title: Exploiting Single-Cell Quantitative Data to Map Genetic Variants Having Probabilistic Effects.
abstract: Despite the recent progress in sequencing technologies, genome-wide association studies (GWAS) remain limited by a statistical-power issue: many polymorphisms contribute little to common trait variation and therefore escape detection. The small contribution sometimes corresponds to incomplete penetrance, which may result from probabilistic effects on molecular regulations. In such cases, genetic mapping may benefit from the wealth of data produced by single-cell technologies. We present here the development of a novel genetic mapping method that allows to scan genomes for single-cell Probabilistic Trait Loci that modify the statistical properties of cellular-level quantitative traits. Phenotypic values are acquired on thousands of individual cells, and genetic association is obtained from a multivariate analysis of a matrix of Kantorovich distances. No prior assumption is required on the mode of action of the genetic loci involved and, by exploiting all single-cell values, the method can reveal non-deterministic effects. Using both simulations and yeast experimental datasets, we show that it can detect linkages that are missed by classical genetic mapping. A probabilistic effect of a single SNP on cell shape was detected and validated. The method also detected a novel locus associated with elevated gene expression noise of the yeast galactose regulon. Our results illustrate how single-cell technologies can be exploited to improve the genetic dissection of certain common traits. The method is available as an open source R package called ptlmapper.
authors.affiliation: Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Chuffart
authors.affiliation: Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Magali
authors.identifier: 0000-0003-3165-3218
authors.initials: M
authors.lastname: Richard
authors.affiliation: Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.|University Grenoble Alpes, CNRS, TIMC-IMAG lab, UMR 5525, Grenoble, France.
authors.forename: Daniel
authors.initials: D
authors.lastname: Jost
authors.affiliation: Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Burny
authors.affiliation: Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Hélène
authors.identifier: 0000-0003-2029-5646
authors.initials: H
authors.lastname: Duplus-Bottin
authors.affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Ohya
authors.affiliation: Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France.
authors.forename: Gaël
authors.initials: G
authors.lastname: Yvert
mesh_terms: D002874:Chromosome Mapping; D005690:Galactose / Q000235:genetics / Q000378:metabolism*; D008040:Genetic Linkage; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D059010:Single-Cell Analysis
chemical_list: D005690:Galactose