Polony Sequencing and the $1000 Genome

Polony 测序和价值 1000 美元的基因组

• 批准号: 8324730
• 负责人: Jeremy S Edwards
• 金额: $ 84.32万
• 依托单位: UNIVERSITY OF NEW MEXICO HEALTH SCIS CTR
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2014-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8324730
• 关键词: Accounting; Adoption; Bacterial Genome; Base Sequence; Code; Computer software; DNA; DNA Library; Data; Emulsions; Genome; Goals; Human Genome; Individual; Laboratories; Length; Libraries; Ligation; Maps; Medicine; Mus; Nature; Positioning Attribute; Protocols documentation; Publishing; Reading; Reagent; Reporting; Rewards; Risk; Running; Science; Single Nucleotide Polymorphism; Staging; Technology; base; computerized tools; cost; density; experience; genome sequencing; high reward; improved; meetings; novel; open source; public health relevance

DESCRIPTION (provided by applicant): We propose to further develop and utilize ultra-high throughput polony genome sequencing with the primary goal of generating raw data to re-sequence the human genome in about one week (including library prep and sequencing) for less than $1,000. Currently, the technology is well advanced, but further progress is needed to meet our goals. As the critical quantitative milestone of the project, we will report the sequence for a human genome with "a target sequence quality equivalent to or better than that of the mouse assembly published in December 2002 (Nature 420:520, 2002)". The project is divided into four specific aims, which are to (1) increase the polony sequencing read length using a cyclic ligation strategy that involves enzymatic cleavage, (2) improve the library construction and emulsion protocols, (3) increase read density by moving to alternative clonal amplification strategies (other than emulsion PCR or ePCR), and (4) extend our software capabilities to allow SNP calls from our new proposed sequencing raw data. Progress towards our goals is at an advanced stage. We are able to routinely sequence bacterial genomes and we are on the verge of sequencing an entire human genome to the required quality level. Overall, we feel that there are substantial rewards to be gained by pursuing the goals described herein. We have extensive experience with the proposed technologies and we have a clear path toward the $1,000 genome. PUBLIC HEALTH RELEVANCE: Herein we propose to further develop and utilize Polony Sequencing Technology with the primary goal of sequencing the human genome in about one week at a cost of less than $1,000. We propose several approaches that will progressively move us toward and beyond the $1,000 human genome. We firmly believe that polony sequencing technology, as proposed, can achieve the $1,000 genome goal and undoubtedly revolutionize medicine.

描述(申请人提供)：我们建议进一步开发和利用超高通量Polony基因组测序，主要目标是产生原始数据，以便在大约一周内重新测序人类基因组(包括文库准备和测序)，成本低于1,000美元。目前，这项技术很先进，但需要进一步进步才能实现我们的目标。作为该项目的关键定量里程碑，我们将报告人类基因组的序列，其目标序列质量与2002年12月发表的小鼠组件的目标序列质量相当或更好(自然420：520,2002)。该项目分为四个具体目标，即(1)使用包括酶切割的循环连接策略增加Polony测序读取长度，(2)改进文库构建和乳化方案，(3)通过采用替代克隆扩增策略(不同于乳液PCR或EPCR)来增加读取密度，以及(4)扩展我们的软件功能，允许从我们新提出的测序原始数据中调用SNP。实现我们的目标的进展已进入后期阶段。我们能够常规地对细菌基因组进行测序，我们即将对整个人类基因组进行测序，以达到所需的质量水平。总体而言，我们认为，通过追求这里所述的目标可以获得可观的回报。我们在拟议的技术方面拥有丰富的经验，我们有一条通往1,000美元基因组的明确道路。 公共卫生相关性：在此，我们建议进一步开发和利用Polony测序技术，主要目标是在大约一周内以不到1,000美元的成本对人类基因组进行测序。我们提出了几种方法，这些方法将逐步推动我们接近并超越1000美元的人类基因组。我们坚信，Polony测序技术可以实现1000美元的基因组目标，并无疑将给医学带来革命性的变化。

项目成果

Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source.

• DOI: 10.1002/elps.201200172
• 发表时间: 2012-12
• 期刊: ELECTROPHORESIS
• 影响因子: 2.9
• 作者: Aragon, Anthony D.;Torrez-Martinez, Norah;Edwards, Jeremy S.
• 通讯作者: Edwards, Jeremy S.

Minke whale genome and aquatic adaptation in cetaceans.

• DOI: 10.1038/ng.2835
• 发表时间: 2014-01
• 期刊: Nature genetics
• 影响因子: 30.8
• 作者: Yim HS;Cho YS;Guang X;Kang SG;Jeong JY;Cha SS;Oh HM;Lee JH;Yang EC;Kwon KK;Kim YJ;Kim TW;Kim W;Jeon JH;Kim SJ;Choi DH;Jho S;Kim HM;Ko J;Kim H;Shin YA;Jung HJ;Zheng Y;Wang Z;Chen Y;Chen M;Jiang A;Li E;Zhang S;Hou H;Kim TH;Yu L;Liu S;Ahn K;Cooper J;Park SG;Hong CP;Jin W;Kim HS;Park C;Lee K;Chun S;Morin PA;O'Brien SJ;Lee H;Kimura J;Moon DY;Manica A;Edwards J;Kim BC;Kim S;Wang J;Bhak J;Lee HS;Lee JH
• 通讯作者: Lee JH

Sequencing by ligation variation with endonuclease V digestion and deoxyinosine-containing query oligonucleotides.

• DOI: 10.1186/1471-2164-12-598
• 发表时间: 2011-12-12
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Ho A;Murphy M;Wilson S;Atlas SR;Edwards JS
• 通讯作者: Edwards JS