Resources for Comparative Mendelian Disease Genomics

比较孟德尔疾病基因组学资源

• 批准号: 8998309
• 负责人: LAURA G REINHOLDT
• 金额: $ 85.39万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8998309
• 关键词: Achondroplasia; Address; Affect; Albers-Schonberg disease; Ally; American; Bone Diseases; Breeding; CRISPR/Cas technology; Clinic; Clinical; Code; Copy Number Polymorphism; DNA Sequence Analysis; Data; Databases; Detection; Diagnosis; Disease; Disease model; Etiology; Family; Gene Transfer Techniques; Genes; Genetic; Genetic Engineering; Genetic Heterogeneity; Genome; Genomics; Goals; Hereditary Malignant Neoplasm; High-Throughput DNA Sequencing; Human; Human Genetics; Human Genome; Inbred Strain; Inherited; Lesion; Libraries; Maps; Mendelian disorder; Methods; Modeling; Molecular; Molecular Diagnosis; Mouse Strains; Mus; Mutation; Mutation Detection; Neonatal; Osteochondromatosis; Other Genetics; Partner in relationship; Patients; Perinatal; Phenotype; Population; Process; Proteins; Public Health; Research; Resources; Source; Source Code; Techniques; Technology; Testing; Translating; Untranslated RNA; Validation; Variant; accurate diagnosis; base; comparative; congenital heart disorder; consanguineous family; cost effective; design; exome; exome sequencing; experience; gene discovery; genome editing; genome sequencing; improved; in vivo; mouse genome; mutant; neonate; nervous system disorder; new technology; public health relevance; research study; reverse genetics; segregation; skin disorder; success; tool; transcriptome sequencing; whole genome

 DESCRIPTION (provided by applicant): 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 overall success rate for human Mendelian disease gene discovery by whole-exome sequencing remains at slightly less than 50 percent. 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. Still, as in humans, the success rate for Mendelian disease gene discovery in the mouse is only slightly better than 50 percent. Possible limitations of whole-exome sequencing for disease gene discovery in both the mouse and human genomes include shortcomings of variant calling tools, insufficient resources describing `normal' genome variation, and the likely existence of regulatory mutations that, residing outside of protein-codin regions, escape detection by exome-sequencing. With the promise of exploring and surmounting these limitations, our long-term goal is to develop genomic resources that facilitate functionalization of both the coding and non-coding portions of the mouse genome through forward genetic discovery approaches and reverse genetic validation. More specifically, the objectives of this proposal are to expand the scope of gene discovery beyond exome-imposed limitations, and to use these data to develop a mouse genome variation database, and other optimized resources, that will deliver improved mutation discovery success rates. Moreover, we will apply these new technologies to explore de novo mutations and perinatal lethal phenotypes in a large population of mouse neonates, as well as identifying the heritable molecular lesions in established, genetically defined Mendelian disease models. In both settings, we will validate and model the mutations using modern CRISPR/Cas9 and other genetic engineering approaches.

 描述（由申请人提供）：约有2000万至3000万美国人患有孟德尔遗传性疾病，具有广泛的临床后果，包括先天性心脏病、先天性骨病、遗传性皮肤病、遗传性神经系统疾病、遗传性癌症等。在过去的几年中，高通量全外显子组测序已被用于分子诊断，并作为发现新的致病基因的研究工具。自六年前首次成功应用该技术以来，已确定了100多种孟德尔疾病的基本遗传基础。尽管取得了这些进展，但通过全外显子组测序发现人类孟德尔疾病基因的总体成功率仍然略低于50%。与这些临床病例相反，小鼠中孟德尔疾病基因的发现是由遗传定义的近交系背景、用于分离分析的大型血缘谱系以及通过使用令人兴奋的新CRISPR/Cas9方法和更传统的基因工程技术进行的疾病建模提供动力的。在这些相关技术的帮助下，近年来全外显子组测序的应用使小鼠突变发现率提高了近十倍。尽管如此，与人类一样，在小鼠中发现孟德尔疾病基因的成功率仅略高于50%。在小鼠和人类基因组中发现疾病基因的全外显子组测序的可能局限性包括变异调用工具的缺点，描述“正常”基因组变异的资源不足，以及可能存在的调节突变，这些突变位于蛋白质编码区之外，逃脱了外显子组测序的检测。随着探索和克服这些限制的承诺，我们的长期目标是开发基因组资源，通过正向遗传发现方法和反向遗传验证促进小鼠基因组编码和非编码部分的功能化。更具体地说，该提案的目标是扩大基因发现的范围，超越外显子组施加的限制，并使用这些数据来开发小鼠基因组变异数据库和其他优化资源，这将提高突变发现的成功率。此外，我们将应用这些新技术来探索大量新生小鼠中的新生突变和围产期致死表型，以及在已建立的遗传定义的孟德尔疾病模型中鉴定可遗传的分子病变。在这两种情况下，我们将使用现代CRISPR/Cas9和其他基因工程方法验证和建模突变。