Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

• Published in: Scientific reports Vol. 5; no. 1; p. 12810
• Main Authors: Broeckx, Bart J.G., Hitte, Christophe, Coopman, Frank, Verhoeven, Geert E.C., De Keulenaer, Sarah, De Meester, Ellen, Derrien, Thomas, Alfoldi, Jessica, Lindblad-Toh, Kerstin, Bosmans, Tim, Gielen, Ingrid, Van Bree, Henri, Van Ryssen, Bernadette, Saunders, Jimmy H., Van Nieuwerburgh, Filip, Deforce, Dieter
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 03.08.2015; Nature Publishing Group
• Subjects: 5' Untranslated Regions; 631/208/212/2301; 631/61/514/2254; 631/61/514/2256; 692/308/2056; Animals; Antisense RNA; Base Composition; Base pairs; Design; Dogs - genetics; Exome; Exons; Genetic Variation; Genomes; Genomics - methods; High-Throughput Nucleotide Sequencing - methods; Humanities and Social Sciences; Life Sciences; miRNA; multidisciplinary; Non-coding RNA; Proteins - genetics; Reproducibility of Results; RNA, Untranslated; Science
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep12810

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.