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- Title
Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.
- 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
- 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.
- Subjects
NON-coding RNA; PROTEIN engineering; GENETIC code; MAMMAL genomes; EXONS (Genetics); RNA sequencing
- Publication
Scientific Reports, 2015, p12810
- ISSN
2045-2322
- Publication type
Article
- DOI
10.1038/srep12810