A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves.
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 pr...
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2019
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Online Access: | https://escholarship.org/uc/item/0hf68790 https://escholarship.org/content/qt0hf68790/qt0hf68790.pdf https://doi.org/10.1111/age.12834 |
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ftcdlib:oai:escholarship.org:ark:/13030/qt0hf68790 2024-09-15T18:01:24+00:00 A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. Jagannathan, V Drögemüller, C Leeb, T Dog Biomedical Variant Database Consortium (DBVDC) 695 - 704 2019-12-01 application/pdf https://escholarship.org/uc/item/0hf68790 https://escholarship.org/content/qt0hf68790/qt0hf68790.pdf https://doi.org/10.1111/age.12834 unknown eScholarship, University of California qt0hf68790 https://escholarship.org/uc/item/0hf68790 https://escholarship.org/content/qt0hf68790/qt0hf68790.pdf doi:10.1111/age.12834 public Animal genetics, vol 50, iss 6 Dog Biomedical Variant Database Consortium Animals Dogs Wolves Disease Models Animal Phylogeny Genes Lethal Whole Genome Sequencing Canis lupus familaris Mendelian animal model bioinformatics functional annotation genetic diversity precision medicine rare disease variant database Human Genome Genetics 2.1 Biological and endogenous factors Aetiology Zoology Veterinary Sciences Dairy & Animal Science article 2019 ftcdlib https://doi.org/10.1111/age.12834 2024-06-28T06:28:18Z 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 23133692 single-nucleotide variants (SNVs) and 10048038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1million single-nucleotide and ~1.4million 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 247141 SNVs and 99562 short indels having moderate or high impact on 11267 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. Article in Journal/Newspaper Canis lupus University of California: eScholarship Animal Genetics 50 6 695 704 |
institution |
Open Polar |
collection |
University of California: eScholarship |
op_collection_id |
ftcdlib |
language |
unknown |
topic |
Dog Biomedical Variant Database Consortium Animals Dogs Wolves Disease Models Animal Phylogeny Genes Lethal Whole Genome Sequencing Canis lupus familaris Mendelian animal model bioinformatics functional annotation genetic diversity precision medicine rare disease variant database Human Genome Genetics 2.1 Biological and endogenous factors Aetiology Zoology Veterinary Sciences Dairy & Animal Science |
spellingShingle |
Dog Biomedical Variant Database Consortium Animals Dogs Wolves Disease Models Animal Phylogeny Genes Lethal Whole Genome Sequencing Canis lupus familaris Mendelian animal model bioinformatics functional annotation genetic diversity precision medicine rare disease variant database Human Genome Genetics 2.1 Biological and endogenous factors Aetiology Zoology Veterinary Sciences Dairy & Animal Science Jagannathan, V Drögemüller, C Leeb, T Dog Biomedical Variant Database Consortium (DBVDC) A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
topic_facet |
Dog Biomedical Variant Database Consortium Animals Dogs Wolves Disease Models Animal Phylogeny Genes Lethal Whole Genome Sequencing Canis lupus familaris Mendelian animal model bioinformatics functional annotation genetic diversity precision medicine rare disease variant database Human Genome Genetics 2.1 Biological and endogenous factors Aetiology Zoology Veterinary Sciences Dairy & Animal Science |
description |
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 23133692 single-nucleotide variants (SNVs) and 10048038 short indels, including 93% undescribed variants. On average, each individual dog genome carried ∼4.1million single-nucleotide and ~1.4million 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 247141 SNVs and 99562 short indels having moderate or high impact on 11267 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. |
format |
Article in Journal/Newspaper |
author |
Jagannathan, V Drögemüller, C Leeb, T Dog Biomedical Variant Database Consortium (DBVDC) |
author_facet |
Jagannathan, V Drögemüller, C Leeb, T Dog Biomedical Variant Database Consortium (DBVDC) |
author_sort |
Jagannathan, V |
title |
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
title_short |
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
title_full |
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
title_fullStr |
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
title_full_unstemmed |
A comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
title_sort |
comprehensive biomedical variant catalogue based on whole genome sequences of 582 dogs and eight wolves. |
publisher |
eScholarship, University of California |
publishDate |
2019 |
url |
https://escholarship.org/uc/item/0hf68790 https://escholarship.org/content/qt0hf68790/qt0hf68790.pdf https://doi.org/10.1111/age.12834 |
op_coverage |
695 - 704 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
Animal genetics, vol 50, iss 6 |
op_relation |
qt0hf68790 https://escholarship.org/uc/item/0hf68790 https://escholarship.org/content/qt0hf68790/qt0hf68790.pdf doi:10.1111/age.12834 |
op_rights |
public |
op_doi |
https://doi.org/10.1111/age.12834 |
container_title |
Animal Genetics |
container_volume |
50 |
container_issue |
6 |
container_start_page |
695 |
op_container_end_page |
704 |
_version_ |
1810438559872581632 |