Rapid Identification and Quantification of Organisms from Heterogeneous DNA

异质 DNA 中生物体的快速鉴定和定量

• 批准号: 9275722
• 负责人: Darryl Andrew Reeves
• 金额: $ 2.18万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-07-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9275722
• 关键词: Algorithms; Base Composition; Cities; Communities; Complex; Computational Technique; Computing Methodologies; DNA; DNA Sequence; Data; Data Set; Development; Disease; Frequencies; Genome; Goals; Health; High-Throughput DNA Sequencing; High-Throughput Nucleotide Sequencing; Human; Human body; Length; Life; Linear Algebra; Linear Models; Location; Methods; Modeling; Molecular; Monitor; New York City; Organism; Pathogen detection; Play; Public Health; Publishing; Reading; Research; Role; Sampling; Sequence Alignment; Testing; Time; Update; Virus; Work; base; computer framework; expectation; genome sequencing; microbial; microbial community; microbiome; novel; open source; pathogen; practical application; statistics; tool; vector; vector genome

DESCRIPTION (provided by applicant): The specific objective of this proposal is to create a method for quickly identifying the species composition of organisms present in high-throughput DNA sequencing data. The main hypothesis is that every organism has a unique k-mer frequency vector that can be constructed from the organism's genome to quickly identify the organism in heterogeneous DNA sequencing samples using methods from linear algebra and statistics. The goals of this research are to build a computational framework for storing and manipulating k-mer frequency vectors, develop a regression model for identifying organisms and estimating their abundance from heterogeneous, short-read DNA sequencing samples, and apply this method for city-wide pathogen detection as part of the New York City "PathoMap" project.

描述（由申请人提供）：该提案的具体目标是创建一种方法，以快速识别高通量DNA测序数据中存在的生物的物种组成。主要的假设是，每个生物体都有一个独特的K-mer频率矢量，可以使用线性代数和统计数据的方法快速从生物体的基因组构建，以快速识别异质DNA测序样品中的生物。这项研究的目标是建立一个计算框架，用于存储和操纵K-MER频率向量，开发一个回归模型，以识别生物体并估算它们从异质，短读的DNA测序样品中估算其丰度，并将这种方法应用于纽约市的一部分“病原”项目。

项目成果

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report.

• DOI: 10.1186/s40168-016-0168-z
• 发表时间: 2016-06-03
• 期刊: Microbiome
• 影响因子: 15.5
• 作者: MetaSUB International Consortium

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

• DOI: 10.1016/j.cels.2015.01.001
• 发表时间: 2015-07-29
• 期刊: Cell systems
• 影响因子: 9.3
• 作者: Afshinnekoo E;Meydan C;Chowdhury S;Jaroudi D;Boyer C;Bernstein N;Maritz JM;Reeves D;Gandara J;Chhangawala S;Ahsanuddin S;Simmons A;Nessel T;Sundaresh B;Pereira E;Jorgensen E;Kolokotronis SO;Kirchberger N;Garcia I;Gandara D;Dhanraj S;Nawrin T;Saletore Y;Alexander N;Vijay P;Hénaff EM;Zumbo P;Walsh M;O'Mullan GD;Tighe S;Dudley JT;Dunaif A;Ennis S;O'Halloran E;Magalhaes TR;Boone B;Jones AL;Muth TR;Paolantonio KS;Alter E;Schadt EE;Garbarino J;Prill RJ;Carlton JM;Levy S;Mason CE
• 通讯作者: Mason CE