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

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 exom...

Full description

Saved in:
Bibliographic Details
Published in:Scientific reports 2015-08, Vol.5 (1), p.12810-12810, Article 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: Article
Language:English
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
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:2045-2322
2045-2322
DOI:10.1038/srep12810