Tags

Type your tag names separated by a space and hit enter

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves.
Anim Genet 2019; 50(6):695-704AG

Abstract

The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs.

Authors+Show Affiliations

Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.No affiliation info available

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31486122

Citation

Jagannathan, V, et al. "A Comprehensive Biomedical Variant Catalogue Based On Whole Genome Sequences of 582 Dogs and Eight Wolves." Animal Genetics, vol. 50, no. 6, 2019, pp. 695-704.
Jagannathan V, Drögemüller C, Leeb T, et al. A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Anim Genet. 2019;50(6):695-704.
Jagannathan, V., Drögemüller, C., & Leeb, T. (2019). A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Animal Genetics, 50(6), pp. 695-704. doi:10.1111/age.12834.
Jagannathan V, et al. A Comprehensive Biomedical Variant Catalogue Based On Whole Genome Sequences of 582 Dogs and Eight Wolves. Anim Genet. 2019;50(6):695-704. PubMed PMID: 31486122.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. AU - Jagannathan,V, AU - Drögemüller,C, AU - Leeb,T, AU - ,, Y1 - 2019/09/05/ PY - 2019/06/21/accepted PY - 2019/12/01/pmc-release PY - 2019/9/6/pubmed PY - 2019/9/6/medline PY - 2019/9/6/entrez KW - Canis lupus familaris KW - Mendelian KW - animal model KW - bioinformatics KW - functional annotation KW - genetic diversity KW - precision medicine KW - rare disease KW - variant database KW - whole genome sequencing SP - 695 EP - 704 JF - Animal genetics JO - Anim. Genet. VL - 50 IS - 6 N2 - The domestic dog serves as an excellent model to investigate the genetic basis of disease. More than 400 heritable traits analogous to human diseases have been described in dogs. To further canine medical genetics research, we established the Dog Biomedical Variant Database Consortium (DBVDC) and present a comprehensive list of functionally annotated genome variants that were identified with whole genome sequencing of 582 dogs from 126 breeds and eight wolves. The genomes used in the study have a minimum coverage of 10× and an average coverage of ~24×. In total, we identified 23 133 692 single-nucleotide variants (SNVs) and 10 048 038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1 million single-nucleotide and ~1.4 million short-indel variants with respect to the reference genome assembly. About 2% of the variants were located in coding regions of annotated genes and loci. Variant effect classification showed 247 141 SNVs and 99 562 short indels having moderate or high impact on 11 267 protein-coding genes. On average, each genome contained heterozygous loss-of-function variants in 30 potentially embryonic lethal genes and 97 genes associated with developmental disorders. More than 50 inherited disorders and traits have been unravelled using the DBVDC variant catalogue, enabling genetic testing for breeding and diagnostics. This resource of annotated variants and their corresponding genotype frequencies constitutes a highly useful tool for the identification of potential variants causative for rare inherited disorders in dogs. SN - 1365-2052 UR - https://www.unboundmedicine.com/medline/citation/31486122/A_comprehensive_biomedical_variant_catalogue_based_on_whole_genome_sequences_of_582_dogs_and_eight_wolves L2 - https://doi.org/10.1111/age.12834 DB - PRIME DP - Unbound Medicine ER -