilities for the T1D and T2D diagnosis terms in the SR (c) and HES (d) data sets for both T1D and T2D GRS analyses. (e,f) Distribution of estimated effect sizes for the T1D and T2D terms in the SR (e) and HES (f) data sets for both T1D and T2D GRS analyses.

Supplementary Figure 7 Effects of T2D on T1D diagnosis misclassification in TreeWAS summary statistics.

Individuals with a type 2 diabetes (T2D) diagnosis were misclassified as having type 1 diabetes (T1D) at different misclassification rates, ranging from 0.5 to 10% of the cohort with a T1D diagnosis. TreeWAS analysis was performed with both T1D and T2D GRSs in the SR and HES data sets. 100 simulations were generated for each misclassification rate. (a,b) Evidence of association at the tree level (BFtree) in the SR (a) and HES (b) data sets for the T1D and T2D GRSs. (c,) Distribution of estimated posterior probabilities for the T1D and T2D diagnosis terms in the SR (c) and HES (d) data sets for both T1D and T2D GRS analyses. (e,f) Distribution of estimated effect sizes for the T1D and T2D terms in the SR (e) and HES (f) data sets for both T1D and T2D GRS analyses.

Supplementary Figure 8 Ancestry analysis of UK Biobank individuals using principal-component analysis.

120,286 individuals plotted in orange were retained in the analysis, and these co-cluster with European-ancestry populations.

Supplementary Figure 9 Prior on effect sizes for the full genetic model.

β1 and β 2 are the log-odds coefficients for heterozygotes and homozygotes, respectively. The heat map indicates the relative density of the prior.

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Cortes, A., Dendrou, C., Motyer, A. et al. Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank. Nat Genet 49, 1311–1318 (2017). https://doi.org/10.1038/ng.3926

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