Computer Cluster and Storage to Support Whole Genome Sequencing and Analysis

支持全基因组测序和分析的计算机集群和存储

• 批准号: 7595696
• 负责人: Eric Sobel
• 金额: $ 23.65万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-14 至 2010-11-13
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7595696
• 关键词: Avian Influenza; Bioinformatics; Biomedical Research; Communities; Computer Systems; Computers; Core Facility; DNA; DNA Sequence; Data; Data Analyses; Diagnosis; Equipment; Funding; Future; Genes; Genetic; Genetic Research; Genome; Genomics; Genotype; Grant; Human Genetics; Influenza; Laboratories; Large-Scale Sequencing; Price; Public Health; Research; Research Project Grants; Risk; Running; Schizophrenia; Scientific Advances and Accomplishments; Scientist; Sequence Analysis; Solid; Structure; Technology; Time; cost; experience; genome sequencing; genome-wide; insight; instrument; instrumentation; new technology; public health relevance; transmission process

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.

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，基因研究的新时代已经来临。这些新仪器为先进科学实验室提供了基因查询的途径，而由于大规模测序的时间和成本过高，这在以前是不可能的。地方实验室现在可以考虑以前属于国家实验室权限的研究。对于希望在基因研究领域处于领先地位的实验室来说，全基因组技术正迅速变得至关重要。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其核心设施中拥有三台全基因组测序仪供其科学家使用，并且正在另一项提案中寻求第四台。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）； Applied Biosystems SOLiD 机器是可能的第四个平台。此外，加州大学洛杉矶分校还可以使用 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 测序仪和基因分型仪本身的成本之外，这项新技术还存在巨大的隐性成本。在每次运行成本相同的情况下，这些机器生成的遗传数据量大约是两年前的 1000 倍。不仅需要巨大的存储容量，还需要相当大的计算能力来彻底分析这些数据。当前的仪器拨款要求为存储阵列和计算集群提供资金，专门用于加州大学洛杉矶分校的全基因组测序和分析。存储阵列总容量为84TB；该计算集群将拥有 128 个 Intel Xeon 3 GHz 核心。这些是企业级仪器，现在可以以合理的价格购买。这些仪器将由人类遗传学生物信息学核心运行，该核心在此类计算系统方面拥有多年经验。加州大学洛杉矶分校正在进行的许多研究项目可以立即从这项技术中受益。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让他们受益。作为一个具体的例子，加州大学洛杉矶分校正在生成和分析由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的数据。此外，该提案中概述的两个项目是流感快速监测和研究中心的一部分，旨在调查禽流感的分布和传播风险。这些关键的公共卫生问题迫切需要所需的文书。加州大学洛杉矶分校科学界对全基因组测序和分析非常兴奋，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：新的大规模并行 DNA 测序技术可以以比以前更短的时间和成本对整个基因组进行测序。这项新技术会产生大量数据，需要大量存储容量和计算能力来存储和分析。将这种 DNA 测序技术以及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。