Dataset Information

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

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.

SUBMITTER: Broeckx BJ

PROVIDER: S-EPMC4522663 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Broeckx Bart J G BJ Hitte Christophe C Coopman Frank F Verhoeven Geert E C GE De Keulenaer Sarah S De Meester Ellen E Derrien Thomas T Alfoldi Jessica J Lindblad-Toh Kerstin K Bosmans Tim T Gielen Ingrid I Van Bree Henri H Van Ryssen Bernadette B Saunders Jimmy H JH Van Nieuwerburgh Filip F Deforce Dieter D

Scientific reports 20150803

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- ...[more]

PMID: 26235384

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Project description:A growing body of evidence suggests that news media which includes a sympathetic portrayal of a mother bereaved by substance use can increase public support for harm reduction initiatives. However, the extent to which such news media coverage occurs in Canada is unknown, and research has not documented how the news media in Canada covers such stories. We undertook a mixed-method secondary analyses of 5681 Canadian newspaper articles on harm reduction (2000-2016). Quantitative analyses described the volume and content of harm reduction reporting featuring a mother whose child's death was related to substance use while qualitative thematic analysis provided in-depth descriptions of the discourses underlying such news reporting. Newspaper articles featuring a mother whose child's death was related to substance use were rarely published (n = 63; 1.1% of total harm reduction media coverage during the study period). Deductive content analysis of these 63 texts revealed that coverage of naloxone distribution (42.9%) and supervised drug consumption services (28.6%) were prioritized over other harm reduction services. Although harm reduction (services or policies) were advocated by the mother in most (77.8%) of these 63 texts, inductive thematic analysis of a subset (n = 52) of those articles revealed that mothers' advocacy was diminished by newspaper reporting that emphasized their experiences of grief, prioritized individual biographies over structural factors contributing to substance use harms, and created rhetorical divisions between different groups of people who use drugs (PWUD). Bereaved mothers' advocacy in support of harm reduction programs and services may be minimized in the process of reporting their stories for newspaper readers. Finding ways to report bereaved mothers' stories in ways that are inclusive of all PWUD while highlighting the role of broad, structural determinants of substance use has the potential to shift public opinion and government support in favour of these life-saving services.

Dataset Information

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

Publications

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

Similar Datasets

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