01 Sequencing and Microarray Facility

项目摘要：测序和微阵列设施(SMF) 测序和微阵列设备(SMF)的任务是使用最先进的仪器和 创新的技术专业知识，为研究人员提供来自 全面的基因组服务，包括基于Illumina平台的下一代测序 (NGS)服务(全基因组、全外显子组、RNA-Seq、芯片-Seq和单细胞分析)、SANGER-AND 基于Illumina的基因重测序和微阵列平台(基因表达、microRNA、甲基化、单 核苷酸多态和拷贝数分析)。针对这些服务，SMF不断创新和发展 定制的方案，根据需要，使研究人员能够获得可靠的基因组数据的标本 通常在癌症中心组织库中发现，如FFPE组织、血清、血浆和尿液，分析物 它们往往是低质量和/或低数量的。SMF的NGS服务需求比去年同期增长了1374% 前一批款周期。 SMF的董事是Vicki Huff博士，联席董事是Sharon Dent博士和Nicholas Navin博士，以及 经理是埃里卡·汤普森女士。工具包括两个NovaSeq、一个HighSeq4000、两个HiSeq2000、 一台NextSeq500，一台MiSeq，两台ABI 3730，一个数字液滴聚合酶链式反应系统，一台Fluidigm C1单细胞自动制备机和 EVOS FL自动成像系统、纳米串计数器MAX分析系统、10倍基因组铬 系统、一个Affymetrix流体工作站和两个机器人工作站(Agilent Bravo和Eppendorf epMotion 5075 TMX)。其中许多是用该机构为SMF提供的3171,019美元购买的 自2013年以来的设备。其中一台NovaSeq6000是在NIH S10 HEI授予的奖项下购买的。 SMF支持了482名MD Anderson调查人员的研究，其中361人是CCSG项目成员 代表所有16个CCSG项目。在上一个赠款周期中，工作人员-管理层基金会为649种出版物提供了捐助，其中78% 在IF&>；5的期刊上发表，其中29%在IF&>；10的期刊上发表。 提供了7,138,252美元SMF预算的93%。CCSG的支持率为6.8%(486,766美元)。因为93%的人 SMF处理的样本来自同行审查的用户，CCSG基金杠杆作用很好。在44日元的赠款中， SMF要求CCSG提供497,812美元(估计为其预算的6.6%)。 在接下来的赠款周期中，SMF将继续巩固其提供尖端基因组服务的记录 以支持高影响力的科学。目前的计划包括：1)继续制定专门议定书 和服务，包括免疫图谱、单细胞拷贝数分析、单细胞ATAC-Seq和单细胞 细胞CRISPR测序，以及阶段性外显体和全基因组，准确的大结构变异 (2)扩展SMF服务，以包括增强的数据处理。 通过这些措施，我们将继续为研究人员提供独特和卓越的基因组服务 他们对SMF寄予厚望。

PROJECT SUMMARY: THE SEQUENCING AND MICROARRAY FACILITY (SMF) The mission of the Sequencing and Microarray Facility (SMF) is to use state-of-the-art instrumentation and innovative technical expertise to provide investigators with the highest quality genomic data from a comprehensive range of genomic services, which include Illumina platform-based next-generation sequencing (NGS) services (whole genome, whole exome, RNA-Seq, ChIP-Seq, and single-cell analysis), Sanger- and Illumina-based gene resequencing, and microarray platforms (gene expression, microRNA, methylation, single- nucleotide polymorphism, and copy number analyses). For these services, the SMF innovates and develops customized protocols, as needed, to enable investigators to obtain reliable genomic data on specimens that are commonly found in cancer center tissue banks such as FFPE tissues, serum, plasma, and urine, the analytes from which are often of low quality and/or quantity. Demand for SMF's NGS service has increased 1374% over the prior grant cycle. The SMF director is Dr. Vicki Huff, co-directors are Drs. Sharon Dent and Nicholas Navin, and the Facility Manager is Ms. Erika Thompson. Instrumentation includes two NovaSeqs, a HighSeq4000, two HiSeq2000s, a NextSeq500, a MiSeq, two ABI 3730s, a digital droplet PCR System, a Fluidigm C1 Single-Cell Auto Prep and EVOS FL Auto Imaging Systems, a Nanostring nCounter MAX Analysis System, a 10X Genomics Chromium System, an Affymetrix Fluidics Station, and two robotic workstations (Agilent Bravo and Eppendorf epMotion 5075 TMX). Many of these were purchased using the $3,171,019 the institution has provided the SMF for equipment since 2013. One of the NovaSeq6000s was purchased with an NIH S10 HEI grant award. The SMF supported the research of 482 MD Anderson investigators, 361 of whom are CCSG program members representing all 16 CCSG programs. In the past grant cycle, SMF contributed to 649 publications, 78% of which were published in journals with IF >5 and 29% of which were published in journals with IF >10. Chargeback fees provided 93% of the SMF budget of $7,138,252. CCSG support was 6.8% ($486,766). Because 93% of the samples processed by the SMF were from peer-reviewed users, CCSG funds were well leveraged. In grant Yr44, the SMF is requesting $497,812 from the CCSG (estimated 6.6% of its budget). In the coming grant cycle, the SMF will continue to build on its record of providing cutting-edge genomic services to support high-impact science. Current plans include 1) continuing the development of specialized protocols and services, including immune profiling, single-cell copy number analysis, single-cell ATAC-Seq, and single- cell CRISPR sequencing, as well as phased exomes and whole genomes, accurate large structural variant identification, and digital spatial profiling, and 2) expanding SMF services to include enhanced data processing. With these measures, we will continue to provide investigators with the unique and exceptional genomic services they have come to expect from the SMF.