Future-Proofing the Sustainability of the MRC High Throughput Sequencing Hub in Scotland

苏格兰 MRC 高通量测序中心的可持续性发展

• 批准号: MR/K001744/1
• 负责人: Mark Blaxter
• 金额: $ 69.14万
• 依托单位: University of Edinburgh
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FK001744%2F1
• 关键词: Future; Proofing; Sustainability; MRC; Throughput

The GenePool is the leading next generation genomics facility in Scotland, and one of the largest academic facilities in the UK. The GenePool is funded by the MRC as a High Throughput Sequencing Hub, with specific remit to deliver collaborative access to next generation sequencing and informatics across the MRC science area. This application is for renewal for 24 months of the initial 3-year funding, to bed in the advances made in setting up the MRC Hub, and to move the facility to full cost-recovery. We will focus on delivering first-rate data and analysis on cutting edge science, to a wide range of collaborators both new and established, using the transformative tools of Illumina sequencing and high-throughput computing. We will build upon our MRC Hub and "spokes" model, fostering bioinformatics training and next generation genomics understanding across our target area.We request core support for promotional and outreach activities, including a new bioinformatics staff member jointly appointed between the Liverpool and Edinburgh MRC Hubs who will organise and deliver advanced training in next generation genomics to PhD students and postdoctoral researchers. We will deliver proactive Next Generation Sequencing Clinics in academic research institutes and departments across Scotland. We will continue to support the Next Generation Bioinformatics User Group meetings, including inviting international speakers and delivering 2-day research workshops on selected technologies. The MRC network of 'spokes' bioinformaticians in institutions across Scotland will be expanded. We will produce promotional materials for distribution to potential collaborators and grant applicants, and use our web site and social media portals to promote the MRC HTS Hub approach to next generation genomics.We will develop standard operating procedures for new techniques, and to explicitly and rigorously cross-check manufacturers' claims. We have good relationships with the major technology and reagent suppliers and will use these to negotiate early access to new products. We will perform in-house trials of new kits, in direct comparison to existing protocols, and make the results known to our collaborator base. We will work with companies and collaborators to bed in and develop new approaches to the generation of and analysis of next generation sequencing data.The next generation sequencing revolution is based on two principles: transformative technologies and skilled staff. We have a mature charging model that includes elements of instrument depreciation and staff time, and generate a working surplus (for investment in the facility) each year. We have already transitioned several staff from core grant to cost recovery support. In the period of 24 months of the renewal, we will transition three further core MRC staff posts to full recovery (one bioinformatician and two high-level research technologists). Two new posts will be created to ensure best service to our collaborators, particularly given the vastly increased throughput of the Illumina HiSeq platform. A laboratory manager will ensure fitness-for-purpose of our LIMS installation, manage the wide portfolio of instrumentation (including robotics, qPCR, analytical platforms and other ancillary instrumentation), and provide oversight of the full laboratory workflow process. A business manager will administer the large number of active projects within the facility, in particular dealing with the financial side, managing the LIMS, and keeping collaborators up-to-date with project progress. Both of these new posts are planned to transition rapidly to full cost recovery in two years. Initiation of these posts will free the GenePool Scientific manager (Dr Karim Gharbi) and the Director (Prof Mark Blaxter) to focus on speeding the transformation of researchers' ideas into viable projects, well-analysed studies and high-hitting publications.

