The trading of individual animal genotype information often involves only the exchange of the called genotypes and not necessarily the additional information required to effectively call structural variants. The main aim here was to determine if it is possible to impute copy number variants (CNVs) using the flanking single nucleotide polymorphism (SNP) haplotype structure in cattle. While this objective was achieved using high-density genotype panels (i.e., 713,162 SNPs), a secondary objective investigated the concordance of CNVs called with this high-density genotype panel compared to CNVs called from a medium-density panel (i.e., 45,677 SNPs in the present study). This is the first study to compare CNVs called from high-density and medium-density SNP genotypes from the same animals. High (and medium-density) genotypes were available on 991 Holstein-Friesian, 1015 Charolais, and 1394 Limousin bulls. The concordance between CNVs called from the medium-density and high-density genotypes were calculated separately for each animal. A subset of CNVs which were called from the high-density genotypes was selected for imputation. Imputation was carried out separately for each breed using a set of high-density SNPs flanking the midpoint of each CNV. A CNV was deemed to be imputed correctly when the called copy number matched the imputed copy number. For 97.0% of CNVs called from the high-density genotypes, the corresponding genomic position on the medium-density of the animal did not contain a called CNV. The average accuracy of imputation for CNV deletions was 0.281, with a standard deviation of 0.286. The average accuracy of imputation of the CNV normal state, i.e. the absence of a CNV, was 0.982 with a standard deviation of 0.022. Two CNV duplications were imputed in the Charolais, a single CNV duplication in the Limousins, and a single CNV duplication in the Holstein-Friesians; in all cases the CNV duplications were incorrectly imputed. The vast majority of CNVs called from the high-density genotypes were not detected using the medium-density genotypes. Furthermore, CNVs cannot be accurately predicted from flanking SNP haplotypes, at least based on the imputation algorithms routinely used in cattle, and using the SNPs currently available on the high-density genotype panel.

中文翻译：

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使用高密度或中密度单核苷酸多态性基因型面板检测到的拷贝数变异与牛侧翼高密度单核苷酸多态性单倍型插补拷贝数变异的潜力之间的一致性率

个别动物基因型信息的交易通常仅涉及被叫基因型的交换，而不一定涉及有效调用结构变体所需的其他信息。此处的主要目的是确定是否可以使用牛侧翼单核苷酸多态性（SNP）单倍型结构来估算拷贝数变异（CNV）。尽管使用高密度基因型检测组（即713,162个SNP）实现了这一目标，但第二个目标研究了使用该高密度基因型检测组与中密度检测组（即45,677个SNP）中CNV的一致性。本研究）。这是第一项比较来自同一动物的高密度和中密度SNP基因型的CNV的研究。991 Holstein-Friesian，1015 Charolais和1394 Limousin公牛有高（中等密度）基因型。对于每只动物，分别计算了从中密度基因型和高密度基因型调用的CNV之间的一致性。选择从高密度基因型调用的CNV子集进行插补。使用每个CNV中点侧翼的一组高密度SNP对每个品种分别进行插补。当被叫副本号与估算的副本号匹配时，CNV被认为是正确估算的。对于从高密度基因型中检出的97.0％的CNV，在动物中密度上相应的基因组位置不含被称为CNV的基因。CNV缺失估算的平均准确度为0.281，标准偏差为0.286。CNV正常状态（即不存在CNV）的平均估算准确度为0.982，标准偏差为0.022。夏洛来牛（Charolais）进行了两次CNV复制，利穆赞（Limousins）中进行了一次CNV复制，在荷斯坦-弗里斯兰人（Holstein-Friesians）中进行了一次CNV复制。在所有情况下，CNV重复均被错误估算。使用中密度基因型无法检测到从高密度基因型调用的绝大多数CNV。此外，至少基于牛中常规使用的插补算法以及使用当前在高密度基因型面板上可获得的SNP，不能从侧翼SNP单倍型准确预测CNV。Limousins中有一个CNV重复，而Holstein-Friesians中有一个CNV重复；在所有情况下，CNV重复均被错误估算。使用中密度基因型无法检测到从高密度基因型调用的绝大多数CNV。此外，至少基于牛中常规使用的插补算法以及使用当前在高密度基因型面板上可获得的SNP，不能从侧翼SNP单倍型准确预测CNV。Limousins中有一个CNV重复，而Holstein-Friesians中有一个CNV重复；在所有情况下，CNV重复均被错误估算。使用中密度基因型无法检测到从高密度基因型调用的绝大多数CNV。此外，至少基于牛中常规使用的插补算法以及使用当前在高密度基因型面板上可获得的SNP，不能从侧翼SNP单倍型准确预测CNV。