ArticleScientific reports2015
Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- IP3 receptor depletion in a spontaneous canine model of Charcot-Marie-Tooth disease 1J with amelogenesis imperfecta.PLoS genetics · 2025Article
- Whole exome sequencing as a screening tool in dogs: A pilot study.Computational and structural biotechnology journal · 2025Article
- VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals.BMC bioinformatics · 2023Article
- Identification of a Novel Idiopathic Epilepsy Risk Locus and a Variant in theAnimals : an open access journal from MDPI · 2023Article
- The genomic landscape of canine diffuse large B-cell lymphoma identifies distinct subtypes with clinical and therapeutic implications.Lab animal · 2022Article
- In-frame deletion in canine PITRM1 is associated with a severe early-onset epilepsy, mitochondrial dysfunction and neurodegeneration.Human genetics · 2021Article
- Missense variant in LOXHD1 is associated with canine nonsyndromic hearing loss.Human genetics · 2021Article
- A domestic cat whole exome sequencing resource for trait discovery.Scientific reports · 2021Article
- Genomic and Transcriptomic Characterization of Canine Osteosarcoma Cell Lines: A Valuable Resource in Translational Medicine.Frontiers in veterinary science · 2021Article
- Article
- Whole genome sequencing for mutation discovery in a single case of lysosomal storage disease (MPS type 1) in the dog.Scientific reports · 2020Article
- Recessive missense LAMP3 variant associated with defect in lamellar body biogenesis and fatal neonatal interstitial lung disease in dogs.PLoS genetics · 2020Article
- Article
- Honey bee predisposition of resistance to ubiquitous mite infestations.Scientific reports · 2019Article
- Canine models of human amelogenesis imperfecta: identification of novel recessive ENAM and ACP4 variants.Human genetics · 2019Article
- A homozygous missense variant in the alkaline phosphatase gene ALPL is associated with a severe form of canine hypophosphatasia.Scientific reports · 2019Article
- An exome sequencing based approach for genome-wide association studies in the dog.Scientific reports · 2017Article
- Exome sequencing reveals independent SGCD deletions causing limb girdle muscular dystrophy in Boston terriers.Skeletal muscle · 2017Article
- A monograph proposing the use of canine mammary tumours as a model for the study of hereditary breast cancer susceptibility genes in humans.Veterinary medicine and science · 2017Review
- Exome sequencing reveals a nebulin nonsense mutation in a dog model of nemaline myopathy.Mammalian genome : official journal of the International Mammalian Genome Society · 2016Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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