Establishing Single Molecule Real Time Sequencing for the North of the UK

在过去的5年里，新的测序技术的应用已经改变了分子生物学，这些技术使DNA和RNA的测序速度比以前可能的要快得多，而且成本大大降低。随着第三代测序方法的出现，我们现在正处于第二波变革性技术浪潮的尖端，可以实现单分子、实时测序。这些进展为在BBSRC汇款中工作的研究人员创造了机会。该提案寻求在利物浦大学基因组研究中心(CGR)内放置一个太平洋生物科学RS II高通量测序平台，该设施已为英国研究界提供DNA测序和分析服务超过5年。CGR被嵌入利物浦大学(http://www.liv.ac.uk/technology-directorate/)，的科技局(TD)，以确保学院利用资产，从而推动学术卓越。在考虑持续进修基金的财政可持续性时，运输署会考虑一些较不明显的回报，例如出版、学生培训和拨款建议，作为学院核心业务的重要组成部分，同时亦会考虑其他回报，例如入场费。因此，利物浦大学坚定地致力于将基因组学作为一项使能技术。因此，CGR是英国同类设施中最大的之一，拥有20名核心员工。CGR每年处理200-300个项目，从小型泵启动/研发项目到涉及数百个样本的排序和分析的大型项目。为了最大限度地利用CGR的能力和专门知识以及实验室和生物信息学工作人员的广泛技能，建议的研究人员与学术领域的研究人员合作，协助他们设计、执行和分析基因组数据集。CGR目前提供一系列高通量测序平台：Roche 454FLX+、Illumina HiSeq和MiSeq以及Ion Torrent平台。我们在此次竞标中的合作伙伴爱丁堡基因组公司，由Genpool和Roslin的方舟基因组学公司融合而成，以非常可比的方式运作，两个设施和这项计划的申请者之间已经存在着广泛的联系。我们现在请求为购买太平洋生物科学公司RS II贡献46%的资金，以扩大目前的平台范围。PacBio系统是市场上唯一可用的平台，它将提供无需放大的样品制备，并具有非常长时间读取输出的潜力。因此，该技术非常适合于符合BBSRC优先事项的核心战略领域的应用，即食品安全、生物能源和工业生物技术以及支撑健康的基础生物科学。申请者实验室内的大部分研究是由BBSRC资助的。我们已经确定了这项技术的五个关键应用，例如复杂基因组的结构和调控[(如小麦)或小菜蛾(小菜蛾)，这是十字花科作物最重要的害虫之一]，了解牲畜的单倍型，以及调查适用于健康和生物技术的微生物群落组成。除了支持利物浦大学的研究外，申请者还得到了北方大学和苏格兰各地的广泛支持，强调了进一步的项目将受益于该技术的应用。工业合作伙伴(Oxitec，一家中小企业和联合利华)和利物浦大学都承诺提供支持。因此，这是一项极具成本效益和相关性的投资，将把一台用户需求很高的仪器放在一个环境中，该环境具有提供高质量科学的可靠记录，拥有熟练的员工，并为学术界和工业界提供了明确的访问模式。

Over the last 5 years molecular biology has been transformed by the application of new sequencing technologies which allow DNA and RNA to be sequenced much faster than was previously possible and at a significantly reduced cost. We are now at the cusp of a second transformative wave of technologies with the availability of third generation sequencing methodologies that enable single molecule, real-time sequencing. These developments create opportunities for researchers working within the BBSRC remit.The proposal seeks to place a Pacific Biosciences RS II high-throughput sequencing platform within the Centre for Genomic Research (CGR) at the University of Liverpool, a facility that has provided DNA sequencing and analysis services to the UK research community for over 5 years. The CGR is embedded within the Technology Directorate (TD) at the University of Liverpool (http://www.liv.ac.uk/technology-directorate/), to ensure utilisation of assets by the Faculty and thus drive academic excellence. In considering the financial sustainability of an SRF, the TD considers a number of less tangible returns, such as publications, student training and grant proposals as important components of the Faculty's core business, alongside returns such as access fees. There is hence a strong commitment by the University of Liverpool to genomics as an enabling technology. As such, the CGR is one of the largest facilities of its type in the UK, with a core staff of 20 people. The CGR handles 200 - 300 projects per year, ranging from small pump-priming / R&D projects to large-scale projects involving the sequencing and analysis of several hundred samples. To make best use of the capacity and expertise residing in the CGR and the wide skill sets of laboratory and bioinformatics staff, the proposal Investigators collaborate with researchers across the academic spectrum to assist them in devising, executing and analysing genomic datasets. The CGR currently offers access to a range of high-throughput sequencing platforms: Roche 454FLX+, Illumina HiSeq and MiSeq as well as the Ion Torrent platforms. Our partner in this bid, Edinburgh Genomics, formed from the fusion of GenePool and Roslin's ARK-Genomics, operates in a very comparable manner and extensive links already existing between the two facilities and applicants on this proposal.We now request a 46% contribution to the purchase of a Pacific Biosciences RS II to extend the current range of platforms. The PacBio system is the only available platform on the market that will offer amplification-free sample preparation in combination with the potential for very long read output. Hence, the technology is ideally suited to the application in areas of core strategic fit with BBSRC priorities, namely Food Security, Bioenergy and Industrial Biotechnology as well as Basic Biosciences underpinning Health. The majority of research within the laboratories of the applicants is funded by the BBSRC. We have identified five key applications of the technology such as the structure and regulation of complex genomes [(eg wheat) or the diamondback moth (Plutella xylostella), one of the most important pests of cruciferous crops], understanding haplotypes in livestock as well as investigating the composition of microbial communities as applicable to health and biotechnology.In addition to underpinning research at the University of Liverpool, the applicants have also received widespread support from across Northern Universities and Scotland, highlighting further projects that will benefit from the application of the technology. Industrial partners (Oxitec, an SME, and Unilever) have pledged support, as has the University of Liverpool. As a consequence, this is a highly cost effective and relevant investment that will place an instrument with high user demand in an environment with a proven track record of delivering high quality science with skilled staff and a clear access model for academia and industry.