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

Bart J. G. Broeckx , Christophe Hitte (1) , Frank Coopman , Geert E. C. Verhoeven , Sarah de Keulenaer , Ellen de Meester , Thomas Derrien (1) , Jessica Alföldi (2) , Kerstin Lindblad-Toh (2, 3) , Tim Bosmans , Ingrid Gielen , Henri van Bree , Bernadette van Ryssen , Jimmy H. Saunders , Filip van Nieuwerburgh , Dieter Deforce

1 IGDR - Institut de Génétique et Développement de Rennes
2 BROAD INSTITUTE - Broad Institute of MIT and Harvard
3 Science for Life Laboratory

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

Domaines: Sciences du Vivant [q-bio]

Bart J. G. Broeckx, Christophe Hitte, Frank Coopman, Geert E. C. Verhoeven, Sarah de Keulenaer, et al.. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Scientific Reports, 2015, 5 (1), pp.12810. ⟨10.1038/srep12810⟩. ⟨hal-01187322⟩