Resources for Comparative Mendelian Disease Genomics

项目总结 大约2000-3000万美国人受到孟德尔遗传性疾病的影响，具有广泛的临床意义 后果包括先天性心脏病、先天性骨病、遗传性皮肤病、 遗传性神经疾病、遗传性癌症等。在过去的几年里，高吞吐量、 全外显子组测序已被用于分子诊断和新发现新基因的研究工具 致病基因(S)。自从六年前首次成功应用这项技术以来， 已经确定了100多种孟德尔疾病的基本遗传基础。尽管有这些进步，但 孟德尔病全外显子组测序的临床产率不到40%。与这些形成对比的是 在临床病例中，在小鼠身上发现孟德尔病基因是由基因定义的近亲繁殖提供动力的 菌株背景，用于分离分析的大型血缘家系，以及通过 使用令人振奋的CRISPR/CAS9新方法和更传统的基因工程技术。使用 这些相关技术，近几年来全外显子组测序的应用，提高了基因分型的速度。 在小鼠身上发现的突变增加了近十倍。然而，孟德尔病基因发现的成功率 鼠标的比例仅略高于50%。疾病全外显子组测序的可能局限性 在小鼠中发现的基因包括各种调用工具的缺点，描述数据资源不足 “正常”的基因组变异，以及可能存在逃脱外显子检测的结构变异- 测序。带着探索和超越这些限制的承诺，我们的长期目标是创造 基因组资源将通过利用Forward促进自然发生的变异的功能化 基因发现和反向基因验证。更具体地说，这个项目的目标是继续 解决导致孟德尔病的变异的可靠发现和功能验证的问题 小鼠的表型，重点是那些通过外显子组测序逃脱检测的变异。我们会 利用新的负担得起的第三代长读测序技术发现结构 Variants(SVS)；并进一步开发将这些新数据类型集成到数据驱动框架中的管道 形成可供研究界使用的变异解释和候选基因优先排序。 最后，我们将利用体内新的高通量、基于CRISPR的工程和表型来 从我们最有趣和最相关的候选基因子集中证明疾病的原因。

PROJECT SUMMARY Approximately 20-30 million Americans are affected by Mendelian genetic disorders with broad clinical consequences including congenital heart disease, congenital bone diseases, inherited skin diseases, hereditary neurological disorders, hereditary cancers, and others. Over the last several years, high-throughput, whole-exome sequencing has been used for molecular diagnosis and as a research tool for discovery of new disease-causative gene(s). Since the first successful application of this technology six years ago, the fundamental genetic bases for over 100 Mendelian diseases have been identified. Despite these advances, the clinical yield for human Mendelian disease by whole-exome sequencing is less than 40%. In contrast to these clinical cases, the discovery of Mendelian disease genes in mice is powered by genetically defined inbred strain backgrounds, large consanguineous pedigrees for segregation analysis, and disease modeling through the use of exciting new CRISPR/Cas9 approaches and more traditional genetic engineering techniques. With these allied technologies, the application of whole-exome sequencing in recent years has increased the rate of mutation discovery in mouse by nearly ten-fold. Yet, the success rate for Mendelian disease gene discovery in the mouse is only slightly higher than 50 percent. Possible limitations of whole-exome sequencing for disease gene discovery in mouse include shortcomings of variant calling tools, insufficient data resources describing `normal' genome variation, and the likely existence of structural variants that escape detection by exome- sequencing. With the promise of exploring and surmounting these limitations, our long-term goal is to create genomic resources that will facilitate functionalization of naturally occurring variation by employing forward genetic discovery and reverse genetic validation. More specifically, the objectives of this project are to continue to tackle the problem of robust discovery and functional validation of variants that cause Mendelian disease phenotypes in mice with an emphasis on those variants that escape detection by exome sequencing. We will harness newly affordable, third-generation, long-read sequencing technologies for the discovery of structural variants (SVs); and further develop pipelines that integrate these new datatypes into a data-driven framework formouse variant interpretation and candidate gene prioritization that is available to the research community. Finally, we will take advantage of new high throughput in vivo, CRISPR-based engineering and phenotyping to prove disease-causation from among a subset of our most interesting and relevant candidate genes.