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Molecular Tools for Genome Partitioning

用于基因组分区的分子工具

基本信息

批准号：
7663041
负责人：
Jay Ashok Shendure
金额：
$ 18.98万
依托单位：
UNIVERSITY OF WASHINGTON
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：
2008-07-23 至 2010-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7663041
关键词：
Address Algorithms Area Biological Candidate Disease Gene Clinical Code Complement Complex DNA Resequencing DNA Sequence Development Diagnostic Disease Drops Exons Experimental Designs Generations Genes Genetic Genetic Polymorphism Genetic Research Genetic Variation Genome Genomics Genotype Goals Gold Human Human Genome Individual Length Libraries Malignant Neoplasms Maps Medical Medicine Methods Molecular Oligonucleotides Pathway interactions Performance Positioning Attribute Proteins Protocols documentation Public Health Reaction Reading Research Research Personnel Role Sample Size Shotgun Sequencing Somatic Mutation Specificity Technology Variant Work base cost design disease phenotype genetic linkage analysis genome wide association study human disease improved interest mammalian genome meetings next generation novel novel strategies public health relevance research study tool

项目摘要

DESCRIPTION (provided by applicant): A new generation of technologies is poised to reduce the cost of DNA sequencing by over two orders of magnitude. However, the routine sequencing of full human genomes will continue to be prohibitively expensive in the context of studies that require even modest sample sizes. However, it is frequently the case that investigators are interested in identifying germline variation or somatic mutations in a particular subset of the genome. Examples of genomic subsets that are highly relevant in the context of specific studies include: (a) a locus to which a disease phenotype has been mapped (i.e. a contiguous genomic region); and (b) the exons of genes belonging to a specific disease-related pathway (i.e. a large set of short, discontiguous sequences). Such subsets total to megabases in length, raising the question of how they can be efficiently isolated without performing hundreds to thousands of PCR reactions per genome. Our ability to take advantage of the power of next-generation sequencing technologies is markedly impaired by the lack of a corresponding targeting method, analogous to PCR that is matched to the scale at which the new sequencing platforms will routinely operate. To address this critical need, we will explore several novel strategies for "genome partitioning". Our goal is to develop these strategies into broadly available methods that enable the selective and uniform amplification of complex, arbitrary subsets of a mammalian genome in a single reaction. Our specific aims are: (1) to develop an enzymatic method for the uniform amplification of large sets of exon sequences from a human genome; (2) to develop a hybridization-based method for the selective amplification of contiguous megabase-scale regions from a human genome; (3) to integrate these methods with next-generation sequencing technologies, validating their utility by performing targeted variation discovery in a small number of individuals. PUBLIC HEALTH RELEVANCE: As we enter an era of "personalized medicine", DNA sequencing technology will be increasingly important to public health, contributing towards the unraveling of the genetic basis of human disease, as well as serving an increasing role in clinical diagnostics. Next-generation sequencing technologies have the potential to markedly accelerate genetics research, but are markedly hindered by the lack of equivalently powerful methods to target specific subsets of the human genome. We propose here to develop technologies that meet this critical need.

描述（由申请人提供）：新一代技术有望将DNA测序的成本降低两个数量级以上。然而，在需要适度样本量的研究背景下，人类全基因组的常规测序将继续昂贵得令人望而却步。然而，通常情况下，研究人员感兴趣的是在基因组的特定子集中识别种系变异或体细胞突变。在特定研究背景下高度相关的基因组亚群的例子包括：(a)已绘制疾病表型的位点（即连续的基因组区域）；(b)属于特定疾病相关途径的基因外显子（即一大组短的不连续序列）。这些亚群的长度达到了百万碱基，这就提出了一个问题，即如何在每个基因组不进行数百到数千次PCR反应的情况下有效地分离它们。由于缺乏相应的靶向方法，我们利用下一代测序技术的能力明显受损，这种方法类似于PCR，与新测序平台常规操作的规模相匹配。为了解决这一关键需求，我们将探索几种“基因组分区”的新策略。我们的目标是将这些策略发展成广泛可用的方法，从而能够在一次反应中选择性地、均匀地扩增哺乳动物基因组的复杂、任意亚群。我们的具体目标是：(1)开发一种酶法，用于从人类基因组中均匀扩增大量外显子序列；(2)开发一种基于杂交的方法，用于从人类基因组中选择性扩增连续的兆级区域；(3)将这些方法与下一代测序技术相结合，通过在少数个体中进行靶向变异发现来验证其实用性。

项目成果

期刊论文数量（9）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Targeted enrichment of specific regions in the human genome by array hybridization.

通过阵列杂交有针对性地富集人类基因组中的特定区域。

DOI：
10.1002/0471142905.hg1803s66
发表时间：
2010
期刊：
Current protocols in human genetics
影响因子：
0
作者：
Igartua,Catherine;Turner,EmilyH;Ng,SarahB;Hodges,Emily;Hannon,GregoryJ;Bhattacharjee,Arindam;Rieder,MarkJ;Nickerson,DeborahA;Shendure,Jay
通讯作者：
Shendure,Jay

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

DOI：
10.1186/gb-2010-11-12-r119
发表时间：
2010
期刊：
Genome biology
影响因子：
12.3
作者：
Adey A;Morrison HG;Asan;Xun X;Kitzman JO;Turner EH;Stackhouse B;MacKenzie AP;Caruccio NC;Zhang X;Shendure J
通讯作者：
Shendure J

Exome sequencing identifies the cause of a mendelian disorder.