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

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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 approximate to 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 approximate 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.
Keywords
GENOME, SEQUENCE, DOG, PERFORMANCE

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Chicago
Broeckx, Bart, Christophe Hitte, Frank Coopman, Geert Verhoeven, Sarah De Keulenaer, Ellen De Meester, Thomas Derrien, et al. 2015. “Improved Canine Exome Designs, Featuring ncRNAs and Increased Coverage of Protein Coding Genes.” Scientific Reports 5.
APA
Broeckx, B., Hitte, C., Coopman, F., Verhoeven, G., De Keulenaer, S., De Meester, E., Derrien, T., et al. (2015). Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. SCIENTIFIC REPORTS, 5.
Vancouver
1.
Broeckx B, Hitte C, Coopman F, Verhoeven G, De Keulenaer S, De Meester E, et al. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. SCIENTIFIC REPORTS. 2015;5.
MLA
Broeckx, Bart, Christophe Hitte, Frank Coopman, et al. “Improved Canine Exome Designs, Featuring ncRNAs and Increased Coverage of Protein Coding Genes.” SCIENTIFIC REPORTS 5 (2015): n. pag. Print.
@article{6896112,
  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 approximate to 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 approximate 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.},
  articleno    = {12810},
  author       = {Broeckx, Bart and Hitte, Christophe and Coopman, Frank and Verhoeven, Geert and De Keulenaer, Sarah and De Meester, Ellen and Derrien, Thomas and Alfoldi, Jessica and Lindblad-Toh, Kerstin and Bosmans, Tim and Gielen, Ingrid and van Bree, Henri and Van Ryssen, Bernadette and Saunders, Jimmy and Van Nieuwerburgh, Filip and Deforce, Dieter},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  language     = {eng},
  pages        = {10},
  title        = {Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes},
  url          = {http://dx.doi.org/10.1038/srep12810},
  volume       = {5},
  year         = {2015},
}

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