PT - JOURNAL ARTICLE
AU - Kim, Hwasoon
AU - Grueneberg, Alexander
AU - Vazquez, Ana I.
AU - Hsu, Stephen
AU - de los Campos, Gustavo
TI - Will Big Data Close the Missing Heritability Gap?
AID - 10.1534/genetics.117.300271
DP - 2017 Nov 01
TA - Genetics
PG - 1135--1145
VI - 207
IP - 3
4099 - http://www.genetics.org/content/207/3/1135.short
4100 - http://www.genetics.org/content/207/3/1135.full
SO - Genetics2017 Nov 01; 207
AB - 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.