| Title: | Will Big Data Close the Missing Heritability Gap? |
| Journal: | Genetics |
| Published: | 11 Sep 2017 |
| Pubmed: | https://pubmed.ncbi.nlm.nih.gov/28893854/ |
| DOI: | https://doi.org/10.1534/genetics.117.300271 |
| URL: | https://www.genetics.org/content/genetics/207/3/1135.full.pdf |
Publication 8482
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Abstract
Despite the important discoveries reported by genome-wide association (GWA) studies, for most traits and diseases the prediction R-squared (R-sq.) achieved with genetic scores remains considerably lower than the trait heritability. Modern biobanks will soon deliver unprecedentedly large biomedical data sets: Will the advent of big data close the gap between the trait heritability and the proportion of variance that can be explained by a genomic predictor? We addressed this question using Bayesian methods and a data analysis approach that produces a surface response relating prediction R-sq. with sample size and model complexity (e.g., number of SNPs). We applied the methodology to data from the interim release of the UK Biobank. Focusing on human height as a model trait and using 80,000 records for model training, we achieved a prediction R-sq. in testing (n = 22,221) of 0.24 (95% C.I.: 0.23-0.25). Our estimates show that prediction R-sq. increases with sample size, reaching an estimated plateau at values that ranged from 0.1 to 0.37 for models using 500 and 50,000 (GWA-selected) SNPs, respectively. Soon much larger data sets will become available. Using the estimated surface response, we forecast that larger sample sizes will lead to further improvements in prediction R-sq. We conclude that big data will lead to a substantial reduction of the gap between trait heritability and the proportion of interindividual differences that can be explained with a genomic predictor. However, even with the power of big data, for complex traits we anticipate that the gap between prediction R-sq. and trait heritability will not be fully closed.</p>
5 Authors
- Hwasoon Kim
- Alexander Grueneberg
- Ana I. Vazquez
- Stephen Hsu
- Gustavo de los Campos
Enabling scientific discoveries that improve human health