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- Sayyab, ShumailaSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics,National University of Sciences and Technology (NUST) (author)
Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis
- Article/chapterEnglish2016
Publisher, publication year, extent ...
- 2016-03-01
- Oxford University Press (OUP),2016
- Genetics Society of America: G3 / Genetics Society of America,2024
Numbers
- LIBRIS-ID:oai:slubar.slu.se:76812
- https://res.slu.se/id/publ/76812URI
- https://doi.org/10.1534/g3.115.025643DOI
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- Language:English
- Summary in:English
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- Over 250 Mendelian traits and disorders, caused by rare alleles have been mapped in the canine genome. Although each disease is rare in the dog as a species, they are collectively common and have major impact on canine health. With SNP-based genotyping arrays, genome-wide association studies (GWAS) have proven to be a powerful method to map the genomic region of interest when 10-20 cases and 10-20 controls are available. However, to identify the genetic variant in associated regions, fine-mapping and targeted resequencing is required. Here we present a new approach using whole-genome sequencing (WGS) of a family trio without prior GWAS. As a proof-ofconcept, we chose an autosomal recessive disease known as hereditary footpad hyperkeratosis (HFH) in Kromfohrländer dogs. To our knowledge, this is the first time this family trio WGS-approach has been used successfully to identify a genetic variant that perfectly segregates with a canine disorder. The sequencing of three Kromfohrländer dogs from a family trio (an affected offspring and both its healthy parents) resulted in an average genome coverage of 9.2X per individual. After applying stringent filtering criteria for candidate causative coding variants, 527 single nucleotide variants (SNVs) and 15 indels were found to be homozygous in the affected offspring and heterozygous in the parents. Using the computer software packages ANNOVAR and SIFT to functionally annotate coding sequence differences, and to predict their functional effect, resulted in seven candidate variants located in six different genes. Of these, only FAM83G:c155G. C (p.R52P) was found to be concordant in eight additional cases, and 16 healthy Kromfohrländer dogs.
Subject headings and genre
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- Viluma, AgneseSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)93279 (author)
- Bergvall, KerstinSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för kliniska vetenskaper (KV),Department of Clinical Sciences(Swepub:slu)47499 (author)
- Brunberg, EmmaNorwegian Institute for Agricultural and Environmental Research (Bioforsk)(Swepub:slu)51128 (author)
- Andersson, GöranSwedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)50422 (author)
- Bergström, Tomas F.Swedish University of Agricultural Sciences,Sveriges lantbruksuniversitet,Institutionen för husdjursgenetik (HGEN),Department of Animal Breeding and Genetics(Swepub:slu)48194 (author)
- Sveriges lantbruksuniversitetInstitutionen för husdjursgenetik (HGEN) (creator_code:org_t)
- Sveriges lantbruksuniversitet
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- In:G3: Oxford University Press (OUP)6, s. 521-5272160-1836
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