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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre 1, 2 Lilia Brinza 3 Camille Marchet 4 Janice Kielbassa 5 Sylvère Bastien 6, 2 Mathilde Boutigny 7, 2 David Monnin 8 Adil El Filali 9 Claudia Marcia Carareto 10 Cristina Vieira 1, 2, 11 Franck Picard 12 Natacha Kremer 8 Fabrice Vavre 8, 2 Marie-France Sagot 7, 2 Vincent Lacroix 2, 7
1 Eléments transposables, évolution, populations
GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
2 ERABLE - Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale
Inria Grenoble - Rhône-Alpes
3 BIOASTER Microbiology Technology Institute [Lyon]
4 GenScale - Scalable, Optimized and Parallel Algorithms for Genomics
Inria Rennes – Bretagne Atlantique , IRISA-D7 - GESTION DES DONNÉES ET DE LA CONNAISSANCE
5 Centre Léon Bérard [Lyon]
6 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
7 Baobab
PEGASE - Département PEGASE [LBBE]
8 Génétique et évolution des interactions hôtes-parasites
GINSENG - Département génétique, interactions et évolution des génomes [LBBE]
9 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
10 UNESP - Universidade Estadual Paulista Júlio de Mesquita Filho [São José do Rio Preto]
11 IUF - Institut Universitaire de France
12 Statistique en grande dimension pour la génomique
PEGASE - Département PEGASE [LBBE]
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 se-quencing 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.
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https://hal.inria.fr/hal-01352586
Contributor : Marie-France Sagot <>
Submitted on : Monday, August 8, 2016 - 3:35:24 PM
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CNRS | INSTITUT-TELECOM | UNIV-RENNES1 | INRIA | IRISA | BIOENVIS | INSERM | UR1-UFR-ISTIC | CENTRALESUPELEC | UNIV-LYON1 | UNIV-RENNES | IRISA-D7 | UDL | INSA-RENNES

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Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, et al.. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence. Nucleic Acids Research, Oxford University Press, 2016, ⟨10.1093/nar/gkw655⟩. ⟨hal-01352586⟩

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