Genome-wide association studies for common diseases and complex traits

Key Points

  • Genome-wide association studies are rapidly becoming feasible as an approach for identifying the genes that underlie common diseases and related quantitative traits. This strategy combines a comprehensive and unbiased survey of the genome with the power to detect common alleles with modest phenotypic effects.

  • Sets of markers for genome-wide association studies can be chosen using various criteria, but the degree to which a particular marker set actually surveys the genome should be evaluated if the label “genome-wide association” is to be applied. Empirical assessments of linkage disequilibrium patterns, such as those that are being performed in the HapMap project, will enable the selection of efficient sets of markers and the evaluation of the comprehensiveness of a given marker set.

  • Study design and interpretation of results must include appropriate statistical thresholds that take multiple-hypothesis testing into account, as can be achieved, for example, by permutation testing. Balancing the need for power to detect modest effects with the cost of genotyping large numbers of markers will probably require a multi-stage design.

  • False-positive results that arise due to population stratification might outnumber true associations, and population stratification should be assessed and corrected for, if needed. Alternatively, family-based designs can be used, but high-quality data are needed to avoid artifacts that are specific to these designs.

  • Gene–gene and gene–environment interactions might be common in complex traits, but unbounded searches for such interactions are unlikely to retain adequate power in studies of hundreds of thousands of markers. Either new methods will be required, or, alternatively, markers with individual effects will need to be identified first, followed by focused searches for interactions.

  • Genome-wide association studies are likely to become a reality in the near future. Care will be required in their design, performance, analysis and interpretation, and well-conceived pilot studies might be valuable for understanding and minimizing the pitfalls of this approach. Nevertheless, genome-wide association studies have the potential to identify many genes for common diseases and quantitative traits.

Abstract

Genetic factors strongly affect susceptibility to common diseases and also influence disease-related quantitative traits. Identifying the relevant genes has been difficult, in part because each causal gene only makes a small contribution to overall heritability. Genetic association studies offer a potentially powerful approach for mapping causal genes with modest effects, but are limited because only a small number of genes can be studied at a time. Genome-wide association studies will soon become possible, and could open new frontiers in our understanding and treatment of disease. However, the execution and analysis of such studies will require great care.

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Figure 1: Testing SNPs for association by direct and indirect methods.
Figure 2: Using a multistage approach to minimize sample sizes.
Figure 3: Effects of population stratification in whole-genome association studies.

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Acknowledgements

We thank David Altshuler, Paul DeBakker, Chris Newton-Cheh and Nick Patterson for useful discussions. J.N.H. is the recipient of a Burroughs Wellcome Career Award in Biomedical Science and a Smith Family Foundation New Investigator Award.

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Correspondence to Joel N. Hirschhorn.

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FURTHER INFORMATION

International HapMap Project

dbSNP database

The ENCODE project

Par Allele Meg Allele genotyping products

Perlegen Whole Genome Scanning

Affymetrix gene chip arrays

Glossary

ASSOCIATION STUDY

A genetic variant is genotyped in a population for which phenotypic information is available (such as disease occurrence, or a range of different trait values). If a correlation is observed between genotype and phenotype, there is said to be an association between the variant and the disease or trait.

QUANTITATIVE TRAIT

A biological trait that shows continuous variation (such as height) rather than falling into distinct categories (such as diabetic or healthy). The genetic basis of these traits generally involves the effects of multiple genes and gene–environment interactions. Examples of quantitative traits that contribute to disease are body mass index, blood pressure and blood lipid levels.

CANDIDATE GENE

A gene for which there is evidence of its possible role in the trait or disease that is under study.

LINKAGE MAPPING

Where genes are mapped by typing genetic markers in families to identify regions that are associated with disease or trait values within pedigrees more often than are expected by chance. Such linked regions are more likely to contain a causal genetic variant.

ADMIXTURE MAPPING

Predicting the recent ancestry of chromosomal segments across the genome to identify regions for which recent ancestry in a particular population correlates with disease or trait values. Such regions are more likely to contain causal variants that are more common in the ancestral population.

PENETRANCE

The proportion of individuals with a specific genotype who manifest the genotype at the phenotypic level. For example, if all individuals with a specific disease genotype show the disease phenotype, then the genotype is said to be 'completely penetrant'.

HERITABILITY

The proportion of the variation in a given characteristic or state that can be attributed to (additive) genetic factors.

LINKAGE DISEQUILIBRIUM

Correlation between nearby variants such that the alleles at neighbouring markers (observed on the same chromosome) are associated within a population more often than if they were unlinked.

HAPLOTYPE

A sequential set of genetic markers that are present on the same chromosome.

TAG SNPs

Single nucleotide polymorphisms that are correlated with, and therefore can serve as a proxy for, much of the known remaining common variation in a region.

ASCERTAINMENT BIAS

A consequence of collecting a nonrandom subsample with a systematic bias, so that results based on the subsample are not representative of the entire sample.

MULTIPLE-HYPOTHESIS TESTING

Testing more than one hypothesis within an experiment. As a result, the probability of an unusual result from within the entire experiment occurring by chance is higher than the individual p-value associated with that result.

BONFERRONI CORRECTION

The simplest correction of individual p-values for multiple-hypothesis testing: pcorrected = 1 − (1 − puncorrected)n, where n is the number of hypotheses tested. This formula assumes that the hypotheses are all independent, and simplifies to pcorrected = npuncorrected when npuncorrected 1.

ODDS RATIO

A measure of relative risk that is usually estimated from case-control studies.

FREQUENTIST

A statistical approach for assessing the likelihood that a hypothesis is correct (such as an association being valid), by assessing the strength of the data that supports the hypothesis and the number of hypotheses that are tested.

BAYESIAN

A statistical approach that assesses the probability of a hypothesis being correct (for example, whether an association is valid) by incorporating the prior probability of the hypothesis and the experimental data supporting the hypothesis.

FOUNDER POPULATIONS

Populations that that have been derived from a limited pool of individuals within the last 100 or fewer generations.

ADMIXTURE

Combining two or more populations into a single group. This has implications for studies of genotype–disease associations if the component populations have different genotypic distributions.

DISCORDANT SIB STUDY

A family-based association approach that uses only sibs who are phenotypically discordant (that is, different). Like the transmission disequilibrium test, this approach is immune to population stratification.

TRANSMISSION DISEQUILIBRIUM TEST

A family-based test for association that is immune to population stratification. The transmission of alleles from heterozygous parents to affected offspring is compared to the expected 1:1 ratio.

HARDY–WEINBERG EQUILIBRIUM

The binomial distribution of genotypes in a population, such that frequencies of genotypes AA, Aa and aa will be p2, 2pq, and q2, respectively, where p is the frequency of allele A, and q is the frequency of allele a. Hardy–Weinberg equilibrium applies in a population when there are no factors such as migration or admixture that cause deviations from p2, 2pq and q2.

EPISTASIS

In statistical genetics, this term refers to an interaction of multiple genetic variants (usually at different loci) such that the net phenotypic effect of carrying more than one variant is different than would be predicted by simply combining the effects of each individual variant (mathematically, this means that the gene–gene interaction is significant).

MULTIFACTOR-DIMENSIONALITY REDUCTION

An approach that attempts to reduce the number of tests required to search for interactions between multiple variables.

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Hirschhorn, J., Daly, M. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6, 95–108 (2005). https://doi.org/10.1038/nrg1521

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