NHGRI/DIR Genomics Core

NHGRI/DIR 基因组学核心

• 批准号: 9152765
• 负责人: settara chandrasekharappa
• 金额: $ 116.84万
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9152765
• 关键词: Acute Myelocytic Leukemia; Adopted; African American; Aliquot; Blood capillaries; Budgets; Clustered Regularly Interspaced Short Palindromic Repeats; Collection; Coloboma; Computer software; Computers; Copy Number Polymorphism; DNA; DNA Library; Data; Data Analyses; Data Set; Diagnosis; Epilepsy; Evaluation; Eye diseases; Fanconi' s Anemia; Fever; Fishes; Frequencies; Future; Gap Junctions; Genome; Genomic Segment; Genomics; Genotype; Goals; Haplotypes; Head and Neck Cancer; Human; Infection; Label; Learning; Leber' s amaurosis; Licensing; Linkage Disequilibrium; Loss of Heterozygosity; Methylation; Mining; Mosaicism; Mus; Mutagenesis; National Human Genome Research Institute; Parents; Patients; Population; Population Analysis; Process; Reaction; Reagent; Research Personnel; Resolution; Resources; Running; SNP genotyping; Sampling; Services; Smith Magenis syndrome; Software Tools; Stratification; Syndrome; Technology; Training; Uniparental Disomy; Ursidae Family; Variant; Zebrafish; base; capillary; cost; exome sequencing; human DNA; induced pluripotent stem cell; insertion/deletion mutation; interest; mouse genome; new technology; novel; physical mapping; programs; screening; targeted sequencing; tool

The Genomics Core primarily offers genotyping services to the NHGRI investigators. To a limited extent, services related to physical mapping, sequencing and access to DNA panels are also available. Genotyping is performed using either of two technologies, Illumina BeadArray for SNPs or ABI capillary electrophoretic sizing of fluorescently tagged PCR products encompassing STRPs or other genomic region(s) of interest. Both Illumina and ABI technologies are widely used by a large number of NHGRI investigators. This year, 18 investigators and three adjuncts representing all nine branches and two programs (NISC and UDP) used Core genotyping services. Over the past four years (FY2012-FY2015), there has been a steady increase in service requests received (353, 583, 707 and 853) and the number of DNA samples processed (9895, 17608, 40350, and 42466). Human SNP genotyping was carried out on eight different BeadArray types using Illumina Infinium technology. We processed 6,188 human DNA samples and generated >3 billion genotypes. In addition, 96 samples were processed using methylation arrays. The genotyping data is used for studies such as linkage, association, copy number variation, deletion intervals, methylation status, variations introduced by the iPS technology, parent-of-origin of deletions, mosaicism, uniparental disomy, and to generate haplotypes for discovering variants from sequence data. In addition to numerous small projects, we do have some large SNP projects. Over the last four years (FY2012-FY2015), we processed 1152, 1536, 2256 and 4032 samples for SNP genotyping for NISC. Since NISC genotypes all samples received for whole exome and targeted sequencing, the sample numbers are likely to increase in the future. Further, a large SNP genotyping project (3,000) samples for an MCIDB lab was started recently. Investigators requesting SNP genotyping bear a portion of the cost by using their own budgets to purchase the SNP chip kits, which include SNP chips and reagents. Samples run on SNP and methylation arrays (6,284 samples) represent only about 15% of the total 42,466 DNA samples processed by the Core this year. The remaining samples (36,182) were processed using ABI technology, which has the capability to separate fluorescently labeled PCR products at single-base resolution. In 2010, we developed an efficient screening strategy for zebrafish mutagenesis, which led to identification of germline transmitting founder fish and the size of insertion/deletion mutations generated by ZFNs and TALENs. Recent introduction of CRISPR/Cas technology for targeted mutagenesis resulted in a huge surge in the number of zebrafish DNA samples processed (5492, 14619, 35539, 28986 for FY2012-2015, respectively). The CRISPR technology is being extended to mouse genome as well. In fact, for the past three years (FY2013-FY2015) the number of mouse (8, 612, 6211) and human (493, 500, 985) samples processed has been steadily increasing. While genotyping was the main activity of the Core, requests for human, mouse, and zebrafish BAC clones were also processed (56, 93, 26 and 2 BAC clones were provided during FY2012-2015). Requests for aliquots of DNA panels (eight, nine, three and two) were also processed during the FY2012-2015 period. We will continue to provide access to BAC libraries and DNA panels, and running sequencing reactions for NHGRI investigators. Since FY2010, the Core has assisted investigators with data analysis and access to software/tools, such as GoldenHelix, Nexus, and GenomeStudio. The Core provided training on Illuminas GenomeStudio, and several researchers at NHGRI are using this software on their own computers. While an earlier purchase of unlimited licenses for GenomeStudio made this possible, the yearly renewal expense of Nexus and GoldenHelix limits their availability to only one computer in the Core. Core helps researchers to take advantage of learning and using these tools, and also helps with the handling, collection, evaluation, and processing of SNP and other data sets. The Core has provided significant data analysis support for 11 investigators over the past three years on different projects, covering copy number variation, linkage disequilibrium analysis, population stratification, and association studies. Analyses for detecting deletions, duplications, loss of heterozygosity, and regions portraying signs of chromosomal mosaicism in DNA samples from patients diagnosed with Fanconi anemia and head and neck cancer were also performed. Other studies include changes associated with the processing of iPS, Acute myeloid leukemia, Smith-Magenis syndrome, Febrile Infection-Related Epilepsy Syndrome, population stratification and variant frequency ranking of the African-American Ancestral SNPs, and eye diseases Coloboma and Leber Congenital Amaurosis (LCA). This service is of huge value to investigators with small projects, as are most users of the Core, who do not have the required tools or expertise for the analysis of large data sets.

