High Throughput Genomic Sequencer at BCM Core Facility

摘要 下一代测序(NGS)技术已经彻底改变了分子生物学、遗传学和 基因组学通过将基因组技术与其他研究领域相结合，实质上将基因组 将中心能力转移到各个研究实验室。所要求的仪器Illumina HiSeq 4000是 最新的下一代测序仪，将取代和补充我们正在成为 过时或在其开发生命周期结束时，并由于其更高的吞吐量而提供具有竞争力的价格 以及更低的单位基本成本。这一新工具将使贝勒医学院(BCM)的团队从 从事研究以了解人类的分子机制的广泛学科 疾病，包括疾病基因克隆、癌症、基因表达、剪接、发育和分化， 和表观遗传学。共享的Illumina HiSeq 4000下一代测序仪将放置在和 由BCM基因组和RNA分析核心(GARP)管理，确保操作顺畅和轻松 在全校范围内访问。最重要的是，Illumina HiSeq 4000保留了我们当前 HiSeq 2500和HiSeq 2000机器，但能够生成两倍以上的序列数据 在大约三分之一的时间里每跑一次。此外，由于Illumina HiSeq 4000采用了图案化的流动电池， 它可以处理群集密度的巨大变化，这是一个重大挑战，也是故障的常见原因 我们目前的模式。我们预计，新仪器将降低故障率，最大限度地减少样品重复， 并将数据生成提高至少两倍。我们将把该系统应用于广泛的应用领域， 包括：1)通过芯片序列识别转录因子的直接下游靶点；2)执行 用RNA-Seq技术分析人体组织和模式生物的转录组；3)鉴定和克隆人 疾病基因全基因组、全外显子组和靶向捕获深度测序；4)调查 选择性剪接与人类疾病；5)环境影响 通过通过全基因组检查表观基因组和营养对怀孕、发育和疾病的影响 硫酸氢盐测序和组蛋白修饰；以及6)单细胞DNA和RNA图谱。我们已经确定了 18个参与小组，他们的研究项目非常多样化，由NIH的11个研究所资助， 包括NICHD、NIDDK、NEI、NCI、NIGMS、NHLBI、NIAMS、NHGRI、NINDS、NIAID和NIH主管的 办公室。由于参与的私人投资机构均从事基础和临床研究，我们相信引入 这一新的NGS仪器的使用将对许多医学相关领域产生直接、广泛和立竿见影的影响。

Abstract Next generation sequencing (NGS) technology has revolutionized the world of molecular biology, genetics, and genomics by the integration of genome technologies with other research fields, essentially bringing genome center capacity to individual research laboratories. The requested instrument, the Illumina HiSeq 4000, is the latest next generation sequencer that will replace and supplement our older instruments that are becoming obsolete or at the end of their development life, and to offer competitive pricing due to its higher throughput and lower per base cost. This new instrument will empower groups at Baylor College of Medicine (BCM) from a broad range of disciplines who conduct research to understand the molecular mechanisms of human diseases, including disease gene cloning, cancer, gene expression, splicing, development and differentiation, and epigenetics. The shared Illumina HiSeq 4000 next generation sequencer will be placed at and administrated by the BCM Genomic and RNA profiling Core (GARP) to ensure smooth operation and easy access school-wide. Most importantly, the Illumina HiSeq 4000 retains all of the flexibilities of our current HiSeq 2500 and HiSeq 2000 machines, but is capable of generating more than twice as much sequence data per run in about one third of the time. In addition, as the Illumina HiSeq 4000 has adopted patterned flow cells, it can handle large variations in cluster density, which is a major challenge and common source of failures of our current models. We anticipate that the new instrument will reduce the failure rate, minimize sample repeat, and increase data generation by at least two fold. We will apply the system to a broad range of applications, including: 1) identifying direct downstream targets of transcription factors by ChIP-Seq; 2) performing transcriptome analysis of human tissues and model organisms by RNA-Seq; 3) identifying and cloning human disease genes by whole genome, whole exome, and targeted capture deep sequencing; 4) investigating alternative splicing and human diseases by splice junction sequencing; 5) examining effects of environment and nutrition on pregnancy, development, and disease by examining the epigenome through whole genome bisulfate sequencing and histone modifications; and 6) single cell DNA and RNA profiling. We have identified 18 participating groups whose research projects are highly diverse and are funded by eleven institutes at NIH, including NICHD, NIDDK, NEI, NCI, NIGMS, NHLBI, NIAMS, NHGRI, NINDS, NIAID, and the NIH director's office. As the participating PIs are all engaged in both basic and clinical research, we believe the introduction of this new NGS instrument will have direct, broad, and immediate impact on many medically relevant fields.