Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study
Data files
Apr 23, 2024 version files 22.48 MB
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Covar.txt
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Immune_Research_Beagles.bed
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Immune_Research_Beagles.bim
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Immune_Research_Beagles.fam
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Phenotypes.txt
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README.md
Abstract
Both genetic and non-genetic factors contribute to individual variation in the immune response to vaccination. Understanding how genetic background influences variation in both the magnitude and persistence of vaccine-induced immunity is vital for improving vaccine development and identifying possible causes of vaccine failure. Dogs provide a relevant biomedical model for investigating mammalian vaccine genetics; canine breed structure and long linkage disequilibrium simplify genetic studies in this species compared to humans. The objective of this study was to estimate the heritability of the antibody response to vaccination against viral and bacterial pathogens and to identify genes driving variation of the immune response to vaccination in Beagles. Sixty puppies were immunized following a standard vaccination schedule with an attenuated combination vaccine containing antigens for canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, canine parvovirus, and four strains of Leptospira bacteria. Serum antibody measurements for each viral and bacterial component were measured at multiple time points. Heritability estimations and GWAS were conducted using SNP genotypes at 279,902 markers together with serum antibody titer phenotypes. The heritability estimates were: (1) to Leptospira antigens, ranging from 0.178 to 0.628; and (2) to viral antigens, ranging from 0.199 to 0.588. There was not a significant difference between the overall heritability of vaccine-induced immune response to Leptospira antigens compared to viral antigens. Genetic architecture indicates that SNPs of low to high effect contribute to immune response to vaccination. GWAS identified two genetic markers associated with vaccine-induced immune response phenotypes. Collectively, these findings indicate that genetic regulation of the immune response to vaccination is antigen-specific and influenced by multiple genes of small effect.
README: Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study
This package of files accompanies the manuscript entitled: "Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study", Jeanna M. Blake, James Thompson, Harm HogenEsch, Kari J. Ekenstedt.
https://doi.org/10.5061/dryad.g79cnp5z5
Genotype data of 57 research Beagles run on the Affymetrix Axiom Canine HD 710K SNP array, with positions in CanFam3.1 reference.
1. Binary PLINK files containing genotype data of 57 research Beagles run on the Affymetrix Axiom Canine HD 710K SNP array with positions in CanFam3.1 reference.
- Immune_Researach_Beagles.fam - family ID, individual ID, sire ID, dam ID, sex (0 if unknown), phenotype value (-9 for missing data, phenotypes included in a separate file)
- Immune_Research_Beagles.bim - chromosome, variant identifier, position in centimorgans ('0' as a dummy value), bp location, allele 1, allele 2
- Immune_Research_Beagles.bed - genotypes for each dog at each SNP
2. Phenotype file with family ID, individual ID, and antibody titers for four strains of Leptospira bacteria, canine adenovirus type 1, canine adenovirus type 2, canine distemper virus, canine parainfluenza virus, and canine parvovirus and multiple timepoints post-vaccination
- Phenotypes.txt
3. Covariate file with family ID, individual ID, vaccine treatment group, and sex used in the analysis
- Covar.txt