title: Predicting quantitative traits from genome and phenome with near perfect accuracy.
abstract: In spite of decades of linkage and association studies and its potential impact on human health, reliable prediction of an individual's risk for heritable disease remains difficult. Large numbers of mapped loci do not explain substantial fractions of heritable variation, leaving an open question of whether accurate complex trait predictions can be achieved in practice. Here, we use a genome sequenced population of ∼7,000 yeast strains of high but varying relatedness, and predict growth traits from family information, effects of segregating genetic variants and growth in other environments with an average coefficient of determination R(2) of 0.91. This accuracy exceeds narrow-sense heritability, approaches limits imposed by measurement repeatability and is higher than achieved with a single assay in the laboratory. Our results prove that very accurate prediction of complex traits is possible, and suggest that additional data from families rather than reference cohorts may be more useful for this purpose.
authors.affiliation: Institute of Computer Science, University of Tartu, Tartu 50409, Estonia.
authors.forename: Kaspar
authors.initials: K
authors.lastname: Märtens
authors.affiliation: Institute for Research on Cancer and Aging, University of Sophia Antipolis, Nice 02 06107, France.
authors.forename: Johan
authors.initials: J
authors.lastname: Hallin
authors.affiliation: Department of Chemistry and Molecular Biology, Gothenburg University, Gothenburg 40530, Sweden.|Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås N-1432, Norway.
authors.forename: Jonas
authors.initials: J
authors.lastname: Warringer
authors.affiliation: Institute for Research on Cancer and Aging, University of Sophia Antipolis, Nice 02 06107, France.
authors.forename: Gianni
authors.initials: G
authors.lastname: Liti
authors.affiliation: Institute of Computer Science, University of Tartu, Tartu 50409, Estonia.|Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK.
authors.forename: Leopold
authors.initials: L
authors.lastname: Parts
mesh_terms: D004171:Diploidy; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D016681:Genome, Fungal; D005838:Genotype; D006801:Humans; D006824:Hybridization, Genetic; D008957:Models, Genetic; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000254:growth & development