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The contribution of genetic variants to disease depends on the ruler

Key Points

  • Although the historically different fields of quantitative genetics and epidemiology are converging to answer fundamental questions about genetic variation in risk underlying human diseases, the plethora of measures to quantify the contribution of variants to disease risk have differing terminology and assumptions, which obfuscate their use and interpretation.

  • In this Analysis, we consider and contrast the most commonly used measures that assess disease risk contributed to the population by individual variants — the heritability of disease liability explained, approximate heritability explained, the sibling recurrence risk explained, the proportion of genetic variance explained on a logarthimic relative risk scale, the area under the receiver–operating curve (AUC) and the population attributable fraction (PAF) — and give numerical examples in breast cancer, Crohn's disease, rheumatoid arthritis and schizophrenia.

  • We discuss the properties of these measures, show how they are connected to each other, consider the situations for which they are best suited and provide an online tool for their calculation.

  • The most appropriate measure to use depends on the importance given to the frequency of a risk variant relative to its effect size on disease and on the baseline to which importance is expressed. These factors should be explicitly considered when assessing the contribution of genetic variants to disease.

  • We recommend investigators to focus primarily on the heritability of liability or genetic variance on the logarthimic relative risk scale explained, as they give estimates that are less sensitive to rare high-risk variants than the other measures considered here. Moreover, we caution against using the PAF for genetic risk variants because it has various undesirable properties.

  • The concept of individual loci providing an explanation for disease is less straightforward than it may seem at first sight, and we recommend investigators to undertake sensitivity analyses that explore how measures of the contribution of genetic variants to risk vary across a range of underlying assumptions.

Abstract

Our understanding of the genetic basis of disease has evolved from descriptions of overall heritability or familiality to the identification of large numbers of risk loci. One can quantify the impact of such loci on disease using a plethora of measures, which can guide future research decisions. However, different measures can attribute varying degrees of importance to a variant. In this Analysis, we consider and contrast the most commonly used measures — specifically, the heritability of disease liability, approximate heritability, sibling recurrence risk, overall genetic variance using a logarithmic relative risk scale, the area under the receiver–operating curve for risk prediction and the population attributable fraction — and give guidelines for their use that should be explicitly considered when assessing the contribution of genetic variants to disease.

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Figure 1: Different measures of genetic effects on disease.
Figure 2: Empirical evaluation of measures of genetic effects.
Figure 3: Application of measures to four diseases.
Figure 4: Aspects of disease heritability: known, hiding and missing.

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Acknowledgements

The authors thank C. Nolan and B. Beyamin for developing the companion website, M. Robinson for help with the figure in Box 1, T. Hoffmann for help in plotting Figure 3, and J. Liu for linkage disequilibrium filtering of the breast cancer SNPs. This work is supported by the US National Institutes of Health grants R01 CA088164, U01 CA127298, U01 GM061390 and P30 CA82103, and by the Australian National Health and Medical Research Council grants 613602, 613601, 1011506, 1050218 and 1048853.

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Correspondence to John S. Witte or Naomi R. Wray.

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Supplementary information

Supplementary information S1 (table)

Measures of overall impact of risk variants for breast cancer. (PDF 216 kb)

Supplementary information S2 (table)

Measures of overall impact of risk variants for Crohn's disease. (PDF 329 kb)

Supplementary information S3 (table)

Measures of overall impact of risk variants for rheumatoid arthritis. (PDF 166 kb)

Supplementary information S4 (table)

Measures of overall impact of risk variants for schizophrenia. (PDF 162 kb)

Glossary

Mendelian loci

Genetic loci that have alleles with discrete effects on the phenotype and that follow Mendel's laws of segregation and independent assortment.

Heritability

The proportion of phenotypic variation in a population that is attributable to genetic variation among individuals.

Disease liability

An underlying or latent continuous variable such that those with a liability above a threshold are considered diseased. The quantitative trait of liability reflects both genetic and environmental factors.

Sibling recurrence risk

The ratio of the probability that a sibling of an individual affected by a disease will also be affected compared to the risk of disease in the general population.

Genetic variance

The variance of trait values that can be ascribed to genetic differences among individuals. The total genetic variance of a trait can be dissected into additive, dominance and other components.

Area under the receiver–operating curve

(AUC). The receiver–operating curve for a predictor (for example, a genetic test) plots the proportion of cases correctly identified by the test against the proportion of controls that are incorrectly classified as cases. The AUC indicates the probability that a factor (for example, a genetic risk score) will predict a higher risk of disease in a randomly selected case than in a control.

Population attributable fraction

(PAF; also known as population attributable risk). For a given disease, risk factor and population, the fraction by which the incidence rate of the disease in the population would be reduced if the risk factor was eliminated.

Overall disease risk

The lifetime probability that an individual will be affected by a disease.

Genetic architectures

The number of risk alleles underlying disease, their allele frequency spectrum, effect sizes and mode of interaction.

Linkage disequilibrium

A measure of whether alleles at two loci coexist in a population in a nonrandom manner. Alleles that are in linkage disequilibrium are found together on the same haplotype more often than expected by chance.

Genomic profile risk

A predicted measure of genetic risk for individuals constructed from a set of loci, the risk alleles and corresponding effect sizes of which have been estimated in an independent sample.

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Witte, J., Visscher, P. & Wray, N. The contribution of genetic variants to disease depends on the ruler. Nat Rev Genet 15, 765–776 (2014). https://doi.org/10.1038/nrg3786

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