title: SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.
abstract: SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be applied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experiments, whereas in many cases, transcriptome sequencing can be used as a cheaper alternative which already enables to identify SNPs located in transcribed regions. In this paper, we propose a method that identifies, quantifies and annotates SNPs without any reference genome, using RNA-seq data only. Individuals can be pooled prior to sequencing, if not enough material is available from one individual. Using pooled human RNA-seq data, we clarify the precision and recall of our method and discuss them with respect to other methods which use a reference genome or an assembled transcriptome. We then validate experimentally the predictions of our method using RNA-seq data from two non-model species. The method can be used for any species to annotate SNPs and predict their impact on the protein sequence. We further enable to test for the association of the identified SNPs with a phenotype of interest.
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Hélène
authors.initials: H
authors.lastname: Lopez-Maestre
authors.affiliation: PT Génomique et Transcriptomique, BIOASTER, Lyon, France.
authors.forename: Lilia
authors.initials: L
authors.lastname: Brinza
authors.affiliation: Université de Rennes, F-35000 Rennes; équipe GenScale, IRISA, Rennes.
authors.forename: Camille
authors.initials: C
authors.lastname: Marchet
authors.affiliation: Synergie-Lyon-Cancer, Universite Lyon 1, Centre Leon Berard, Lyon, France.
authors.forename: Janice
authors.initials: J
authors.lastname: Kielbassa
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Sylvère
authors.initials: S
authors.lastname: Bastien
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Boutigny
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
authors.forename: David
authors.initials: D
authors.lastname: Monnin
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
authors.forename: Adil El
authors.initials: AE
authors.lastname: Filali
authors.affiliation: Department of Biology, UNESP - São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
authors.forename: Claudia Marcia
authors.initials: CM
authors.lastname: Carareto
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Cristina
authors.initials: C
authors.lastname: Vieira
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
authors.forename: Franck
authors.initials: F
authors.lastname: Picard
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.
authors.forename: Natacha
authors.initials: N
authors.lastname: Kremer
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Vavre
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Marie-France
authors.initials: MF
authors.lastname: Sagot
authors.affiliation: Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France vincent.lacroix@univ-lyon1.fr.|EPI ERABLE - Inria Grenoble, Rhône-Alpes.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lacroix
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D005819:Genetic Markers; D016678:Genome; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D059467:Transcriptome
chemical_list: D005819:Genetic Markers