01 Sequencing and Microarray Facility

项目概要：测序和微阵列工厂（SMF） 测序和微阵列设施（SMF）的使命是使用最先进的仪器， 创新的技术专长，为研究人员提供最高质量的基因组数据， 全方位的基因组服务，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、ChIP-Seq和单细胞分析），桑格-和 基于Illumina的基因重测序和微阵列平台（基因表达、microRNA、甲基化、单核苷酸多态性）， 核苷酸多态性和拷贝数分析）。对于这些服务，SMF创新和开发 根据需要定制方案，使研究人员能够获得可靠的标本基因组数据， 通常在癌症中心组织库如FFPE组织、血清、血浆和尿液中发现， 其中通常是低质量和/或低数量的。对SMF的NGS服务的需求增长了1374%， 前一个周期的补助金。 SMF主任是Vicki Huff博士，联合主任是Sharon Dent博士和Nicholas Navin博士， 经理是艾丽卡·汤普森女士。仪器包括两个NovaSeq、一个HighSeq 4000、两个HiSeq 2000， 一台NextSeq 500、一台MiSeq、两台ABI 3730、一台数字液滴PCR系统、一台Fluidigm C1单细胞自动制备仪和 EVOS FL自动成像系统，Nanostring nCounter MAX分析系统，10 X Genomics Chromium 系统、一个Affytechnic Fluidics Station和两个机器人工作站（Agilent Bravo和Eppendorf epMotion 5075 TMX）。其中许多是使用该机构提供的SMF购买的3，171，019美元 自2013年以来的装备。其中一个NovaSeq 6000是用NIH S10 HEI赠款购买的。 SMF支持了482名MD安德森研究人员的研究，其中361人是CCSG计划成员 代表了CCSG的全部16个项目。在过去的赠款周期中，SMF为649份出版物提供了捐助，其中78%是 在IF >5的期刊上发表的论文占29%，在IF >10的期刊上发表的论文占29%。退款费用 提供了SMF预算7，138，252美元的93%。CCSG的支持率为6.8%（486，766美元）。因为93%的 由于SMF处理的样本来自同行评审用户，CCSG资金得到了很好的利用。在格兰特44年， SMF要求CCSG提供497，812美元（估计占其预算的6.6%）。 在即将到来的资助周期中，SMF将继续建立其提供尖端基因组服务的记录 来支持高影响力的科学目前的计划包括：1）继续制定专门的议定书 和服务，包括免疫分析、单细胞拷贝数分析、单细胞ATAC-Seq和单细胞 细胞CRISPR测序，以及定相外显子组和全基因组，精确的大结构变体 2）扩大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的期望。

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.