Project III - Comprehensive Genomic Evaluation of Structural Birth Defects

项目三——结构性出生缺陷的综合基因组评估

• 批准号: 10154930
• 负责人: Katrina M Dipple
• 金额: $ 38.99万
• 依托单位: SEATTLE CHILDREN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-11 至 2025-12-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10154930
• 关键词: Adoption; Affect; Area; Base Pairing; Biopsy; Blood; Cells; Child; Clinical; Code; Congenital Abnormality; Copy Number Polymorphism; DNA; DNA Methylation; DNA Modification Process; DNA Sequence Alteration; DNA sequencing; Data; Diagnosis; Diagnostic; Environmental Risk Factor; Epigenetic Process; Etiology; Evaluation; Gene Abnormality; Gene Expression; Genetic; Genetic Structures; Genetic Variation; Genome; Genomics; Goals; Human; Human Development; Individual; Infant; Introns; Laboratory Scientists; Live Birth; Methods; Methylation; Modification; Molecular; Morbidity - disease rate; Mosaicism; Mutation; National Institute of Child Health and Human Development; Patients; Phenotype; Prevention; Prospective cohort; Protein Isoforms; RNA Splicing; Repetitive Sequence; Source; Structural Congenital Anomalies; Structure; Surgeon; Syndrome; Technology; Tissues; Transformed Cell Line; Untranslated RNA; Variant; Work; base; body system; causal variant; clinical diagnostics; clinical phenotype; clinically relevant; collaborative environment; cost; deep sequencing; exome; exome sequencing; genetic architecture; genetic disorder diagnosis; genetic testing; genetic variant; genome sequencing; genome wide association study; improved; infant morbidity/mortality; mortality; nanopore; new technology; next generation; perinatal period; transcriptome sequencing; whole genome

PROJECT SUMMARY Structural birth defects (SBD) affect 3-6% of live births and are a leading cause of infant morbidity and mortality worldwide. Most SBD are isolated, occur in the first 10 weeks of human development, and are thought to be driven by genetic, epigenetic, and environmental factors. Technical advances in DNA sequencing have propelled our understanding of the genetics of SBD. Array based technologies identified copy number variants that contribute to SBD and enabled genome wide association studies. Massively parallel “Next Generation” (NGS) methods sequence large numbers of short (50-300 base pairs) pieces of DNA simultaneously, permitting sequencing of all coding regions (the exome) or the entire genome at once. Exome and genome sequencing of blood-derived DNA identifies the molecular etiology of ~50% of children multisystemic, syndromic SBD. However, the etiology of most SBD- both isolated and syndromic- remains unknown. A potential reason for this is that short-read based sequencing of blood-derived DNA does not provide a comprehensive view of an individual’s genome. The goal of this proposal is to use novel technologies in prospective cohorts of children with SBD to identify genetic variation not identified by current methods. These “hidden” variants include duplications, inversions, repeat expansions/contractions, and epigenetic modifications that standard short-read based methods cannot identify (Aim 1). Hidden variants also include DNA mutations that arise post-zygotically (“mosaic”) and are not present in blood-derived DNA (Aim 2). We will use long-read based DNA and RNA sequencing methods (PacBio and Oxford Nanopore) on patients with syndromic SBD whose clinical workup (including exome sequencing) has been non-diagnostic. In patients with isolated SBD whose clinical workup has been non-diagnostic, we will apply deep short-read based DNA sequencing of multiple, non-blood derived tissues to identify mosaic variants. This proposal aligns with the stated goals of the NICHD, as our findings will form the basis of new strategies for the diagnosis, treatment, and prevention of human structural birth defects. Our work furthers that goal by identifying previously undetected genetic variation in children with SBD. This is a key first step towards establishing a framework for utilizing these novel technologies in the clinical diagnostic arena.

项目摘要 结构性先天缺陷（SBD）影响了3-6％的活产，是婴儿发病率和死亡率的主要原因 全世界。大多数SBD是孤立的，发生在人类发展的前10周，被认为是 由遗传，表观遗传和环境因素驱动。 DNA测序的技术进步推动了我们对SBD遗传学的理解。基于数组 技术确定了副本编号变体，这些变体有助于SBD并启用了基因组广泛的关联 研究。大量平行的“下一代”（NGS）方法序列序列大量短（50-300个底座 对）简单的DNA片段，允许对所有编码区域（外显子）或整个编码区进行测序 同时基因组。血液来源DNA的外显子组和基因组测序鉴定了分子病因 〜50％的儿童多系统，综合征SBD。但是，大多数SBD的病因既孤立又 综合征仍然未知。 一个潜在的原因是，基于简读的血液衍生DNA测序不提供 对个人基因组的全面看法。 该提案的目的是使用新颖的技术在患有SBD的儿童中 遗传变异未通过当前方法鉴定。这些“隐藏”变体包括重复，反转， 重复扩展/收缩和标准基于短阅读方法的表观遗传修饰不能 识别（目标1）。隐藏的变体还包括在zy旋后出现的DNA突变（“马赛克”），而不是 存在于血液来源的DNA中（AIM 2）。 我们将对患者使用长阅读的DNA和RNA测序方法（PACBIO和牛津纳米孔） 综合征SBD的临床检查（包括外显子组测序）是非诊断的。在患者中 与临床检查无诊断的孤立SBD，我们将采用深度读取的DNA 多个非血液衍生组织的测序以鉴定镶嵌变体。 该建议与NICHD的既定目标保持一致，因为我们的发现将构成新的策略的基础 人类结构出生缺陷的诊断，治疗和预防。我们的工作进一步实现了目标 确定SBD儿童先前未发现的遗传变异。这是迈向的关键第一步 在临床诊断领域建立一个利用这些新技术的框架。