Ubiquitous polygenicity of human complex traits: genome-wide analysis of 49 traits in Koreans

PLoS Genet. 2013;9(3):e1003355. doi: 10.1371/journal.pgen.1003355. Epub 2013 Mar 7.

Abstract

Recent studies in population of European ancestry have shown that 30% ~ 50% of heritability for human complex traits such as height and body mass index, and common diseases such as schizophrenia and rheumatoid arthritis, can be captured by common SNPs and that genetic variation attributed to chromosomes are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analysed 49 human quantitative traits, many of which are relevant to human diseases, in 7,170 unrelated Korean individuals genotyped on 326,262 SNPs. For 43 of the 49 traits, we estimated a nominally significant (P<0.05) proportion of variance explained by all SNPs on the Affymetrix 5.0 genotyping array ([Formula: see text]). On average across 47 of the 49 traits for which the estimate of h(G)(2) is non-zero, common SNPs explain approximately one-third (range of 7.8% to 76.8%) of narrow sense heritability. The estimate of h(G)(2) is highly correlated with the proportion of SNPs with association P<0.031 (r(2) = 0.92). Longer genomic segments tend to explain more phenotypic variation, with a correlation of 0.78 between the estimate of variance explained by individual chromosomes and their physical length, and 1% of the genome explains approximately 1% of the genetic variance. Despite the fact that there are a few SNPs with large effects for some traits, these results suggest that polygenicity is ubiquitous for most human complex traits and that a substantial proportion of the "missing heritability" is captured by common SNPs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Asian Continental Ancestry Group / genetics
  • Body Height / genetics*
  • Body Mass Index
  • Genetic Variation
  • Genome, Human
  • Genome-Wide Association Study*
  • Genotype
  • Humans
  • Korea
  • Models, Genetic
  • Multifactorial Inheritance / genetics*
  • Phenotype
  • Polymorphism, Single Nucleotide

Grant support

We acknowledge funding from the Australian Research Council (grant DP1093502) and the National Health and Medical Research Council (grant 613672). This research was performed within the Consortium for Large Scale Genome-Wide Association Study III (2011E7300400), which was supported by the genotyping data (the Korean Genome Analysis Project, 4845-301) and the phenotypic data (the Korean Genome Epidemiology Study, 4851-302) from the Korea Center for Disease Control. This study was also supported by Next-Generation BioGreen 21 Program (PJ0090192012) from the Rural Development Administration of Korea. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.