权益分类	功能权益	普通用户	{{item.name}}会员
{{category.name}}	{{benefitItem.name}}

Identification of causal genes for nonsyndromic orofacial clefts using Whole Exome Sequencing

使用全外显子组测序鉴定非综合征性口面裂的致病基因

基本信息

批准号：
267241232
负责人：
Privatdozent Dr. Tim Becker
金额：
--
依托单位：
Institut für Humangenetik
依托单位国家：
德国
项目类别：
Research Grants
财政年份：
2015
资助国家：
德国
起止时间：
2014-12-31 至 2019-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/267241232?language=en
关键词：
Identification causal genes nonsyndromic orofacial

项目摘要

Orofacial clefting (OFC) is one of the most common congenital malformations worldwide. In the absence of any surgical intervention, neonatal mortality is reported to be high. Formal genetic / epidemiological studies have shown that the two most common subtypes of OFC, namely nonsyndromic cleft lip with or without cleft palate (nsCL/P) and cleft palate only (nsCPO), have a multifactorial aetiology in which both genetic and environmental factors contribute to the phenotype. The heritability of nsCL/P has been estimated to be more than 90%.Genome-wide association studies (GWAS) and subsequent meta-analyses have recently led to major breakthroughs in deciphering the genetic aetiology of nsCL/P, with 15 susceptibility loci for nsCL/P being identified. However, a large proportion of the nsCL/P heritability still remains to be explained. For nsCPO, the success of GWAS has been limited. The fact that both types of nonsyndromic OFC are often sporadic and the very low rate of reproduction due to high neonatal mortality suggest that a substantial proportion of clefting is caused by individual and rare de novo mutations. GWAS, which are primarily designed to target common variants, are unlikely to detect such alterations.The aim of this study is the identification of causative de novo mutations, risk genes, and functional pathways for nonsyndromic OFC, using a whole exome sequencing (WES) approach. From our large cohort of nonsyndromic OFC patients we will select 50 triads with nsCL/P and 50 triads with nsCPO (parents unaffected respectively) as a discovery cohort. Exome capture will be performed using Agilent SureSelectv5+UTR, targeting 74 Mb of the human genome. WES will be run on the in-house Illumina HiSeq2500 sequencing platform using paired-end technology. Stringent parameters for read alignment, mapping and variant calling will be applied, and variants will only be retained if they are not inherited from either parent. We anticipate that this approach will yield about 150 de novo candidate variants/genes. In order to identify the most promising candidates for follow-up (priority candidate genes), detected variants will be analysed and evaluated by different statistical approaches, such as burden and pathway analyses, locus-specific mutation rates and detrimental scores. Priority candidate genes (estimated number: 50-60) will then be re-sequenced on the Illumina MiSeq system, in a large independent confirmation cohort of 300 individuals with nsCL/P and 300 with nsCPO. The data generated will provide the basis for further in-depth analyses, such as combining with WES data from another European group. Additionally, candidate genes will be checked for association / sub-phenotype specific effects of common variants in our nsCL/P GWAS meta-analyses data.We anticipate that this study's approach will uncover the spectrum of susceptibility variants/genes for nonsyndromic clefting, and substantially improve our understanding of craniofacial development.

口面部裂（OFC）是世界范围内最常见的先天性畸形之一。据报道，在没有任何手术干预的情况下，新生儿死亡率很高。正式的遗传/流行病学研究表明，OFC 的两种最常见亚型，即伴或不伴腭裂的非综合征性唇裂 (nsCL/P) 和单纯腭裂 (nsCPO)，具有多因素病因，其中遗传和环境因素均对表型有影响。据估计，nsCL/P 的遗传率超过 90%。全基因组关联研究 (GWAS) 和随后的荟萃分析最近在破译 nsCL/P 的遗传病因学方面取得了重大突破，确定了 15 个 nsCL/P 的易感位点。然而，很大一部分 nsCL/P 遗传力仍有待解释。对于 nsCPO 而言，GWAS 的成功有限。事实上，这两种类型的非综合征性 OFC 通常都是散发性的，并且由于新生儿死亡率高而导致繁殖率非常低，这表明很大一部分的分裂是由个体和罕见的新生突变引起的。 GWAS 主要针对常见变异而设计，不太可能检测到此类改变。本研究的目的是使用全外显子组测序 (WES) 方法来识别非综合征性 OFC 的致病新突变、风险基因和功能途径。从我们的大型非综合征性 OFC 患者队列中，我们将选择 50 名 nsCL/P 三联征和 50 名 nsCPO 三联征（父母分别未受影响）作为发现队列。将使用 Agilent SureSelectv5+UTR 进行外显子组捕获，目标为 74 Mb 的人类基因组。 WES 将使用配对末端技术在内部 Illumina HiSeq2500 测序平台上运行。将应用读取比对、映射和变体调用的严格参数，并且仅当变体不是从任一父代继承时才会保留变体。我们预计这种方法将产生约 150 个从头候选变体/基因。为了确定最有希望的后续候选基因（优先候选基因），将通过不同的统计方法对检测到的变异进行分析和评估，例如负担和途径分析、位点特异性突变率和有害评分。然后，优先候选基因（估计数量：50-60）将在 Illumina MiSeq 系统上重新测序，这是一个由 300 名 nsCL/P 个体和 300 名 nsCPO 个体组成的大型独立确认队列。生成的数据将为进一步深入分析提供基础，例如与另一个欧洲小组的 WES 数据相结合。此外，还将检查候选基因的 nsCL/P GWAS 荟萃分析数据中常见变异的关联/亚表型特异性影响。我们预计这项研究的方法将揭示非综合征性裂的易感性变异/基因的范围，并大大提高我们对颅面发育的理解。