Contribution of Rare Copy Number Variants to Isolated Human Malformations

BackgroundCongenital malformations are present in approximately 2–3% of liveborn babies and 20% of stillborn fetuses. The mechanisms underlying the majority of sporadic and isolated congenital malformations are poorly understood, although it is hypothesized that the accumulation of rare genetic, genomic and epigenetic variants converge to deregulate developmental networks. Methodology/Principal FindingsWe selected samples from 95 fetuses with congenital malformations not ascribed to a specific syndrome (68 with isolated malformations, 27 with multiple malformations). Karyotyping and Multiplex Ligation-dependent Probe Amplification (MLPA) discarded recurrent genomic and cytogenetic rearrangements. DNA extracted from the affected tissue (46%) or from lung or liver (54%) was analyzed by molecular karyotyping. Validations and inheritance were obtained by MLPA. We identified 22 rare copy number variants (CNV) [>100 kb, either absent (n = 7) or very uncommon (n = 15, de novo while the remaining were inherited from a healthy parent. The highest frequency was observed in fetuses with heart hypoplasia (8/17, 62.5%), with two events previously related with the phenotype. Double events hitting candidate genes were detected in two samples with brain malformations. Globally, the burden of deletions was significantly higher in fetuses with malformations compared to controls. Conclusions/SignificanceOur data reveal a significant contribution of rare deletion-type CNV, mostly inherited but also de novo, to human congenital malformations, especially heart hypoplasia, and reinforce the hypothesis of a multifactorial etiology in most cases.【背景】先天性畸形在活产婴儿中发生率约为2%~3%，在死胎胎儿中占比达20%。多数散发性、孤立性先天性畸形的发病机制尚不明确，目前假说认为，罕见遗传、基因组及表观遗传变异的累积会导致发育网络失调。 【方法学与主要结果】我们选取了95例无特定综合征的先天性畸形胎儿样本，其中孤立性畸形68例、多发性畸形27例。通过核型分析与多重连接依赖探针扩增（Multiplex Ligation-dependent Probe Amplification，MLPA）排除了复发性基因组及细胞遗传学重排。对取自受累组织（46%）或肺/肝组织（54%）的DNA进行分子核型分析，并通过MLPA完成验证及遗传溯源。本研究共鉴定出22个罕见拷贝数变异（copy number variant，CNV），其长度均>100 kb，其中7个为完全缺失型，15个极为罕见；变异包含新发变异，其余均来自健康亲本的遗传。检出率最高的表型为胎儿心脏发育不全，17例该表型胎儿中共检出8例（62.5%），其中2个变异此前已被报道与该表型相关。在2例脑畸形胎儿样本中，检测到同时累及候选基因的双变异事件。总体而言，畸形胎儿的缺失型CNV负担显著高于对照组。 【结论与意义】本研究数据表明，罕见缺失型CNV（多数为遗传获得，亦存在新发变异）对人类先天性畸形具有显著贡献，尤以心脏发育不全为甚，进一步支持了多数病例为多因素病因的假说。