Genomic analysis of microphthalmia, anophthalmia and coloboma

小眼症、无眼症和缺损的基因组分析

• 批准号: 10280960
• 负责人: ANNE M. SLAVOTINEK
• 金额: $ 47.67万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-30 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10280960
• 关键词: Affect; Animal Model; Anophthalmos; Architecture; Bilateral; Biological; Biological Assay; Biological Models; Biology; CRISPR/Cas technology; Candidate Disease Gene; Catalogs; Categories; Cells; Clinical Management; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Collaborations; Coloboma; Color; Congenital Abnormality; Copy Number Polymorphism; Cytogenetics; Data; Data Set; Defect; Development; Developmental Biology; Diagnosis; Dideoxy Chain Termination DNA Sequencing; Dominant-Negative Mutation; Evaluation; Exons; Eye; Eye Development; Eye diseases; Failure; Family member; Fissural; Future; Gene Expression; Gene Transfer Techniques; Genes; Genetic; Genetic Heterogeneity; Genetic Predisposition to Disease; Genomics; Genotype; Immunohistochemistry; Impairment; In Vitro; Injections; Investigation; Karyotype; Knowledge; Larva; Medical Genetics; Methodology; Microphthalmos; Modeling; Morphogenesis; Morphology; Nucleic Acid Regulatory Sequences; Nucleotides; Oligonucleotides; Optics; Parents; Pathogenesis; Pathogenicity; Patient Care; Patients; Phenotype; Prognosis; Quality of life; RNA; RNA Splicing; Regulatory Element; Reporter; Research Personnel; Research Support; Resources; Reverse Transcriptase Polymerase Chain Reaction; Risk; Role; Site; Spliced Genes; Structure; Testing; Therapeutic Trials; Time; Untranslated RNA; Validation; Variant; Vision; Visual impairment; Work; Zebrafish; causal variant; exome sequencing; experience; gain of function; genetic testing; genetic variant; genome sequencing; genomic data; genomic variation; improved; in silico; in vivo; insertion/deletion mutation; loss of function; malformation; medical complication; mutant; novel; programs; segregation; spatiotemporal; therapy development; transcription factor; transcriptome sequencing; whole genome

SUMMARY Microphthalmia, anophthalmia and coloboma (MAC) are highly important birth defects because of the lifelong effects of severely reduced vision. MAC can be caused by pathogenic sequence variants and copy number variants affecting transcription factors and other genes involved in eye development. Patients with MAC typically undergo genetic testing with microarrays, gene panels and exome sequencing, but a genetic etiology is not identified for many patients. A complete catalogue of the genomic variation underlying MAC is critical for optimizing patient care, facilitating future therapeutic trials and to provide novel information supporting research into the developmental biology of eye defects. In this proposal, we will use whole genome sequencing (WGS) and in vitro and in vivo functional studies to advance our understanding of the genomic architecture of MAC. Our first Aim involves the use of WGS to obtain complete genomic data, including coding and non-coding sequence variants, copy number variants and structural cytogenetic variation, in a minimum of 200 patients with MAC. We will prioritize patients with MAC who have multiple affected family members, consanguineous parents, bilateral eye involvement, and negative prior genetic testing. This aim will enable us to investigate the full range of genomic variation in MAC and to determine whether non-coding variation and structural cytogenetic variation contribute to the genetic etiology of these birth defects. In our second Aim, we will use zebrafish with CRISPR to investigate the effects of loss and gain of function for novel candidate genes for MAC and to determine the effects of specific, coding sequence variants on eye development. We will comprehensively phenotype control and mutant larvae and perform RNA-Seq to study alterations in downstream gene expression. We will also study non-coding variation by performing RT-PCR in patient cells, minigene assays and CRISPR/Cas9 with dual reporter transgenesis assays in zebrafish. Our results will generate comprehensive data on the genomic variation that can cause MAC and will provide functional validation of novel genes and variants. This proposal will substantially improve our understanding of eye development, in addition to generating rich resources for future investigations and collaborations between clinicians, developmental biologists and eye researchers.

总结 小眼症、无眼症和缺损（MAC）是非常重要的出生缺陷， 视力严重下降的终身影响。MAC可由致病性序列变异和拷贝数引起 影响转录因子和其他与眼睛发育有关的基因的变异。MAC患者通常 接受基因检测与微阵列，基因面板和外显子组测序，但遗传病因是不是 为许多患者发现。MAC基因组变异的完整目录对于 优化患者护理，促进未来的治疗试验，并提供新的信息支持 研究眼睛缺陷的发育生物学。在这个提议中，我们将使用全基因组测序 (WGS)以及体外和体内功能研究，以促进我们对基因组结构的理解， Mac.我们的第一个目标是使用WGS获得完整的基因组数据，包括编码和非编码 序列变异、拷贝数变异和结构细胞遗传学变异，至少200例患者， Mac.我们将优先考虑有多个受影响家庭成员的MAC患者，近亲父母， 双侧眼睛受累，基因检测阴性。这一目标将使我们能够调查全方位的 的基因组变异，并确定是否非编码变异和结构细胞遗传学变异 导致这些出生缺陷的遗传病因。在我们的第二个目标中，我们将使用斑马鱼与CRISPR， 研究MAC新候选基因功能丧失和获得的影响，并确定其影响 特定的编码序列变异对眼睛发育的影响。我们将全面进行表型控制， 突变的幼虫，并进行RNA-Seq研究下游基因表达的变化。我们还将研究 通过在患者细胞中进行RT-PCR、小基因测定和CRISPR/Cas9与双特异性引物结合， 斑马鱼中的报告基因转基因测定。我们的研究结果将产生关于基因组变异的全面数据 这可能导致MAC，并将提供新基因和变异的功能验证。这项建议会 大大提高我们对眼睛发育的理解，除了为未来创造丰富的资源外， 临床医生、发育生物学家和眼科研究人员之间的调查和合作。