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Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes
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2015 (English)In: Scientific Reports, ISSN 2045-2322, Vol. 5, 12810Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2015. Vol. 5, 12810
National Category
Medical Genetics
URN: urn:nbn:se:uu:diva-260805DOI: 10.1038/srep12810ISI: 000358854200001PubMedID: 26235384OAI: oai:DiVA.org:uu-260805DiVA: diva2:849903
Available from: 2015-08-31 Created: 2015-08-25 Last updated: 2015-08-31Bibliographically approved

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Lindblad-Toh, Kerstin
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Science for Life Laboratory, SciLifeLabDepartment of Medical Biochemistry and Microbiology
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