基因组学核心主要为NHGRI研究人员提供基因分型服务。在有限的范围内，还提供与物理绘图、测序和获取DNA样本有关的服务。使用两种技术中的任一种进行基因分型，用于SNP的Illumina BeadArray或荧光标记的PCR产物的ABI毛细管电泳大小测定，所述荧光标记的PCR产物包含STRP或其他感兴趣的基因组区域。Illumina和ABI技术都被大量的NHGRI研究人员广泛使用。今年，代表所有九个分支和两个项目（NISC和UDP）的18名研究人员和三名专家使用了核心基因分型服务。在过去四年（2012 - 2015财年），收到的服务请求（353、583、707和853）和处理的DNA样本数量（9895、17608、40350和42466）稳步增加。 使用Illumina Infinium技术对八种不同的BeadArray类型进行人类SNP基因分型。我们处理了6,188个人类DNA样本，产生了超过30亿个基因型。此外，使用甲基化阵列处理96个样品。基因分型数据用于研究，如连锁、关联、拷贝数变异、缺失间隔、甲基化状态、iPS技术引入的变异、缺失的起源亲本、嵌合体、单亲二体，并用于生成单倍型以从序列数据发现变体。除了许多小项目外，我们还有一些大型的SNP项目。在过去的四年中（FY 2012-FY 2015），我们处理了1152、1536、2256和4032份样本用于NISC的SNP基因分型。由于NISC对所有接受全外显子组和靶向测序的样本进行基因分型，因此样本数量在未来可能会增加。此外，MCIDB实验室的一个大型SNP基因分型项目（3，000个）样品最近开始。要求SNP基因分型的研究者通过使用他们自己的预算来购买SNP芯片试剂盒来承担部分费用，SNP芯片试剂盒包括SNP芯片和试剂。 在SNP和甲基化阵列上运行的样本（6，284个样本）仅占今年核心处理的42，466个DNA样本的15%左右。剩余样本（36，182）使用ABI技术进行处理，该技术能够以单碱基分辨率分离荧光标记的PCR产物。2010年，我们开发了一种有效的斑马鱼诱变筛选策略，这导致了生殖系传播创始人鱼的鉴定以及ZFN和TALEN产生的插入/缺失突变的大小。最近引入的CRISPR/Cas技术用于靶向诱变，导致处理的斑马鱼DNA样本数量激增（2012 -2015财年分别为5492、14619、35539、28986）。CRISPR技术也正在扩展到小鼠基因组。事实上，在过去三年（2013 - 2015财年）中，处理的小鼠（8，612，6211）和人（493，500，985）样本数量一直在稳步增加。 虽然基因分型是核心的主要活动，但也处理了对人类、小鼠和斑马鱼BAC克隆的请求（2012 -2015财年期间提供了56、93、26和2个BAC克隆）。在2012 -2015财政年度期间，还处理了DNA样本组等分试样（8份、9份、3份和2份）的请求。我们将继续为NHGRI研究人员提供BAC文库和DNA面板，并运行测序反应。 自2010财年以来，Core已协助调查人员进行数据分析并访问软件/工具，例如GoldenHelix、Nexus和GenomeStudio。核心提供Illuminas GenomeStudio的培训，NHGRI的几位研究人员正在自己的计算机上使用该软件。虽然早期购买的GenomeStudio的无限许可证使这成为可能，Nexus和GoldenHashion的年度续订费用限制了它们的可用性，只有一台计算机的核心。Core帮助研究人员利用学习和使用这些工具，并帮助处理，收集，评估和处理SNP和其他数据集。在过去的三年里，核心研究中心为11名研究人员提供了重要的数据分析支持，涉及不同的项目，包括拷贝数变异、连锁不平衡分析、人群分层和关联研究。还对诊断为范可尼贫血和头颈癌的患者的DNA样本中的缺失、重复、杂合性丢失和描绘染色体嵌合现象迹象的区域进行了检测分析。其他研究包括与处理iPS、急性髓性白血病、Smith-Magenis综合征、发热性惊厥相关癫痫综合征、非裔美国人祖先SNP的人群分层和变异频率排名以及眼病Coloboma和Leber先天性黑蒙（LCA）相关的变化。这项服务对于小项目的调查人员和核心数据库的大多数用户都具有巨大价值，因为他们不具备分析大型数据集所需的工具或专门知识。