DOI: 10.5061/dryad.g79cnp5z5
title: Heritability and genome-wide association study of vaccine-induced immune response in Beagles: A pilot study

description: 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.
description: # 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](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