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: 10914942
• 负责人: ANNE M. SLAVOTINEK
• 金额: $ 32.73万
• 依托单位: CINCINNATI CHILDRENS HOSP MED CTR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10914942
• 关键词: Affect; Animal Model; Anophthalmos; Architecture; Bilateral; Bioinformatics; Biological; Biological Assay; Biological Models; Biology; CRISPR/Cas technology; Candidate Disease Gene; Catalogs; Categories; Cells; Clinical Management; 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; Future; Gene Expression; Gene Transfer Techniques; Genes; Genetic; Genetic Heterogeneity; Genetic Predisposition to Disease; Genomics; Genotype; Immunohistochemistry; Impairment; In Vitro; 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; Qualifying; Quality of life; RNA; RNA Splicing; Regulatory Element; Reporter; Research Personnel; Research Support; Resources; Reverse Transcriptase Polymerase Chain Reaction; Risk; Role; SNP array; Site; Spliced Genes; Testing; Time; Untranslated RNA; Validation; Variant; Vision; Visual impairment; Work; Zebrafish; causal variant; exome sequencing; experience; gain of function; gene discovery; genetic testing; genome sequencing; genomic data; genomic variation; improved; in silico; in vivo; insertion/deletion mutation; larval control; loss of function; malformation; medical complication; novel; ophthalmic examination; prime editing; programs; segregation; spatiotemporal; therapy development; transcription factor; transcriptome sequencing; treatment planning; virulence gene; 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 therapies, and providing information to support 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 variants, in a minimum of 200 patients with MAC and their biological parents. We will prioritize patients with MAC who have had negative prior genetic testing, multiple affected family members, consanguineous parents and bilateral eye involvement to increase our changes of identifying novel variants and genes. This aim will enable us to investigate the full range of genomic variation in MAC and to determine the contribution of non-coding variation and structural cytogenetic variation to the genetic etiology of these birth defects. In our second Aim, we will use zebrafish with gene editing and CRISPR/Cas9 to investigate the effects of loss and gain of function for novel candidate genes for MAC and to determine the effects of specific sequence variants on eye development. We will comprehensively phenotype crispant and control larvae and perform RNA-Seq to study alterations in downstream gene expression. We will also study non-coding variation by performing bioinformatic studies, minigene assays, RT-PCR in patient cells as appropriate, and dual-color 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 优化病人护理，促进未来的治疗，并提供信息，以支持研究， 眼缺陷的发育生物学在这项提议中，我们将使用全基因组测序（WGS）和体外 和体内功能研究，以促进我们对MAC基因组结构的理解。我们的首要目标 涉及使用WGS来获得完整的基因组数据，包括编码和非编码序列变体， 拷贝数变异和结构细胞遗传学变异，在至少200例MAC患者及其 亲生父母我们将优先考虑MAC患者，他们之前的基因检测结果为阴性， 受影响的家庭成员，近亲父母和双眼受累增加了我们的变化， 识别新的变异体和基因。这一目标将使我们能够调查全方位的基因组变异， MAC，并确定非编码变异和结构细胞遗传学变异的贡献， 这些出生缺陷的遗传病因。在我们的第二个目标中，我们将使用基因编辑的斑马鱼， CRISPR/Cas9研究MAC的新候选基因的功能丧失和获得的影响， 确定特定序列变异对眼睛发育的影响。我们将全面表型 crispant和对照幼虫，并进行RNA-Seq研究下游基因表达的变化。我们将 还通过在患者细胞中进行生物信息学研究、微基因测定、RT-PCR来研究非编码变异 适当时，以及在斑马鱼中的双色报告基因转基因测定。我们的研究结果将产生全面的 关于可能导致MAC的基因组变异的数据，并将提供新基因的功能验证， 变体。这项建议将大大提高我们对眼睛发育的理解， 为未来的研究和临床医生之间的合作，发展 生物学家和眼科研究人员。