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

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

Edité par CCSD ; Nature Publishing Group -

International audience. 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

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