基因库是苏格兰领先的下一代基因组学设施，也是英国最大的学术设施之一。GenePool由MRC资助，作为高通量测序中心，具有特定的权限，以提供跨MRC科学领域的下一代测序和信息学的协作访问。申请将最初的3年期拨款续期24个月，以落实设立MRC中心所取得的进展，并使该设施完全收回成本。我们将专注于使用Illumina测序和高通量计算的变革性工具，向广泛的新老合作伙伴提供一流的前沿科学数据和分析。我们将建立我们的MRC中心和“辐条”模式，在我们的目标领域促进生物信息学培训和下一代基因组学理解。我们要求为推广和拓展活动提供核心支持，包括由利物浦和爱丁堡MRC中心联合任命的一名新的生物信息学工作人员，他将为博士生和博士后研究人员组织和提供下一代基因组学的高级培训。我们将在苏格兰的学术研究机构和部门提供前瞻性的下一代测序诊所。我们将继续支持下一代生物信息学用户组会议，包括邀请国际演讲者并就选定的技术举办为期两天的研究研讨会。苏格兰各机构的MRC“辐条”生物信息学家网络将得到扩展。我们将制作宣传材料分发给潜在的合作者和资助申请人，并使用我们的网站和社交媒体门户网站来推广MRC HTS中心对下一代基因组学的方法。我们将制定新技术的标准操作程序，并明确和严格地交叉检查制造商的声明。我们与主要的技术和试剂供应商有良好的关系，并将利用这些来谈判新产品的早期准入。我们将对新试剂盒进行内部试验，直接与现有方案进行比较，并将结果告知我们的合作伙伴。我们将与公司和合作者合作，共同开发下一代测序数据生成和分析的新方法。下一代测序革命基于两个原则：变革性技术和熟练的员工。我们有一个成熟的收费模式，包括仪器折旧和员工时间，每年产生工作盈余（用于设施投资）。我们已经将几名工作人员从核心赠款转移到成本回收支持。在续期的24个月里，我们将把另外3个MRC核心人员岗位（1个生物信息学家和2个高级研究技术人员）全面恢复。我们将设立两个新职位，以确保为我们的合作伙伴提供最好的服务，特别是考虑到Illumina HiSeq平台的吞吐量大幅提高。实验室经理将确保LIMS安装的适用性，管理广泛的仪器组合（包括机器人，qPCR，分析平台和其他辅助仪器），并监督整个实验室工作流程。业务经理将管理设施内大量的活动项目，特别是处理财务方面，管理LIMS，并使合作者了解项目进展情况。这两个新员额计划在两年内迅速过渡到完全收回成本。这些职位的设立将使基因库科学经理（Karim Gharbi博士）和主任（Mark Blaxter教授）能够集中精力加快将科学家的想法转化为可行的项目、经过充分分析的研究和高影响力的出版物。

项目成果

A comparison of in vitro nucleosome positioning mapped with chicken, frog and a variety of yeast core histones.

• DOI: 10.1016/j.jmb.2013.07.019
• 发表时间: 2013-11-15
• 期刊: Journal of molecular biology
• 影响因子: 5.6
• 作者: Allan J;Fraser RM;Owen-Hughes T;Docherty K;Singh V
• 通讯作者: Singh V

A systematic analysis of the human immune response to Plasmodium vivax.

• DOI: 10.1172/jci152463
• 发表时间: 2023-10-16
• 期刊: JOURNAL OF CLINICAL INVESTIGATION
• 影响因子: 15.9
• 作者: Bach, Florian A.;Sandoval, Diana Munoz;Mazurczyk, Michalina;Themistocleous, Yrene;Rawlinson, Thomas A.;Harding, Adam C.;Kemp, Alison;Silk, Sarah E.;Barrett, Jordan R.;Edwards, Nick J.;Ivens, Alasdair;Rayner, Julian C.;Minassian, Angela M.;Napolitani, Giorgio;Draper, Simon J.;Spence, Philip J.
• 通讯作者: Spence, Philip J.

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

• DOI: 10.1371/journal.pcbi.1004143
• 发表时间: 2015-04
• 期刊: PLoS computational biology
• 影响因子: 4.3
• 作者: Attwood TK;Bongcam-Rudloff E;Brazas ME;Corpas M;Gaudet P;Lewitter F;Mulder N;Palagi PM;Schneider MV;van Gelder CW;GOBLET Consortium
• 通讯作者: GOBLET Consortium

MicroRNA-100-5p indirectly modulates the expression of Il6, Ptgs1/2 and Tlr4 mRNA in the mouse follicular dendritic cell-like cell line, FL-Y.

• DOI: 10.1111/imm.12342
• 发表时间: 2015-01
• 期刊: Immunology
• 影响因子: 6.4
• 作者: Aungier SR;Ohmori H;Clinton M;Mabbott NA
• 通讯作者: Mabbott NA

Genomic associations with bill length and disease reveal drift and selection across island bird populations.

• DOI: 10.1002/evl3.38
• 发表时间: 2018-03
• 期刊: Evolution letters
• 影响因子: 5
• 作者: Armstrong C;Richardson DS;Hipperson H;Horsburgh GJ;Küpper C;Percival-Alwyn L;Clark M;Burke T;Spurgin LG
• 通讯作者: Spurgin LG