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SCODA DNA extraction to normalize species representation

SCODA DNA 提取使物种代表性标准化

基本信息

批准号：
7691838
负责人：
ANDRE MARZIALI
金额：
$ 36.63万
依托单位：
BOREAL GENOMICS INC.
依托单位国家：
美国
项目类别：
财政年份：
2008
资助国家：
美国
起止时间：
2008-09-26 至 2012-07-31
项目状态：
已结题

项目摘要

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元基因组分析，需要在构建文库之前对物种丰度进行标准化，以避免代表过多的生物体的冗余，从而实现成本效益高的测序，也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，并且可以丰富低丰度序列的DNA池，以确保可以检测到尽可能多的生物。我们的目标是应用我们用于浓缩和纯化核酸的SCoda技术，在单一自动化步骤中执行综合提取和片段长度选择，以减少从受污染的样本生产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定浓度的核酸，作为一种手段来丰富极低丰度物种的DNA种群，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元基因组分析，需要在构建文库之前对物种丰度进行标准化，以避免过度代表的生物体的冗余，从而实现具有成本效益的测序，还可能允许检测和测序丰度极低的物种。因此，需要一种稳健的DNA纯化方法，这种方法可以有效地提取DNA，同时拒绝在提取过程中可以选择长度的污染物，并且可以丰富低丰度生物的DNA池。我们的目标是应用我们的SCoda技术来浓缩和纯化核酸，以在一个自动化步骤中满足这些要求，从而产生一个成本效益高的过程来生产用于分析人类微生物组的高质量序列文库。