PDF(Pubmed)
Abstract：
NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects.
We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences.
Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model.
Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.
We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with known NODAL variants and CHD from institutional research and clinical cohorts to investigate an allelic series. For those with candidate contributory variants, variant allele confirmation and segregation analysis were studied by Sanger sequencing in available family members. Array comparative genomic hybridization and droplet digital PCR were utilized for copy number variants (CNV) validation and characterization. We performed Human Phenotype Ontology (HPO)-based quantitative phenotypic analyses to dissect allele-specific phenotypic differences.
Missense, nonsense, splice site, indels, and/or structural variants of NODAL were identified as potential causes of heterotaxy and other laterality defects in 33 CHD cases. We describe a recurrent complex indel variant for which the nucleic acid secondary structure predictions implicate secondary structure mutagenesis as a possible mechanism for formation. We identified two CNV deletion alleles spanning NODAL in two unrelated CHD cases. Furthermore, 17 CHD individuals were found (16/17 with known Hispanic ancestry) to have the c.778G > A:p.G260R NODAL missense variant which we propose reclassification from variant of uncertain significance (VUS) to likely pathogenic. Quantitative HPO-based analyses of the observed clinical phenotype for all cases with p.G260R variation, including heterozygous, homozygous, and compound heterozygous cases, reveal clustering of individuals with biallelic variation. This finding provides evidence for a genotypic-phenotypic correlation and an allele-specific gene dosage model.
Our data further support a role for rare deleterious variants in NODAL as a cause for sporadic human laterality defects, expand the repertoire of observed anatomical complexity of potential cardiovascular anomalies, and implicate an allele specific gene dosage model.
摘要：
背景：NODAL信号在脊椎动物的胚胎模式和心脏发育中起关键作用。导致TGF-β/NODAL信号传导途径扰动的遗传变异已重复显示在人类中引起偏侧性缺陷。为了进一步探索这种关联并改善遗传诊断，本研究旨在鉴定和表征大量具有侧向性缺陷的个体中更广泛的NODAL变异.
方法：我们使用以家庭为基础的方法，重新分析了321例临床诊断为偏侧性先天性心脏病（CHD）的先证者外显子组，罕见的变异基因组分析。在该队列中，我们添加了12名来自机构研究和临床队列的具有已知NODAL变体和CHD的受影响受试者，以调查等位基因系列。对于那些具有候选贡献变体的人，通过Sanger测序对现有家族成员进行变异等位基因确认和分离分析.阵列比较基因组杂交和液滴数字PCR用于拷贝数变体(CNV)验证和表征。我们进行了基于人类表型本体论（HPO）的定量表型分析，以剖析等位基因特异性表型差异。
结果：错觉，胡说，拼接部位，indels,在33例CHD病例中，NODAL的和/或结构变体被确定为异位和其他侧向缺陷的潜在原因。我们描述了一种复发的复杂indel变体，其核酸二级结构预测暗示二级结构诱变是一种可能的形成机制。我们在两个无关的CHD病例中鉴定了两个跨越NODAL的CNV缺失等位基因。此外，发现17例CHD个体(16/17已知西班牙裔)的c.778G>A：p。G260RNODAL错义变体，我们建议将其从意义不确定的变体（VUS）重新分类为可能的致病性。对所有p.G260R变异病例的临床表型进行基于HPO的定量分析，包括杂合的,纯合子，和复合杂合子病例，揭示具有双等位基因变异的个体的聚类。这一发现为基因型-表型相关性和等位基因特异性基因剂量模型提供了证据。
结论：我们的数据进一步支持NODAL中罕见的有害变体作为散发性人类侧向缺陷的原因的作用，扩大观察到的潜在心血管异常的解剖复杂性，并暗示等位基因特异性基因剂量模型。
方法：我们使用以家庭为基础的方法，重新分析了321例临床诊断为偏侧性先天性心脏病（CHD）的先证者外显子组，罕见的变异基因组分析。在该队列中，我们添加了12名来自机构研究和临床队列的具有已知NODAL变体和CHD的受影响受试者，以调查等位基因系列。对于那些具有候选贡献变体的人，通过Sanger测序对现有家族成员进行变异等位基因确认和分离分析.阵列比较基因组杂交和液滴数字PCR用于拷贝数变体(CNV)验证和表征。我们进行了基于人类表型本体论（HPO）的定量表型分析，以剖析等位基因特异性表型差异。
结果：错觉，胡说，拼接部位，indels,在33例CHD病例中，NODAL的和/或结构变体被确定为异位和其他侧向缺陷的潜在原因。我们描述了一种复发的复杂indel变体，其核酸二级结构预测暗示二级结构诱变是一种可能的形成机制。我们在两个无关的CHD病例中鉴定了两个跨越NODAL的CNV缺失等位基因。此外，发现17例CHD个体(16/17已知西班牙裔)的c.778G>A：p。G260RNODAL错义变体，我们建议将其从意义不确定的变体（VUS）重新分类为可能的致病性。对所有p.G260R变异病例的临床表型进行基于HPO的定量分析，包括杂合的,纯合子，和复合杂合子病例，揭示具有双等位基因变异的个体的聚类。这一发现为基因型-表型相关性和等位基因特异性基因剂量模型提供了证据。
结论：我们的数据进一步支持NODAL中罕见的有害变体作为散发性人类侧向缺陷的原因的作用，扩大观察到的潜在心血管异常的解剖复杂性，并暗示等位基因特异性基因剂量模型。
