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.

Genepool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机构之一。 GenePool由MRC资助为高通量测序中心，并具有特定的职责，可以在MRC科学领域提供对下一代测序和信息学的协作访问。该申请是为了在最初的3年资金中续签24个月，在设置MRC枢纽的进步中就读，并将设施移至全部成本恢复。我们将使用Illumina测序和高通量计算的变革性工具来将一流的数据和有关尖端科学的一流数据和分析进行新的合作者。我们将基于MRC枢纽和“发言”模型，在目标领域促进生物信息学培训以及下一代基因组学的理解。我们向促销和外展活动提供核心支持，包括在利物浦和爱丁堡MRC之间共同任命的新生物信息知识的工作人员，他们将在下一代基因组和PHD学生中提供先进的培训，并提供高级培训。我们将在苏格兰的学术研究机构和部门提供积极主动的下一代测序诊所。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提供有关选定技术的2天研究研讨会。苏格兰机构的“发言人”生物信息学家的MRC网络将扩大。我们将生产促销材料，以向潜在的合作者和授予申请人分发，并使用我们的网站和社交媒体门户网站来推广MRC HTS Hub方法，以促进下一代基因组学。我们将为新技术制定标准操作程序，并明确，严格地进行交叉检查制造商的主张。我们与主要技术和试剂供应商有良好的关系，并将使用它们来协商早期获得新产品的机会。我们将与现有协议直接比较新工具包进行内部试验，并使我们的合作者基础已知结果。我们将与公司和合作者合作，在下一代测序数据的生成和分析中闲逛并开发新的方法。下一代测序革命基于两个原则：变革性技术和熟练的员工。我们有一个成熟的充电模型，其中包括仪器折旧和员工时间的要素，并每年产生工作盈余（用于设施的投资）。我们已经将几名员工从Core Grant转变为成本恢复支持。在续签的24个月期间，我们将过渡三个核心MRC员工职位以完全康复（一名生物信息学家和两名高级研究技术人员）。将创建两个新的帖子，以确保为我们的合作者提供最佳服务，特别是考虑到Illumina Hiseq平台的吞吐量大大增加。实验室经理将确保我们的LIMS安装的健身能力，管理广泛的仪器组合（包括机器人技术，QPCR，分析平台和其他辅助仪器），并对完整的实验室工作流程进行监督。业务经理将管理该设施内的大量活动项目，特别是与财务方面，管理LIMS，并使合作者保持最新的项目进度。这两个新职位均计划在两年内迅速过渡到全部成本恢复。这些职位的发起将释放Genepool科学经理（Karim Gharbi博士）和主任（Mark Blaxter教授），专注于将研究人员的思想转变为可行的项目，良好的研究和高级出版物的转变。

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