Will Big Data Close the Missing Heritability Gap?. Issue 3 (11th September 2017)

• Record Type: Journal Article
• Authors: Kim, Hwasoon; Grueneberg, Alexander; Vazquez, Ana I; Hsu, Stephen; de los Campos, Gustavo
• Is Part Of: Genetics. Volume 207:Issue 3(2017)
• Page Start: 1135
• Page End: 1145
• Publication Date: 2017-09-11
• Subjects: prediction of complex traits -- big data -- genomic prediction -- whole-genome regressions -- UK Biobank -- Bayesian -- BGLR -- GenPred -- Shared Data Resources -- Genomic Selection; Genetics -- Periodicals; 576.5
• DOI: 10.1534/genetics.117.300271
• Languages: English
• ISSNs: 0016-6731

Abstract

Abstract: Modern biobanks that collect genotype-phenotype information from hundreds of thousands of individuals bring unprecedented opportunities for genomic... 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.