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Pitfalls of predicting complex traits from SNPs

Abstract

The success of genome-wide association studies (GWASs) has led to increasing interest in making predictions of complex trait phenotypes, including disease, from genotype data. Rigorous assessment of the value of predictors is crucial before implementation. Here we discuss some of the limitations and pitfalls of prediction analysis and show how naive implementations can lead to severe bias and misinterpretation of results.

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Figure 1: Flowchart of SNP-based prediction analysis.
Figure 2: The overlap pitfall: non-independence of discovery and validation samples.

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Acknowledgements

The authors acknowledge funding from the Australian National Health and Medical Research Council (1047956, 1011506, 613601, 613602, 1048853, 1052684, 1050218), Australian Research Council (FT0991360, DP130102666) and the US National Institutes of Health (NIH; R01 HG006399, R01 GM 075091, P01 GM 099568, R01 MH100141). The authors thank J. Witte for helpful comments. Funding support for the genome-wide association study (GWAS) of gene and environment initiatives in type 2 diabetes is provided through the NIH Genes, Environment and Health Initiative (GEI; U01HG004399). The human subjects participating in the GWAS are derived from the Nurses' Health Study (NHS) and Health Professionals' Follow-up Study (HPFS), and these studies are supported by NIH grants CA87969, CA55075 and DK58845. Assistance with phenotype harmonization and genotype cleaning, as well as with general study coordination, was provided by the gene–environment association studies, GENEVA Coordinating Center (U01 HG004446). Assistance with data cleaning was provided by the US National Center for Biotechnology Information (NCBI). Funding support for genotyping, which was carried out at the Broad Institute of MIT and Harvard, was provided by the NIH GEI (U01HG004424). The data sets used for the analyses described in this manuscript were obtained from dbGap accession number phs000091. The Atherosclerosis Risk in Communities Study (ARIC) was carried out as a collaborative study supported by US National Heart, Lung, and Blood Institute (NHLBI) contracts (HHSN268201100005C, HHSN268201100006C, HHSN268201100007C, HHSN268201100008C, HHSN268201100009C, HHSN268201100010C, HHSN268201100011C, HHSN268201100012C), R01HL087641, R01HL59367 and R01HL086694; National Human Genome Research Institute contract U01HG004402; and NIH contract HHSN268200625226C. The authors thank the staff and participants of the ARIC study for their important contributions. Infrastructure was partly supported by grant number UL1RR025005, a component of the NIH and NIH Roadmap for Medical Research. The Framingham Heart Study (FHS) is conducted and supported by the NHLBI in collaboration with Boston University (Contract No. N01-HC-25195). This article was not prepared in collaboration with investigators of the FHS and does not necessarily reflect the opinions or views of the FHS, Boston University or the NHLBI. Funding for SHARe Affymetrix genotyping was provided by NHLBI Contract N02-HL-64278. SHARe Illumina genotyping was provided under an agreement between Illumina and Boston University. The authors are grateful to S. Pollack, C. Palmer and J. Hirschhorn for assistance with FHS data.

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Supplementary information

Supplementary Information S1 (Box)

Derivation of expected R2 when discovery data are used both for SNP selection and prediction (Box 2). (PDF 271 kb)

Supplementary Information S2 (table)

Analysis of height from Framingham Heart Study (Box 3) (PDF 185 kb)

Supplementary Information S3 (box)

Analysis of dairy cattle data (Fig 2a) (PDF 271 kb)

Glossary

Ancestry principal components

Principal components derived from the genome relationship matrix that account for the genetic substructure of the data. In case–control studies, these principal components can reflect genotyping artefacts, such as plate, batch and genotyping centre, that could be confounded with case–control status.

Conventionally unrelated

Individuals that are not closely related: for example, more distantly related than third cousins.

Cross-validated

Cross-validation involves testing the validity of a prediction in the absence of an independent external validation sample. This is done by dividing the sample into k independent subsets (balanced with respect to case–control status in disease data). Each of the k subsets is used in turn as a validation sample for a predictor derived from the remaining k– 1 subsets.

Cryptic relatedness

When a sample is thought to comprise unrelated individuals on the basis of recorded pedigree relationships but in fact includes close relatives: for example, second cousin or closer.

Effective population size

The number of individuals in an idealized population with random mating and no selection that would lead to the same rate of inbreeding as observed in the real population.

Estimated breeding values

Estimates of the additive genetic value for a particular trait that an individual will pass on to descendants.

Heritability

The proportion of phenotypic variance attributable to additive genetic variation.

Independent sample

In the context of risk prediction, this is a sample from the same population but excluding individuals that are closely related. It is necessary for the individuals in different samples from the same population to share common ancestors, and indeed this distant sharing underpins the efficacy of a risk predictor.

Independent SNPs

Uncorrelated single-nucleotide polymorphisms (SNPs) in linkage equilibrium.

Linkage disequilibrium

(LD). The nonrandom association of alleles at different loci.

Polygenic prediction analysis

Any analysis method that predicts genetic risk or breeding values on the basis of the combined contribution of many loci.

Profile scoring

A polygenic prediction method for prediction of genetic value or risk for each individual (a 'profile') in a validation sample generated from the sum of the alleles they carry weighted by the association effect size estimated in a discovery sample.

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Wray, N., Yang, J., Hayes, B. et al. Pitfalls of predicting complex traits from SNPs. Nat Rev Genet 14, 507–515 (2013). https://doi.org/10.1038/nrg3457

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