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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
Published on: January 16, 2019
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Copy number variation and variant discovery in Bullmastiff dogs
S-A Mortlock1,2, P Williamson1,2, M S Khatkar2
1Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, 2006, Australia.
Animal Genetics
|February 23, 2019
Summary
This study identified nearly 3000 copy number variants (CNVs) and millions of other genetic variants in Bullmastiff dogs. Some variants may be breed-specific, offering insights into canine genetics and traits.
Area of Science:
- Canine Genomics
- Veterinary Genetics
- Molecular Biology
Background:
- Understanding genomic variation in dog breeds is crucial for elucidating genetic contributions to diversity and phenotypic traits.
- The Bullmastiff breed's unique characteristics necessitate detailed genetic investigation.
Purpose of the Study:
- To identify sources of genetic variation within the Bullmastiff breed.
- To characterize copy number variants (CNVs) and other genetic variants using high-density genotyping and whole-genome sequencing.
- To discover potential breed-specific variants and their implications for canine traits and diseases.
Main Methods:
- Analysis of high-density signal intensity data (Canine HD BeadChip) to identify copy number variants (CNVs).
- Whole-genome sequencing to identify single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and insertion/deletion variants (INDELs).
- Collation of CNVs to identify copy number variant regions (CNVRs) and assess their locations relative to transcribed regions and genes.
Main Results:
- Approximately 3000 CNVs were identified in Bullmastiff dogs.
- 82 CNV regions (CNVRs) were detected, with 50% located in transcribed regions and encompassing 432 genes.
- Fifty novel CNVRs, potentially breed-specific, were identified.
- An average of 5 million putative variants (SNPs, MNPs, INDELs) per dog were identified via whole-genome sequencing.
- A subset of CNVR variants showed predicted modifying effects on gene pathways relevant to breed traits.
Conclusions:
- The study successfully identified numerous genetic variants, including novel CNVRs, in the Bullmastiff breed.
- These identified genetic variants provide valuable molecular markers for future investigations into Bullmastiff traits and diseases.
- The findings contribute to a deeper understanding of canine genetic diversity and the molecular basis of breed-specific characteristics.
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