Computer Cluster and Storage to Support Whole Genome Sequencing and Analysis

描述（由申请人提供）：随着大规模并行，高通量，全基因组DNA测序仪的到来，基因研究的新时代正在到来。这些新仪器为先进的科学实验室提供了遗传研究的途径，由于大规模测序的时间和成本过高，直到现在还不可能实现。地方实验室现在可以考虑以前是国家实验室权限的研究。全基因组技术正迅速成为希望在基因研究中处于领先地位的实验室的关键。作为一个世界级的遗传学中心，加州大学洛杉矶分校目前在核心设施中有三台全基因组测序仪可供其科学家使用，第四台正在另一项提案中寻求。加州大学洛杉矶分校目前有两台Illumina基因组分析仪（又名Solexa）和一台罗氏基因组测序仪FLX（又名454）；应用生物系统公司的SOLiD机器可能是第四个平台。此外，加州大学洛杉矶分校还使用Illumina BeadLab 1000进行全基因组高通量基因分型。不幸的是，除了全基因组DNA测序仪和基因型本身的成本之外，这项新技术还有一个巨大的隐性成本。这些机器产生的基因数据量大约是两年前的1000倍，每次运行的成本相同。不仅需要巨大的存储容量，而且还需要相当大的计算能力来彻底分析这个数量的数据。目前的仪器设备拨款要求为存储阵列和计算集群提供资金，用于加州大学洛杉矶分校的全基因组测序和分析。存储阵列的总容量为84 TB；计算集群将拥有128个英特尔至强3ghz内核。这些都是企业级的工具，现在价格合理。这些仪器将由人类遗传学生物信息学核心运行，该核心在这类计算系统方面有多年的经验。加州大学洛杉矶分校有许多正在进行的研究项目可以立即受益于这项技术。还有一大批从事生物医学研究的科学家，这项技术将在不久的将来对他们有益。作为一个特殊的例子，加州大学洛杉矶分校正在美国国立卫生研究院资助的精神分裂症基因全基因组搜索中生成和分析数据。此外，本提案中概述的两个项目是调查禽流感分布和传播风险的快速流感监测和研究中心的一部分。这些关键的公共卫生问题迫切需要所需的工具。加州大学洛杉矶分校的科学界对全基因组测序和分析感到非常兴奋，他们渴望使用拟议的设备将加州大学洛杉矶分校的生物医学研究带入基因组发现的下一个时代。公共卫生相关性：新的大规模平行DNA测序技术使全基因组测序在以前可能的时间和成本的一小部分。这项新技术产生了大量的数据，需要很大的存储容量和计算能力来存储和分析。将这种DNA测序技术和分析结果数据的能力引入加州大学洛杉矶分校生物医学研究界，将使科学家能够更深入地了解基因组的结构和功能，并促进对公共卫生问题的理解、诊断和治疗。

DESCRIPTION (provided by applicant): A new era of genetic research is now upon us with the arrival of massively parallel, high throughput, whole genome DNA sequencers. These new instruments allow avenues of genetic inquiry for advanced scientific laboratories that were impossible until now due to the prohibitive time and cost of large-scale sequencing. Local labs can now consider studies that were previously the purview of national labs. Whole genome technology is quickly becoming crucial to labs that wish to be current in genetic research. As befits a world- class center of genetics, UCLA currently has three whole genome sequencers in Core facilities available to its scientists, and a fourth is being sought in a separate proposal. At UCLA there are currently two Illumina Genome Analyzers (aka Solexa) and one Roche Genome Sequencer FLX (aka 454); an Applied Biosystems SOLiD machine is the possible fourth platform. In addition, UCLA has genome-wide, high throughput genotyping available using the Illumina BeadLab 1000. Unfortunately there is a large hidden cost of this new technology beyond the cost of the whole genome DNA sequencers and genotypers themselves. The amount of genetic data generated by these machines is roughly 1000-fold greater than was available only two years ago at the same cost per run. Not only is there need for tremendous storage capacity, but it also requires considerable computational power to thoroughly analyze this quantity of data. The current instrumentation grant requests funds for a storage array and computational cluster to dedicate to whole-genome sequencing and analysis at UCLA. The storage array will have 84 TB total capacity; the computational cluster will have 128 Intel Xeon 3 GHz cores. These are enterprise-level instruments that are now available at reasonable prices. These instruments will be run by the Human Genetics Bioinformatics Core, which has several years experience with these type of computing systems. There are a number of ongoing research projects at UCLA that can immediately benefit from this technology. There is also a large community of scientists engaged in biomedical research for whom this technology will be beneficial in the very near future. As a particular example, UCLA is generating and analyzing the data in an NIH-funded genome-wide search for schizophrenia genes. In addition, two of the projects outlined in this proposal are part of the Center for Rapid Influenza Surveillance and Research investigating the distribution and transmission risks of avian influenza. These critical public health issues have an urgent need for the requested instruments. There is a great deal of excitement for whole genome sequencing and analysis within the UCLA scientific community, they are anxious to use the proposed equipment to move biomedical research at UCLA into the next era of genomic discovery. PUBLIC HEALTH RELEVANCE: New massively parallel DNA sequencing technology allows whole genomes to be sequenced at a fraction of the time and cost previously possible. This new technology generates tremendous amounts of data that requires large storage capacity and computing power to store and analyze. Bringing this DNA sequencing technology, and the power to analyze the resulting data, to the UCLA biomedical research community will allow scientists to develop a deeper insight into the structure and function of the genome, and advance the understanding, diagnosis, and treatment of public health issues.