Exploiting rare human disease genomics to discover novel developmental control genes

在正在进行的基因组计划中，通过下一代测序已经发现了大量与表型相关的罕见基因变异。所分析的表型数量远远超过传统的正向遗传学筛选。我们将结合这些“突变体”的生物信息学分析和非洲爪蟾的高通量基因功能测定，以发现在发育中具有重要的进化保守作用的新基因。该项目的第一阶段将涉及检测基因变异，这些变异被认为极有可能支撑人类的致病表型，但其中涉及的特定基因具有未知的发育功能。该学生将接受培训，从临床和基因组数据中获取、分析和优先处理这些基因变异，这些数据是UoS正在进行的项目的一部分，并通过英国基因组学临床解释合作伙伴关系（GECIPS）产生。在非洲爪蟾中进行建模的变异将根据以下因素进行优先排序：测序质量、致病性和频率的计算机度量、遗传模式和从已发表的文献中收集的生物背景数据。然后，基因编辑将用于敲除热带棘球绦虫中每个生物信息优先的基因。由于这是在100个胚胎中进行的常规测试，它将测试极少数携带这种变异基因的人类所显示的功能是否是真实的和进化上保守的。这些实验在一周内完成，允许高通量。为了更容易地对表型进行详细分析，我们将在具有适当荧光细胞类型的转基因蛙系中进行敲除，我们有大约200个这样的系。这项研究的影响将是发现新的发育基因，并通过将其中许多基因分发给其他发育生物学家（优先考虑SoCoBio中的基因），将它们整合到系统生物学的基因调控网络中，从而巩固我们对健康和疾病的理解。

A huge number of rare gene variants associated with phenotypes has been identified by next generation sequencing in ongoing genome projects. The number of phenotypes analysed far exceeds that in a traditional forward genetics screen. We will combine bioinformatic analysis of these "mutants" and high throughput gene function determination in Xenopus to discover new genes that have important, evolutionarily conserved roles in development.The first phase of the project, will involve the detection of gene variants that are deemed highly likely to underpin pathogenic human phenotypes, but where the specific gene involved is of unknown developmental function. The student will be trained to access, analyse and prioritise these gene variants from clinical and genomic data generated as part of ongoing projects at the UoS and through the Genomics England Clinical Interpretation Partnerships (GECIPS). Variants to undergo modelling in Xenopus will be prioritised on the basis of: sequencing quality, in silico metrics of pathogenicity and frequency, inheritance patterns and biological background data gleaned from the published literature.Gene editing will then be used to make a knockout of each bioinformatically-prioritised gene in X. tropicalis. Since this is routinely done in >100 embryos it will test whether the function suggested by the very small number of humans with this variant gene is both genuine and evolutionarily conserved. These experiments are performed in a week allowing high throughput. To make detailed analysis of the phenotype easier, knockouts will be performed in lines of transgenic frogs with the appropriate fluorescent cell type, we have >200 of these lines.The impact of this study will be discovering novel developmental genes and, by distributing many of them to other developmental biologists (prioritising those in SoCoBio), to integrate them into the gene regulatory networks of systems biology that underpin our understanding of health and disease.