Rapid and inexpensive epi/genetic profiling of the human mitochondrial genome

快速且廉价地对人类线粒体基因组进行表观/遗传分析

基本信息

批准号：
8570219
负责人：
RAVI SACHIDANANDAM
金额：
$ 25.36万
依托单位：
ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-09-09 至 2015-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8570219
关键词：
Adenosine Triphosphate Age Aging Apoptosis Biological Birth Birth Weight Birth length Blood specimen Cell Line Cell physiology Cells Chloroplasts Clinical Clinical Research Code Codon Nucleotides DNA DNA Methylation Defect Development Diabetes Mellitus Disease Doctor of Philosophy Energy-Generating Resources Ensure Epidemiologic Studies Epidemiology Epigenetic Process Eukaryotic Cell Fetal Development Fetus Functional RNA Future Genes Genetic Genome Genomics Goals Head circumference Human Human Cell Line Individual Lead Length Malignant Neoplasms Measures Metabolic Metabolism Methods Methylation Mitochondria Mitochondrial DNA Mitochondrial Diseases Modification Monitor Mutation Myopathy Nature Neurologic Newborn Infant Nuclear Nucleotides Organelles Organism Oxidative Stress Phenotype Placenta Plant Roots Plants Play Point Mutation Pregnancy Proteins Proxy Reading Reporting Research Ribosomal RNA Role Sampling Somatic Mutation Specificity Stress Techniques Tissues Transfer RNA Umbilical Cord Blood United States National Institutes of Health Variant Weights and Measures bisulfite cohort deep sequencing epigenome insertion/deletion mutation insight instrument medical schools mitochondrial genome novel novel strategies public health relevance rapid technique screening

项目摘要

DESCRIPTION (provided by applicant): The primary goal of this proposal ("Rapid and inexpensive epi/genetic profiling of the human mitochondrial genome") is to apply our new method of isolating and sequencing the mitochondrial genome (mtDNA) and epigenome (mtDNA-methylation) to large sets of samples in order to derive biological and clinical insights. We will characterize the variability in the mitochondrial genome and epigenome. The inexpensive and rapid method developed here will enable large-scale epidemiological studies of the role of mtDNA in aging and in the initiation and progression of a variety of human disorders. In specific aim 1 we will develop the techniques to efficiently sequence the mtDNA. We will sequence the mtDNA isolated from commonly used human cell-lines and human blood samples in order to establish a baseline for comparison with future studies. This will also help us understand the nature of variations supported by mtDNA. We will also develop analytical techniques to determine the quality of mtDNA isolation, assemble the reads into a complete genome and identify variations in the genome. In specific aim 2, we will modify and apply the technique of specific aim 1 to bisulfite treated mtDNA. This will allow us to profile DNA-methylation across the mtDNA in an unbiased manner. We will use the same samples as in specific aim 1 to quantify the levels of mtDNA methylation and its variability between samples, both within cell-lines and between individual blood samples. In specific aim 3 will apply the techniques of specific aims 1 and 2 to placental samples from a newborn cohort established at Mount Sinai School of Medicine. Since placentas are rich in mitochondria and hold the key to early development, we believe this will give us insights into developmental differences between newborns. We will correlate the phenotypes (birth weight, length and head circumference) to mtDNA profiles and generate hypotheses on the role of variants in determining the phenotypes. This will be the first epidemiological use of mtDNA profiling. The results of this proposal will have a broad impact on a range of fields, from bacteril genomics and genetics of chloroplasts in plants to disorders such as cancer and diabetes in humans.

描述（由申请人提供）：该提案的主要目的（“人性线粒体基因组的快速且廉价的Epi/遗传分析”）是应用我们的新方法，即分离和测序线粒体基因组（MTDNA）和表观远期组（mtDNA-甲基化）（mTDNA-甲基化），以使大量样品用于生物学和临床上的生物学iNsermets。我们将表征线粒体基因组和表观基因组的变异性。此处开发的廉价和快速方法将使MTDNA在衰老以及各种人类疾病的启动和进展中的作用进行大规模的流行病学研究。在特定目标1中，我们将开发有效测序mtDNA的技术。我们将对从常用的人类细胞线和人类血液样本分离的mtDNA进行测序，以建立与未来研究进行比较的基线。这也将有助于我们了解mtDNA支持的变化的性质。我们还将开发分析技术来确定mtDNA隔离的质量，将读取成完整的基因组并确定基因组中的变化。在特定的目标2中，我们将修改并将特定目标1的技术应用于Bisulfite处理的mtDNA。这将使我们能够以公正的方式介绍MTDNA的DNA-甲基化。我们将使用与特定目标1中相同的样品来量化细胞线和单个血样之间样品之间的mtDNA甲基化水平及其在样品之间的变异性。在特定目标中，3将应用特定目标1和2的技术，以从西奈山医学院成立的新生同胞中的胎盘样品。由于胎盘富含线粒体并拥有早期发展的关键，因此我们认为这将使我们深入了解新生儿之间的发展差异。我们将将表型（出生体重，长度和头圆）与mtDNA谱相关联，并对变体在确定表型中的作用产生假设。这将是mtDNA分析的首次流行病学使用。该提案的结果将对一系列领域产生广泛的影响，从植物中的细菌基因组学和叶绿体的遗传学到人类癌症和糖尿病等疾病。