A multi-marker association method for genome-wide association studies without the need for population structure correction

Nat Commun. 2016 Nov 10;7:13299. doi: 10.1038/ncomms13299.


All common genome-wide association (GWA) methods rely on population structure correction, to avoid false genotype-to-phenotype associations. However, population structure correction is a stringent penalization, which also impedes identification of real associations. Using recent statistical advances, we developed a new GWA method, called Quantitative Trait Cluster Association Test (QTCAT), enabling simultaneous multi-marker associations while considering correlations between markers. With this, QTCAT overcomes the need for population structure correction and also reflects the polygenic nature of complex traits better than single-marker methods. Using simulated data, we show that QTCAT clearly outperforms linear mixed model approaches. Moreover, using QTCAT to reanalyse public human, mouse and Arabidopsis GWA data revealed nearly all known and some previously undetected associations. Following up on the most significant novel association in the Arabidopsis data allowed us to identify a so far unknown component of root growth.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Chromosome Mapping / methods*
  • Gene Frequency
  • Genetic Association Studies / methods*
  • Genome, Plant / genetics
  • Genome-Wide Association Study / methods*
  • Genotype
  • Linear Models
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci / genetics*
  • Reproducibility of Results