CanVAS: A Harmonized and Imputed Canine Variant Atlas

The domestic dog (Canis lupus familiaris) is a powerful model for genetic studies of complex disease,but canine genotype data are distributed across independent studies using incompatible genotypingplatforms, genome builds, strand conventions, and allele coding schemes. Here we present CanVAS, aquality-controlled, harmonized, and imputed canine genotype resource integrating 15 publicly availabledatasets into a single analysis-ready PLINK file set on the CanFam4 (UU_Cfam_GSD_1.0) referenceassembly. The typed backbone contains 15,451 dogs from over 400 breeds, village dog populations,dingoes, wolves, and coyotes, genotyped across 77,215 shared SNPs. Imputation against the Dog10Kwhole-genome sequencing reference panel (1,929 dogs) using Beagle 5.4 expanded the resource to 9.7million variants (DR2 ≥ 0.3, MAF ≥ 0.01), including approximately 3 million rare variants (MAF < 0.05).We describe the complete harmonization pipeline and validate the resource through population structureanalysis and genome-wide runs-of-homozygosity analysis, recovering known breed-level differences ingenomic inbreeding.家犬（Canis lupus familiaris）是复杂疾病遗传研究的极具价值的模型，但犬类基因型数据分散于各项独立研究中，各研究使用的基因分型平台、基因组组装版本、链方向约定以及等位基因编码方案均不兼容。本研究推出了经过质量控制、统一标准化且已完成基因型填充的犬类基因型资源库CanVAS，该资源库将15个公开数据集整合为一套基于CanFam4（UU_Cfam_GSD_1.0）参考基因组组装版本的、可直接用于分析的PLINK文件集。该基因分型核心数据集包含来自400余个品种、乡土犬种群、澳洲野犬、灰狼以及郊狼的15451只犬只，这些样本均通过77215个共享单核苷酸多态性（Single Nucleotide Polymorphism，SNP）位点完成基因分型。研究使用Beagle 5.4软件，以Dog10K全基因组测序参考面板（1929只犬只）为参照进行基因型填充，将该资源库的变异位点数量扩充至970万个（决定系数（Determination Coefficient，DR2）≥0.3，最小等位基因频率（Minor Allele Frequency，MAF）≥0.01），其中包含约300万个稀有变异（MAF<0.05）。本研究详细描述了完整的标准化统一流程，并通过种群结构分析以及全基因组纯合子连续片段（Runs of Homozygosity）分析验证了该资源库的有效性，成功复现了已知的不同品种间基因组近交水平差异。