A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves

Dog Biomedical Variant Database Consortium (DBVDC)

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)695-704
Number of pages10
JournalAnimal Genetics
Volume50
Issue number6
DOIs
StatePublished - Dec 1 2019

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wolves
Genome
Dogs
genome
dogs
Nucleotides
nucleotides
genetic disorders
Lethal Genes
Databases
Genetic Research
Inborn Genetic Diseases
genome assembly
Medical Genetics
Genetic Testing
genes
Genes
Breeding
Canidae
Biomedical Research

Keywords

  • animal model
  • bioinformatics
  • Canis lupus familaris
  • functional annotation
  • genetic diversity
  • Mendelian
  • precision medicine
  • rare disease
  • variant database
  • whole genome sequencing

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Genetics

Cite this

A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. / Dog Biomedical Variant Database Consortium (DBVDC).

In: Animal Genetics, Vol. 50, No. 6, 01.12.2019, p. 695-704.

Research output: Contribution to journalArticle

Dog Biomedical Variant Database Consortium (DBVDC). / A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. In: Animal Genetics. 2019 ; Vol. 50, No. 6. pp. 695-704.
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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.",
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