Predicting Polygenic Risk of Psychiatric Disorders

Genetics provides two major opportunities for understanding human disease-as a transformative line of etiological inquiry and as a biomarker for heritable diseases. In psychiatry, biomarkers are very much needed for both research and treatment, given the heterogenous populations identified by current phenomenologically based diagnostic systems. To date, however, useful and valid biomarkers have been scant owing to the inaccessibility and complexity of human brain tissue and consequent lack of insight into disease mechanisms. Genetic biomarkers are therefore especially promising for psychiatric disorders. Genome-wide association studies of common diseases have matured over the last decade, generating the knowledge base for increasingly informative individual-level genetic risk prediction. In this review, we discuss fundamental concepts involved in computing genetic risk with current methods, strengths and weaknesses of various approaches, assessments of utility, and applications to various psychiatric disorders and related traits. Although genetic risk prediction has become increasingly straightforward to apply and common in published studies, there are important pitfalls to avoid. At present, the clinical utility of genetic risk prediction is still low; however, there is significant promise for future clinical applications as the ancestral diversity and sample sizes of genome-wide association studies increase. We discuss emerging data and methods aimed at improving the value of genetic risk prediction for disentangling disease mechanisms and stratifying subjects for epidemiological and clinical studies. For all applications, it is absolutely critical that polygenic risk prediction is applied with appropriate methodology and control for confounding to avoid repeating some mistakes of the candidate gene era.

Transforming Summary Statistics from Logistic Regression to the Liability Scale: Application to Genetic and Environmental Risk Scores

OBJECTIVE

Stratified medicine requires models of disease risk incorporating genetic and environmental factors. These may combine estimates from different studies, and the models must be easily updatable when new estimates become available. The logit scale is often used in genetic and environmental association studies; however, the liability scale is used for polygenic risk scores and measures of heritability, but combining parameters across studies requires a common scale for the estimates.

METHODS

We present equations to approximate the relationship between univariate effect size estimates on the logit scale and the liability scale, allowing model parameters to be translated between scales.

RESULTS

These equations are used to build a risk score on the liability scale, using effect size estimates originally estimated on the logit scale. Such a score can then be used in a joint effects model to estimate the risk of disease, and this is demonstrated for schizophrenia using a polygenic risk score and environmental risk factors.

CONCLUSION

This straightforward method allows the conversion of model parameters between the logit and liability scales and may be a key tool to integrate risk estimates into a comprehensive risk model, particularly for joint models with environmental and genetic risk factors.

Improving Disease Prediction by Incorporating Family Disease History in Risk Prediction Models with Large-Scale Genetic Data

Despite the many successes of genome-wide association studies (GWAS), the known susceptibility variants identified by GWAS have modest effect sizes, leading to notable skepticism about the effectiveness of building a risk prediction model from large-scale genetic data. However, in contrast to genetic variants, the family history of diseases has been largely accepted as an important risk factor in clinical diagnosis and risk prediction. Nevertheless, the complicated structures of the family history of diseases have limited their application in clinical practice. Here, we developed a new method that enables incorporation of the general family history of diseases with a liability threshold model, and propose a new analysis strategy for risk prediction with penalized regression analysis that incorporates both large numbers of genetic variants and clinical risk factors. Application of our model to type 2 diabetes in the Korean population (1846 cases and 1846 controls) demonstrated that single-nucleotide polymorphisms accounted for 32.5% of the variation explained by the predicted risk scores in the test data set, and incorporation of family history led to an additional 6.3% improvement in prediction. Our results illustrate that family medical history provides valuable information on the variation of complex diseases and improves prediction performance.

On the Transformation of Genetic Effect Size from Logit to Liability Scale

Genetic effects on the liability scale are informative for describing the genetic architecture of binary traits, typically diseases. However, most genetic association analyses on binary traits are performed by logistic regression, and there is no straightforward method that transforms both effect size estimate and standard error from the logit scale to the liability scale. Here, we derive a simple linear transformation of the log odds ratio and its standard error for a single nucleotide polymorphism (SNP) to an effect size and standard error on the liability scale. We show by analytic calculations and simulations that this approximation is accurate when the disease is common and the SNP effect is small. We also apply this method to estimate the contribution of a SNP near the RET gene to the variance of Hirschsprung disease liability, and the age-specific contributions of APOE4 on the variance of Alzheimer's disease liability. We discuss the approximate linear inter-relationships between genotype and effect sizes on the observed binary, logit, and liability scales, and the potential applications of the linear approximation to statistical power calculation for binary traits.

A Bivariate Twin Study of Lifetime cannabis Initiation and Lifetime Regular Tobacco Smoking Across Three Different Countries

Regular cigarette smoking and cannabis consumption are strongly positively related to each other, yet few studies explore their underlying variation and covariation. We evaluated the genetic and environmental decomposition of variance and covariance of these two traits in twin data from three countries with different social norms and legislation. Data from the Netherlands Twin Register, FinnTwin12/16, and the Minnesota Center for Twin Family Research (total N = 21,617) were analyzed in bivariate threshold models of lifetime regular smoking initiation (RSI) and lifetime cannabis initiation (CI). We ran unstratified models and models stratified by sex and country. Prevalence of RSI was lowest in the Netherlands and prevalence of CI was highest in Minnesota. In the unstratified model, genetic (A) and common environmental factors (C) contributed substantially to the liabilities of RSI (A = 0.47, C = 0.34) and CI (A = 0.28, C = 0.51). The two liabilities were significantly phenotypically (rP = 0.56), genetically (rA = 0.74), and environmentally correlated in the unstratified model (rC = 0.47and rE = 0.48, representing correlations between common and unique environmental factors). The magnitude of phenotypic correlation between liabilities varied by country but not sex (Minnesota rP ~ 0.70, Netherlands rP ~ 0.59, Finland rP ~ 0.45). Comparisons of decomposed correlations could not be reliably tested in the stratified models. The prevalence and association of RSI and CI vary by sex and country. These two behaviors are correlated because there is genetic and environmental overlap between their underlying latent liabilities. There is heterogeneity in the genetic architecture of these traits across country.