title: Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.
abstract: By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of ≈ 152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to ≈ 71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies.
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Bart J G
authors.initials: BJ
authors.lastname: Broeckx
authors.affiliation: Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Hitte
authors.affiliation: Department of Applied Biosciences, Faculty of Bioscience Engineering, University College Ghent, Ghent, Belgium.
authors.forename: Frank
authors.initials: F
authors.lastname: Coopman
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Geert E C
authors.initials: GE
authors.lastname: Verhoeven
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Sarah
authors.initials: S
authors.lastname: De Keulenaer
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Ellen
authors.initials: E
authors.lastname: De Meester
authors.affiliation: Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Alfoldi
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA [2] Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.affiliation: Department of Medicine and Clinical Biology of Small Animals, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Tim
authors.initials: T
authors.lastname: Bosmans
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Ingrid
authors.initials: I
authors.lastname: Gielen
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Henri
authors.initials: H
authors.lastname: Van Bree
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Bernadette
authors.initials: B
authors.lastname: Van Ryssen
authors.affiliation: Department of Medical Imaging and Small Animal Orthopaedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
authors.forename: Jimmy H
authors.initials: JH
authors.lastname: Saunders
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Filip
authors.initials: F
authors.lastname: Van Nieuwerburgh
authors.affiliation: Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
authors.forename: Dieter
authors.initials: D
authors.lastname: Deforce
mesh_terms: D000818:Animals; D001482:Base Composition; D004285:Dogs / Q000235:genetics*; D059472:Exome; D014644:Genetic Variation; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D011506:Proteins / Q000235:genetics*; D022661:RNA, Untranslated; D015203:Reproducibility of Results
chemical_list: D011506:Proteins; D022661:RNA, Untranslated