title: The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies.
abstract: Genome-wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) associated with complex traits. However, the genetic heritability of most of these traits remains unexplained. To help guide future studies, we address the crucial question of whether future GWAS can detect new SNP associations and explain additional heritability given the new availability of larger GWAS SNP arrays, imputation, and reduced genotyping costs. We first describe the pairwise and imputation coverage of all SNPs in the human genome by commercially available GWAS SNP arrays, using the 1000 Genomes Project as a reference. Next, we describe the findings from 6 years of GWAS of 172 chronic diseases, calculating the power to detect each of them while taking array coverage and sample size into account. We then calculate the power to detect these SNP associations under different conditions using improved coverage and/or sample sizes. Finally, we estimate the percentages of SNP associations and heritability previously detected and detectable by future GWAS under each condition. Overall, we estimated that previous GWAS have detected less than one-fifth of all GWAS-detectable SNPs underlying chronic disease. Furthermore, increasing sample size has a much larger impact than increasing coverage on the potential of future GWAS to detect additional SNP-disease associations and heritability.
authors.affiliation: Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94158-9001, USA.
authors.forename: Karla J
authors.initials: KJ
authors.lastname: Lindquist
authors.forename: Eric
authors.initials: E
authors.lastname: Jorgenson
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Hoffmann
authors.forename: John S
authors.initials: JS
authors.lastname: Witte
mesh_terms: D002908:Chronic Disease; D015894:Genome, Human; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012107:Research Design; D018401:Sample Size