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

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. Wiley 10.1111/age.12834

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

UniBE Contributor:

Jagannathan, Vidya; Drögemüller, Cord and Leeb, T

Subjects:

500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture
500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

1365-2052

Publisher:

Wiley

Language:

English

Submitter:

Tosso Leeb

Date Deposited:

21 Nov 2019 11:12

Last Modified:

21 Nov 2019 11:12

Publisher DOI:

10.1111/age.12834

PubMed ID:

31486122

Uncontrolled Keywords:

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

BORIS DOI:

10.7892/boris.135289

URI:

https://boris.unibe.ch/id/eprint/135289

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