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By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High\u2010throughput sequencing (<jats:styled-content style=\"fixed-case\">HTS<\/jats:styled-content>) technologies, such as genotype\u2010by\u2010sequencing (<jats:styled-content style=\"fixed-case\">GBS<\/jats:styled-content>), facilitate expanded explorations of genomic variation among populations. Hybridization\u2010based <jats:styled-content style=\"fixed-case\">GBS<\/jats:styled-content> techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to \u201ccapture\u201d specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300\u2010kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on\u2010target enrichment with relatively even sequence coverage across all targeted loci and samples (mean\u00a0=\u00a050\u00d7), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content>s). Challenges remained in accurately describing microsatellite variation using this technique; however, longer\u2010read <jats:styled-content style=\"fixed-case\">HTS<\/jats:styled-content> technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune\u2010related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.<\/jats:p>","DOI":"10.1002\/ece3.3583","type":"journal-article","created":{"date-parts":[[2017,12,2]],"date-time":"2017-12-02T05:08:42Z","timestamp":1512191322000},"page":"572-583","source":"Crossref","is-referenced-by-count":7,"title":["Development of a genotype\u2010by\u2010sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure"],"prefix":"10.1002","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6779-1455","authenticated-orcid":false,"given":"Michael E.","family":"Donaldson","sequence":"first","affiliation":[{"name":"Environmental and Life Sciences Graduate Program Trent University  Peterborough ON Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yessica","family":"Rico","sequence":"additional","affiliation":[{"name":"CONACYT Instituto de Ecolog\u00eda A.C. 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