TIGR/JTC Large Scale Sequencing Production Center

描述(申请人提供)：本申请中描述的大规模基因组测序生产中心(Center)的目标是：(1)为高度优先的真核生物物种的研究提供经过验证的大规模DNA测序和生物信息学专业知识，以一致地产生尽可能高质量的基因组序列草案和完成的基因组序列以及注释；(2)向公共领域快速发布基因组序列数据、序列跟踪、组装和相关注释；(3)向科学界提供根据这一拨款开发的试剂和软件；以及(4)研究和实施能够显著提高测序吞吐量，同时降低测序成本的新方法和技术。该中心将通过应用强大而复杂的大规模基因组测序和分析管道来实现这些目标，该管道由一组研究人员开发，他们是该领域的世界领先者，总共测得的基因组比任何其他测序中心都多。到目前为止，这些物种包括40多种微生物，13种寄生和真菌病原体，2种植物(拟南芥和水稻)，2种昆虫(黑腹果蝇和冈比亚按蚊)，4种哺乳动物(人、鼠、鼠和狗)，总计超过1亿次测序反应和超过100亿碱基对的组装基因组序列。本申请中描述的测序活动将在新创建的J.Craig Venter科学基金会联合技术中心(JTC)进行，该中心是TIGR的附属机构。JTC实验室的设计旨在支持高通量生产管道，用于猎枪和BAC末端测序项目，以及基于聚合酶链式反应的重测序和SNP发现，在其运营的第一年，每年可进行4500万次测序反应。JTC的设计规模为每年超过1.2亿次测序反应。TIGR/JTC测序生产中心每个通道的初始成本不到0.94美元，完成成本为每个基地0.0.001美元，这些成本在边远地区大幅降低。

DESCRIPTION (provided by applicant): The goals of the Large-Scale Genome Sequencing Production Center (Center) described in this application are to: (1) provide proven expertise in large-scale DNA sequencing and bioinformatics to the study of high priority eukaryotic species to consistently produce draft and finished genome sequences and annotation of the highest possible quality; (2) rapidly release genome sequence data, sequence traces, assemblies, and associated annotation to the public domain; (3) provide reagents and software developed under this grant to the scientific community; and (4) investigate and implement novel methods and technologies that can significantly increase sequencing throughput while decreasing sequencing costs. The Center will accomplish these goals through the application of a robust and sophisticated pipeline for large-scale genome sequencing and analysis that has been developed by a team of investigators that are world leaders in this field and have collectively sequenced more genomes than any other sequencing center. These include more than 40 microbial species, 13 parasitic and fungal pathogens, 2 plant species (Arabidopsis thaliana and rice), 2 insect species (Drosophila melanogaster and Anopheles gambiae), and 4 mammalian species (human, mouse, rat, and dog) to date, totaling more than 100 million sequencing reactions and over 10 billion base pairs of assembled genome sequence. Sequencing activities described in this application will be carried out at the newly created J. Craig Venter Science Foundation Joint Technology Center (JTC), a TIGR affiliate. The JTC laboratories have been designed to support high-throughput production pipelines for shotgun and BAC end sequencing projects and for PCR-based resequencing and SNP discovery at a level of 45 million sequencing reactions per year in its first year of operation. The JTC is designed to scale to over 120 million sequencing reactions per year. The initial per lane costs for the TIGR/JTC Sequencing Production Center are less than $0.94 and finishing costs are $.0.001 per basepair with significant reductions in the outlying years.