SCODA DNA extraction to normalize species representation

SCODA DNA 提取使物种代表性标准化

• 批准号: 7572798
• 负责人: ANDRE MARZIALI
• 金额: $ 40.7万
• 依托单位: BOREAL GENOMICS INC.
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-09-26 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7572798
• 关键词: Acrylamide; Acrylamides; Archaea; Automation; Award; Bacteria; Binding; Complementary DNA; DNA; DNA Sequence; DNA purification; Data; Depth; Detection; Distal; Ensure; Facility Construction Funding Category; Funding; Gel; Gene Mutation; Genome; Genomics; Human; Human Microbiome; Individual; Lead; Length; Libraries; Link; Metagenomics; Methods; Molecular Weight; Nucleic Acids; Numbers; Organism; Population; Preparation; Process; Public Health; Pulsed-Field Gel Electrophoresis; Range; Rate; Recovery; Research; Sampling; Science; Shotgun Sequencing; Technology; Temperature; Testing; Time; Validation; concept; cost; cost effective; innovation; instrument; novel; prototype

DESCRIPTION (provided by applicant): To perform a metagenomic analysis of the Human Microbiome, normalization of species abundances prior to library construction is required to allow for both cost effective sequencing by avoiding redundancy of over represented organisms, and also to allow the detection and sequencing of very low abundance species. As a result, there exists a need for a robust DNA purification method that can efficiently extract DNA while rejecting contaminants, that can length select during the extraction process, and that can enrich DNA pools for low abundance sequences to ensure that as many organisms as possible can be detected. We aim to apply our SCODA technology for concentrating and purifying nucleic acids to perform integrated extraction and fragment length selection in a single automated step, in order to reduce the time and labor required to produce clone libraries from contaminated samples. In addition, we aim to develop sequence- specific concentration of nucleic acids as a means to enrich DNA populations for very low abundance species, and for targeted recovery of low abundance genomes. PUBLIC HEALTH RELEVANCE: To perform a metagenomic analysis of the Human Microbiome, normalization of species abundances prior to library construction is required to allow for both cost effective sequencing by avoiding redundancy of over represented organisms, and may also allow the detection and sequencing of very low abundance species. As a result, there exists a need for a robust DNA purification method that can efficiently extract DNA while rejecting contaminants that can length select during the extraction process, and that can enrich DNA pools for low abundance organisms. We aim to apply our SCODA technology for concentrating and purifying nucleic acids to satisfy these requirements in a single automated step, resulting in a cost-effective process for producing high quality sequence libraries for analysis of the Human Microbiome.

描述（由申请人提供）：要对人类微生物组进行宏基因组分析，需要在图书馆构造之前对物种丰度的归一化，以通过避免过度代表的生物的冗余性来允许进行成本效益的测序，并允许对非常低丰度物种的检测和测序进行检测和测序。结果，需要采用可靠的DNA纯化方法，该方法可以在拒绝污染物时有效提取DNA，该方法可以在提取过程中进行长度选择，并且可以富含低丰度序列的DNA池，以确保能够检测到尽可能多的生物体。我们旨在应用我们的SCODA技术来集中和纯化核酸，以在单个自动化步骤中进行集成的提取和碎片长度选择，以减少从受污染的样品中产生克隆文库所需的时间和人工。此外，我们旨在开发核酸的序列浓度，作为富集非常低丰度的DNA群体的一种手段，并旨在靶向低丰度基因组的靶向恢复。公共卫生相关性：要对人类微生物组进行宏基因组分析，需要在图书馆构造之前对物种丰度的归一化，以通过避免过度代表的生物的冗余性来允许进行成本效益的测序，并且还可以允许对非常低的丰度物种进行检测和测序。结果，需要采用可靠的DNA纯化方法，该方法可以有效提取DNA，同时拒绝在提取过程中可以长度选择的污染物，并且可以丰富DNA池的低丰度生物体。我们旨在将SCODA技术应用于集中和纯化的核酸，以在单一自动化的步骤中满足这些要求，从而产生一个具有成本效益的过程，用于生成高质量的序列文库，以分析人类微生物组。