SEQUENCING MOUSE GENOMIC CLONES

描述(改编自《调查员摘要》)：的主要目标 本项目的研究内容是系统地对基因片段进行测序 与人类基因组测序区域同线的小鼠基因组。 测序将通过继续Roe博士的 实验室，总部设在俄克拉荷马大学化学系和 诺曼校园的生物化学，与诺曼大学的实验室合作 约翰·霍普金斯大学的里夫斯博士。在过去的一年里，这个非正式的 合作已经产生了超过200kbp的鼠标序列 与人类22q11同线的染色体DNA。罗博士现在希望 将此协作正规化并开始将技术从其 小组与约翰·霍普金斯大学联合协调开始小鼠基因组研究 进行更大规模的测序，并将此序列数据提供给 社区。全长基因组克隆测序将在 俄克拉荷马大学的基因组克隆文库和末端测序 将在约翰·霍普金斯大学演出。为了实现这一目标， 调查人员现在提议： 1.扩展加州大学的兆库测序能力 俄克拉荷马州高级基因组技术中心将包括一个致力于 小鼠基因组测序。ACGT是建立在毕业生的基础上的 以学生/博士后培训为基础的基因组测序方法 成功地完成了大约200万个人类DNA碱基 化脓性链球菌的序列和大约一倍的覆盖率 和淋病奈瑟氏菌的基因组。通过雇用和 完善他们已经建立的方案，调查人员可以完成 01年和02年至少6个含有BAC的小鼠基因组序列 已经有NSF EPSCoR资助的ABI377，并将其 03年和04年的测序率，以及额外的自动DNA 定序器。因此，他们将对大约4.5M的小鼠基因组进行测序 这与同时测序的人类基因组区域在 建议的4年资助期。 2.继续发展、改进和实施自动化程序 用于DNA分离、DNA序列分析、数据采集和数据 分析，从而提高他们的DNA测序效率。 3.向社区快速发布带注释的DNA序列数据 遵循线虫的范例。 有了现有的技术，调查人员可以清楚地记录 这个项目的可行性，基于他们自己的生产力， 华盛顿大学(C.elegans)和桑格中心(C. 优雅，和人类)。目前最终序列的每个碱基的成本是 略低于1美元，计算方法是将NCHGR的总资金计入 调查员，包括间接成本和按比例计算的设备 总授权期，并除以存放在 GenBank。随着技术和效率的适度提高， 调查人员可以现实地预计，老鼠的一个重要区域 基因组DNA可以在4年的拟议资助期内按 最终序列的每个碱基的成本低于50美分。在这段时间里， 他们还将继续培训下一代科学家 发展新的测序方法和方法所需的基本理论和方法 进行数据分析。

DESCRIPTION (Adapted from the Investigator's Abstract): The major goal of the research in this project is to systematically sequence regions of the mouse genome that are syntenic with sequenced regions of the human genome. The sequencing will be accomplished by continuing the link between Dr. Roe's laboratory, based at the University of Oklahoma Department of Chemistry and Biochemistry on the Norman campus, in a partnership with the laboratory of Dr. Reeves at John Hopkins University. During the past year, this informal collaboration has resulted in the sequence of over 200 kbp of mouse chromosomal DNA that is syntenic with human 22q11. Dr. Roe now wishes to formalize this collaboration and begin transferring the technology from his group to John Hopkins by jointly coordinating efforts to begin mouse genomic sequencing on a larger scale and provide this sequence data to the community. Full length genomic clone sequencing will be performed at the University of Oklahoma and the genomic clone libraries and end sequencing will be performed at the John Hopkins University. To achieve this goal, the investigators now propose to: 1. Expand the megabase sequencing capabilities at the University of Oklahoma Advanced Center for Genome Technology to include a group dedicated to mouse genomic sequencing. ACGT is built upon the graduate student/postdoctoral training-based approach to genomic sequencing that has led to successfully completing approximately 2 million bases of human DNA sequence and approximately one-fold coverage of the Streptococcus pyogenes and Neisseria gonorrhoeae genomes within the last year. By employing and refining their already established protocols, the investigators can complete the sequence of at least 6 mouse genomic containing BACs in years 01 and 02 with an already available NSF EPSCoR funded ABI377 and double their sequencing rate in years 03 and 04 with an additional automated DNA sequencer. Thus, they will sequence approximately 4.5 M of the mouse genome that is syntenic with concurrently sequenced human genomic regions within the proposed 4 year funding period. 2. To continue to develop, improve and implement the automated procedures for DNA isolation, DNA sequence analysis, data acquisition, and data analysis, thereby increasing their DNA sequencing efficiency. 3. To rapidly release annotated DNA sequence data to the community following the C. elegans paradigm. With the existing technology, the investigators can clearly document the feasibility of this project, based on their own productivity, that of the Washington University (C. elegans), and the Sanger Center (yeast, C. elegans, and human). The present cost per base of final sequence is slightly under $1 as calculated by taking the total NCHGR funding to the investigator, including indirect cost and pro-rating equipment over the total grant period, and dividing by the total number of bases deposited in GenBank. With the modest improvement in technology and efficiency, the investigators can realistically expect that a significant region of mouse genomic DNA can be sequenced within the 4 year proposed grant period at a cost of under 50 cents per base of final sequence. Throughout this period, they also will continue to train the next generation of scientists in the basic theories and methods needed to evolve new approaches to sequencing and to data analysis.