Utilization of Advanced Technologies for the Understanding of Human Structural Birth Defects

利用先进技术了解人类结构性出生缺陷

基本信息

批准号：
10541184
负责人：
DAVID R. BEIER
金额：
$ 160.4万
依托单位：
SEATTLE CHILDREN'S HOSPITAL
依托单位国家：
美国
项目类别：
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/10541184
关键词：
3-Dimensional Affect Alprostadil Biological Biological Models Biology Blood Cells Child Clinical Computer Vision Systems Congenital Abnormality Copy Number Polymorphism DNA DNA Sequence Alteration DNA sequencing Data Data Analyses Data Set Defect Development Developmental Biology Diagnosis Disease Embryo Embryonic Development Epigenetic Process Evaluation Fetus Frequencies Genes Genetic Transcription Genetic Variation Genomics Goals Harvest Human Human Development Image Investigation Knowledge Literature Machine Learning Methods Modification Morphology Mus Mutant Strains Mice Mutation Organogenesis Orthologous Gene Pathway interactions Patients Phenotype Pregnancy Probability Prospective cohort Proteins Reproducibility Research Institute Research Personnel SHH gene Sampling Science Shapes Structural Congenital Anomalies Syndrome Techniques Technology Three-Dimensional Image Three-Dimensional Imaging Tissues Training Universities Variant Washington X-Ray Computed Tomography automated segmentation cell type cohort computational anatomy deep learning exome sequencing genome sciences human disease human population genetics indexing insight machine learning model microCT morphometry mosaic mosaic variant mouse model mutant new technology novel organ growth response single-cell RNA sequencing smoothened signaling pathway transcriptome sequencing

项目摘要

PROJECT SUMMARY The unifying theme of this proposal is the aim to use state-of-the-art technologies to investigate the basic biology of mammalian organ development and human structural birth defects. Our approach is wide-ranging, and aims to demonstrate how utilization of powerful technologies can inform many disorders. Importantly, this proposal marries a number of strengths of investigators at Seattle Children’s Research Institute and the University of Washington Department of Genome Sciences; specifically, expertise in the diagnosis and understanding of human congenital malformation syndromes and mammalian developmental biology, and the application of powerful new techniques for biological investigation. In Project 1, we propose to use single-cell RNA sequencing (sci-RNA-seq) technology to characterize mid- gestation embryos of mice carrying mutations relevant to human structural birth defects. Essentially, we are proposing to utilize sci-RNA-seq as a phenotype, with which one can annotate changes in expression and cell- type representation during abnormal organogenesis. Ideally, these profiles will be comparable to each other, and can potentially provide insight into fundamental biological pathways that are perturbed when developmentally important genes are lost. In Project 2, we will leverage recent advances in 3D imaging, computer vision and machine-learning to make the morphological characterization of mouse mutants more accurate, quantitative, reproducible and accessible. Progeny from the same lines studied in Project 1 will be harvested at E15.5 and imaged using microCT scanning. We will then employ several different data analysis techniques to identify differences in the tissue volume and shapes in the mutant mice compared to synthetic image constructed from a pool of ‘normative’ samples. The goal of Project 3 is to use novel technologies in prospective cohorts of children with structural birth defects to identify genetic variation not ascertained by current methods. These “hidden” variants include structural rearrangements, as well as DNA mutations that arise post-zygotically and are not present in blood-derived DNA. We will use long-read based DNA and RNA sequencing methods, or deep short-read based DNA sequencing of multiple, non-blood derived tissues, on patients with structural birth defects whose clinical workup has been non-diagnostic.

项目概要该提案的统一主题是利用最先进的技术来研究基本原理哺乳动物器官发育和人类结构出生缺陷的生物学我们的方法范围广泛，旨在展示强大技术的利用如何可以解决许多疾病。该提案结合了西雅图儿童研究所和华盛顿大学基因组科学系；特别是诊断和治疗方面的专业知识；了解人类先天畸形综合症和哺乳动物发育生物学，以及应用强大的生物学研究新技术。在项目1中，我们建议使用单细胞RNA测序（sci-RNA-seq）技术来表征中携带与人类结构出生缺陷相关的突变的小鼠的妊娠胚胎本质上是。提议利用 sci-RNA-seq 作为一种表型，用它可以注释表达和细胞的变化理想情况下，这些概况将相互比较，并有可能提供对受干扰的基本生物途径的深入了解发育上重要的基因丢失。在项目 2 中，我们将利用 3D 成像、计算机视觉和机器学习领域的最新进展来制作小鼠突变体的形态学表征更加准确、定量、可重复且易于获取。项目 1 中研究的相同品系的后代将在 E15.5 收获并使用 microCT 成像然后，我们将采用几种不同的数据分析技术来识别组织中的差异。突变小鼠的体积和形状与由“规范”池构建的合成图像相比样品。项目 3 的目标是在患有结构性出生缺陷的儿童的前瞻性队列中使用新技术识别当前方法无法确定的遗传变异，这些“隐藏”变异包括结构变异。重排，以及合子后出现的、血液来源中不存在的 DNA 突变 DNA。我们将使用基于长读长的 DNA 和 RNA 测序方法，或基于深度短读长的 DNA。对患有结构性出生缺陷的患者进行多个非血源组织的测序，这些患者的临床检查未得出诊断结果。