Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Genome Med. 2024 Apr 3;16(1):53. doi: 10.1186/s13073-024-01312-9.
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.
NODAL 信号在脊椎动物胚胎模式形成和心脏发育中起着关键作用。导致 TGF-β/NODAL 信号通路扰动的遗传变异已被反复证明会导致人类的左右侧缺陷。为了进一步探索这种关联并改善遗传诊断，本研究旨在鉴定和描述大量左右侧缺陷个体中更广泛范围的 NODAL 变异。
我们使用基于家系的罕见变异基因组分析，重新分析了一组 321 名仅有临床诊断为先天性心脏疾病（CHD）的个体的外显子组。我们将来自机构研究和临床队列的 12 名已知 NODAL 变异和 CHD 的受影响受试者添加到该队列中，以研究等位基因系列。对于那些具有候选贡献变异的个体，通过在可用的家庭成员中进行 Sanger 测序研究了变异等位基因的确认和分离分析。使用阵列比较基因组杂交和液滴数字 PCR 进行拷贝数变异（CNV）验证和特征分析。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。
在 33 例 CHD 病例中，发现了 NODAL 的错义、无义、剪接位点、插入缺失和/或结构变异，这些变异可能是异位和其他左右侧缺陷的原因。我们描述了一种复发性复杂插入缺失变异，其核酸二级结构预测提示二级结构诱变可能是形成的一种机制。我们在两个不相关的 CHD 病例中发现了跨越 NODAL 的两个 CNV 缺失等位基因。此外，我们发现 17 名 CHD 个体（16/17 具有已知的西班牙裔血统）具有 c.778G> A:p.G260R NODAL 错义变异，我们建议将其从不明意义变异（VUS）重新分类为可能的致病性。对所有具有 p.G260R 变异的病例的观察到的临床表型进行基于 HPO 的定量分析，包括杂合子、纯合子和复合杂合子病例，显示出具有双等位基因变异的个体聚类。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。
我们的数据进一步支持稀有有害变异在 NODAL 中作为导致散发性人类左右侧缺陷的原因的作用，扩展了观察到的潜在心血管异常解剖复杂性的范围，并暗示了等位基因特异性基因剂量模型。
