PDF(Pubmed)
Abstract：
BACKGROUND: Chiari malformation type II (CMII) was originally reported in humans as a rare disorder characterized by the downward herniation of the hindbrain and towering cerebellum. The congenital brain malformation is usually accompanied by spina bifida, a congenital spinal anomaly resulting from incomplete closure of the dorsal aspect of the spinal neural tube, and occasionally by other lesions. A similar disorder has been reported in several animal species, including cattle, particularly as a congenital syndrome. A cause of congenital syndromic Chiari-like malformation (CSCM) in cattle has not been reported to date. We collected a series of 14 CSCM-affected Holstein calves (13 purebred, one Red Danish Dairy F1 cross) and performed whole-genome sequencing (WGS). WGS was performed on 33 cattle, including eight cases with parents (trio-based; group 1), three cases with one parent (group 2), and three single cases (solo-based; group 3).
RESULTS: Sequencing-based genome-wide association study of the 13 Holstein calves with CSCM and 166 controls revealed no significantly associated genome region. Assuming a single Holstein breed-specific recessive allele, no region of shared homozygosity was detected suggesting heterogeneity. Subsequent filtering for protein-changing variants that were only homozygous in the genomes of the individual cases allowed the identification of two missense variants affecting different genes, SHC4 in case 4 in group 1 and WDR45B in case 13 in group 3. Furthermore, these two variants were only observed in Holstein cattle when querying WGS data of > 5,100 animals. Alternatively, potential de novo mutational events were assessed in each case. Filtering for heterozygous private protein-changing variants identified one DYNC1H1 frameshift variant as a candidate causal dominant acting allele in case 12 in group 3. Finally, the presence of larger structural DNA variants and chromosomal abnormalities was investigated in all cases. Depth of coverage analysis revealed two different partial monosomies of chromosome 2 segments in cases 1 and 7 in group 1 and a trisomy of chromosome 12 in the WDR45B homozygous case 13 in group 3.
CONCLUSIONS: This study presents for the first time a detailed genomic evaluation of CSCM in Holstein cattle and suggests an unexpected genetic and allelic heterogeneity considering the mode of inheritance, as well as the type of variant. For the first time, we propose candidate causal variants that may explain bovine CSCM in a certain proportion of affected calves. We present cattle as a large animal model for human CMII and propose new genes and genomic variants as possible causes for related diseases in both animals and humans.
RESULTS: Sequencing-based genome-wide association study of the 13 Holstein calves with CSCM and 166 controls revealed no significantly associated genome region. Assuming a single Holstein breed-specific recessive allele, no region of shared homozygosity was detected suggesting heterogeneity. Subsequent filtering for protein-changing variants that were only homozygous in the genomes of the individual cases allowed the identification of two missense variants affecting different genes, SHC4 in case 4 in group 1 and WDR45B in case 13 in group 3. Furthermore, these two variants were only observed in Holstein cattle when querying WGS data of > 5,100 animals. Alternatively, potential de novo mutational events were assessed in each case. Filtering for heterozygous private protein-changing variants identified one DYNC1H1 frameshift variant as a candidate causal dominant acting allele in case 12 in group 3. Finally, the presence of larger structural DNA variants and chromosomal abnormalities was investigated in all cases. Depth of coverage analysis revealed two different partial monosomies of chromosome 2 segments in cases 1 and 7 in group 1 and a trisomy of chromosome 12 in the WDR45B homozygous case 13 in group 3.
CONCLUSIONS: This study presents for the first time a detailed genomic evaluation of CSCM in Holstein cattle and suggests an unexpected genetic and allelic heterogeneity considering the mode of inheritance, as well as the type of variant. For the first time, we propose candidate causal variants that may explain bovine CSCM in a certain proportion of affected calves. We present cattle as a large animal model for human CMII and propose new genes and genomic variants as possible causes for related diseases in both animals and humans.
摘要：
背景：Chiari畸形II型（CMII）最初在人类中被报道为一种罕见的疾病，其特征是后脑向下突出和高耸的小脑。先天性脑畸形通常伴有脊柱裂，由脊髓神经管背侧不完全闭合引起的先天性脊柱异常，偶尔还有其他病变。在几种动物中已经报道了类似的疾病，包括牛,特别是作为一种先天性综合症。迄今为止，尚未报道牛先天性综合症Chiari样畸形（CSCM）的原因。我们收集了一系列14只受CSCM影响的荷斯坦小牛(13只纯种，一个红色丹麦乳品F1杂交）并进行了全基因组测序（WGS）。对33头牛进行了WGS，包括8例父母（三人基础；第1组），三例有一位父母（第2组），和三个单一案例(以独奏为基础；第3组)。
结果：基于测序的13只荷斯坦牛与CSCM和166只对照的全基因组关联研究显示，基因组区域没有显著相关。假设一个Holstein品种特异性隐性等位基因，未检测到共有纯合性区域,提示异质性.随后过滤仅在单个病例的基因组中纯合的蛋白质变化变体，可以鉴定出影响不同基因的两个错义变体。第1组病例4中的SHC4和第3组病例13中的WDR45B。此外，当查询>5,100只动物的WGS数据时，仅在荷斯坦牛中观察到这两种变体。或者，在每种情况下评估潜在的从头突变事件。在第3组中的病例12中，对杂合的私有蛋白变化变体进行过滤，将一个DYNC1H1移码变体鉴定为候选的因果显性作用等位基因。最后,在所有病例中研究了较大结构DNA变异和染色体异常的存在.覆盖深度分析显示，第1组病例1和7中2号染色体片段的两个不同的部分单体，第3组WDR45B纯合病例13中12号染色体的三体性。
结论：这项研究首次对荷斯坦牛的CSCM进行了详细的基因组评估，并提出了考虑到遗传方式的意外遗传和等位基因异质性，以及变体的类型。第一次,我们提出了候选因果变异，可以解释一定比例的受影响小牛的牛CSCM。我们提出了牛作为人类CMII的大型动物模型，并提出了新的基因和基因组变异作为动物和人类相关疾病的可能原因。
结果：基于测序的13只荷斯坦牛与CSCM和166只对照的全基因组关联研究显示，基因组区域没有显著相关。假设一个Holstein品种特异性隐性等位基因，未检测到共有纯合性区域,提示异质性.随后过滤仅在单个病例的基因组中纯合的蛋白质变化变体，可以鉴定出影响不同基因的两个错义变体。第1组病例4中的SHC4和第3组病例13中的WDR45B。此外，当查询>5,100只动物的WGS数据时，仅在荷斯坦牛中观察到这两种变体。或者，在每种情况下评估潜在的从头突变事件。在第3组中的病例12中，对杂合的私有蛋白变化变体进行过滤，将一个DYNC1H1移码变体鉴定为候选的因果显性作用等位基因。最后,在所有病例中研究了较大结构DNA变异和染色体异常的存在.覆盖深度分析显示，第1组病例1和7中2号染色体片段的两个不同的部分单体，第3组WDR45B纯合病例13中12号染色体的三体性。
结论：这项研究首次对荷斯坦牛的CSCM进行了详细的基因组评估，并提出了考虑到遗传方式的意外遗传和等位基因异质性，以及变体的类型。第一次,我们提出了候选因果变异，可以解释一定比例的受影响小牛的牛CSCM。我们提出了牛作为人类CMII的大型动物模型，并提出了新的基因和基因组变异作为动物和人类相关疾病的可能原因。
