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）：为了对人类微生物组进行宏基因组分析，需要在文库构建之前对物种丰度进行标准化，以通过避免过度代表的生物体的冗余来实现具有成本效益的测序，并且还允许检测和测序丰度非常低的物种。因此，需要一种稳健的DNA纯化方法，该方法可以有效地提取DNA，同时排除污染物，可以在提取过程中进行长度选择，并且可以富集低丰度序列的DNA池，以确保可以检测到尽可能多的生物体。我们的目标是将我们的SCODA技术用于浓缩和纯化核酸，以在单个自动化步骤中进行集成提取和片段长度选择，以减少从污染样品中产生克隆文库所需的时间和劳动力。此外，我们的目标是开发核酸的序列特异性浓度，作为富集非常低丰度物种的DNA群体以及低丰度基因组的靶向回收的手段。公共卫生相关性：为了进行人类微生物组的宏基因组分析，需要在文库构建之前对物种丰度进行标准化，以通过避免过度代表的生物体的冗余来实现成本有效的测序，并且还可以允许对非常低丰度的物种进行检测和测序。因此，需要一种稳健的DNA纯化方法，该方法可以有效地提取DNA，同时排除在提取过程中可以进行长度选择的污染物，并且可以富集低丰度生物体的DNA池。我们的目标是应用我们的SCODA技术浓缩和纯化核酸，以满足这些要求，在一个单一的自动化步骤，从而产生一个具有成本效益的过程，生产高质量的序列库，用于分析人类微生物组。