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，以便通过避免过度代表性的生物体冗余来实现成本有效的测序，并且还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，该方法可以有效提取 DNA，同时拒绝污染物，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 库，以确保可以检测到尽可能多的生物体。我们的目标是应用我们的 SCODA 技术来浓缩和纯化核酸，在一个自动化步骤中执行集成提取和片段长度选择，以减少从受污染的样品中生成克隆文库所需的时间和劳动力。此外，我们的目标是开发序列特异性浓度的核酸，作为富集极低丰度物种 DNA 群体的手段，并有针对性地恢复低丰度基因组。公共卫生相关性：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，以便通过避免过度代表性的生物体冗余来实现成本有效的测序，并且还可以允许检测和测序非常低丰度的物种。因此，需要一种稳健的 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 技术来浓缩和纯化核酸，从而在一个自动化步骤中满足这些要求，从而形成一种经济高效的过程，用于生成用于人类微生物组分析的高质量序列文库。