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  • Review Article
  • Published:

Developing and evaluating polygenic risk prediction models for stratified disease prevention

Nature Reviews Genetics volume 17, pages 392–406 (2016)Cite this article

Subjects

Key Points

  • Evaluation of the utility of genetic risk assessment for disease prevention requires the development of models incorporating both genetic and non-genetic (environmental) risk factors for predicting the absolute risk of diseases. Development of models for absolute risk may require combining data from various sources, including epidemiological cohort, case–control and family-based studies, population-based disease and death registries, and national health surveys.

  • Complex diseases are likely to be associated with thousands or tens of thousands of common single-nucleotide polymorphisms (SNPs), each with small effects, but cumulatively they may explain substantial variation in disease risks. The extreme polygenic architecture of many common diseases implies that the predictive performance of polygenic risk scores (PRSs) will slowly rise in the future with increasingly large studies and will reach a plateau only after genome-wide association studies (GWAS) reach huge sample sizes, possibly involving hundreds of thousands of individuals.

  • Development of optimal PRSs based on data from a given GWAS data set requires careful consideration of the threshold for SNP selection, weights for selected SNPs, linkage disequilibrium and any external knowledge — including functional, annotation and pleiotropic information — that can be utilized to prioritize the SNPs.

  • Development of multifactorial risk models, including PRSs and environmental risk factors, requires characterization of the risk associated with individual factors, exploration of interactions and assessment of the goodness of fit of models. Use of information on disease rates and mortality from population-based registries can improve the generalizability of absolute risk models.

  • Before clinical applications, models need to be assessed for calibrations — that is, their ability to produce an unbiased estimate of risks in prospective cohort studies. The clinical utility of well-calibrated models depends on the degree of risk stratification they can produce for the population, but the optimal criterion for evaluating risk stratification depends on the clinical application under consideration.

Abstract

Knowledge of genetics and its implications for human health is rapidly evolving in accordance with recent events, such as discoveries of large numbers of disease susceptibility loci from genome-wide association studies, the US Supreme Court ruling of the non-patentability of human genes, and the development of a regulatory framework for commercial genetic tests. In anticipation of the increasing relevance of genetic testing for the assessment of disease risks, this Review provides a summary of the methodologies used for building, evaluating and applying risk prediction models that include information from genetic testing and environmental risk factors. Potential applications of models for primary and secondary disease prevention are illustrated through several case studies, and future challenges and opportunities are discussed.

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Figure 1: Steps for building and evaluating absolute risk models for the general population.
Figure 2: Hypothetical distribution of absolute risk for breast cancer.
Figure 3: Effect-size distribution for susceptibility markers and implications for risk prediction.
Figure 4: Role of polygenic risk in determining absolute risk reduction for coronary heart disease and bladder cancer achievable by modification of environmental risk factors.
Figure 5: Role of polygenic risk in determining the optimal age of initiation for screening of breast and colon cancers.

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Acknowledgements

The research was supported by intramural funding from the National Cancer Institute, which is part of the US National Institutes of Health, and a Bloomberg Distinguished Professorship endowment from Johns Hopkins University.

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Authors and Affiliations

  1. Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University,

    Nilanjan Chatterjee

  2. Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, 21205, Maryland, USA

    Nilanjan Chatterjee

  3. Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, 20892, Maryland, USA

    Nilanjan Chatterjee, Jianxin Shi & Montserrat García-Closas

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Study designs and methods used for model building, validation and assessment ofclinical utility in case studies (PDF 71 kb)

Glossary

Penetrance

The proportion of individuals in a population with a genetic variant who develop the disease associated with that variant. Common single-nucleotide polymorphisms (SNPs) are referred to as low-penetrant, as risk alleles typically confer modest risk.

Polygenic disease

A disease caused by a large number of underlying susceptibility genes.

Prospective cohort studies

Studies that collect information on potential risk factors (based on questionnaires, devices and biological samples) in a sample of healthy individuals and then longitudinally follow them to record future disease incidence. Information on risk factors can be updated longitudinally over time.

Heritability

The proportion of phenotypic variation attributed to genetic variation among individuals in a population.

Polygenic risk score

(PRS). A score for predicting disease risk, calculated as the weighted sum of risk alleles with the weights specified by association coefficients.

Ascertainment

Non-random selection of study participants, often arising in genetic studies owing to the selection of subjects based on personal and/or family history of disease.

Ethnically admixed samples

Samples from subjects who have inherited genetic materials from two or more previously separated populations.

Confounding

A false association between a disease and an exposure caused by the presence of a risk factor for the disease that is correlated with the exposure.

Case–control studies

Studies that sample subjects with and without a disease and collect information on potential risk factors in a retrospective fashion.

Incidence rates

(Also known as hazard rates). The rates at which new diseases are observed in a population during a specific time interval (for example, between specific ages).

Proportional hazard model

A model for incidence rate that assumes a multiplicative effect of risk factors on the age-specific incidence rate of a disease.

Hazard ratio

The ratio of hazard rates (also known as incidence rates) between groups of subjects with different risk factor profiles.

Incident case–control studies

Case–control studies that aim to recruit representative samples of new cases that arise in a population during a specified time period.

Odds ratios

Quantitative measures of the strength of association between a binary disease end point and risk factors that can be estimated by logistic regression models.

Prevalent cases

The number of individuals with a disease condition in a population at a given time point.

Selection bias

Bias in risk estimates due to non-random selection of study participants. Case–control studies can be particularly prone to selection bias, as the likelihood of participation may be affected by both disease status and risk factor history.

Logit

The transformation log{p/(1−p)} where p is the probability of disease occurrence in a population.

Liability score

A score that represents the underlying progression of a disease through the accumulation of risks on a continuous scale. The risk of binary disease outcomes can be modelled by assuming the existence of an underlying, normally distributed liability score that leads to the manifestation of disease when it exceeds a threshold.

Probit

The transformation Φ−1(p) where Φ−1 denotes the inverse of the cumulative distribution function for a standard normal random variable and p is the probability of disease occurrence in a population.

Additive interaction

The presence of non-additive effects of multiple risk factors on the risk of a disease. Absence of additive interaction indicates that the risk difference parameter associated with one factor does not vary with that of other factors.

Genome-wide significance

A stringent level of statistical significance, often set at p − val = 5 × 108 for genome-wide association studies (GWAS) of common variants, for the avoidance of false positives.

Linkage disequilibrium

(LD). The non-random association of alleles at different loci, frequently measured by r2, the square of the genotypic correlation between two single-nucleotide polymorphisms (SNPs).

Pleiotropic analysis

Analysis to identify variants associated with two or more distinct phenotypic traits.

Recall bias

Bias in risk estimates that could arise in case–control studies owing to differential recall or reporting of disease status by study participants.

Multiplicative interactions

Presence of the non-multiplicative effects of multiple factors on the risk of a disease. Absence of multiplicative interaction implies that the risk ratio parameter associated with one factor does not depend on that of the other factors.

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Chatterjee, N., Shi, J. & García-Closas, M. Developing and evaluating polygenic risk prediction models for stratified disease prevention. Nat Rev Genet 17, 392–406 (2016). https://doi.org/10.1038/nrg.2016.27

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