NHGRI/DIR Genomics Core

NHGRI/DIR 基因组学核心

• 批准号: 8177744
• 负责人: Lawrence C Brody
• 金额: $ 24.08万
• 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/8177744
• 关键词: Adopted; Arts; Copy Number Polymorphism; DNA; Data; Diamond-Blackfan anemia; Disease; Embryo; Fanconi' s Anemia; Genome; Genomics; Genotype; Goals; Holoprosencephaly; Human Cloning; Human Genome; Human Resources; Length; Libraries; Link; Maps; Mediating; Methylation; Mexican Americans; Microphthalmos; Mining; Mosaicism; Mus; Mutagenesis; National Human Genome Research Institute; Parents; Phenotype; Polydactyly; Process; Reaction; Research; Research Personnel; Resources; Running; SNP genotyping; Sampling; Scanning; Screening procedure; Services; Speed; Technology; Time; Transplantation; Zebrafish; Zinc Fingers; base; cleft lip and palate; congenic; density; genome wide association study; meetings; new technology; novel; physical mapping

The Genomics Core provides resources, services and advice to meet the needs of the NHGRI investigators related to genomics research. The genotyping services offered by the Genomics Core were used extensively and by a large number of investigators. In the past year, there were >100 requests by 15 investigators. The majority of requests were for human genome SNP genotyping. The Core processed 50 requests for genotyping with 1M SNP chips for a total of 730 DNA samples. A wide range of other Illumina SNP chips (370K, 550K, 610K, 1M Quad, 2.5M Quad and methylation) were processed, bringing the total to 850M SNP genotypes for the year. Genotypes were primarily used for scanning for genomic changes (deletions/duplications/mosaicism) using high density SNP chips, however, the data is useful for answering a variety of other questions related to linkage, association, copy number and methylation changes. Our investigators study a variety of disease conditions where the genotype data was utilized: Polydactyly, microphthalmia, cleft lip and palate, holoprosencephaly, undiagnosed diseases (UDP), Diamond-Blackfan anemia, Fanconi anemia, NF1 among others. The Core continues to provide STRP based genotyping as well. Although there were over 40 requests for STRP genotyping, these were typically for smaller number of samples. These STRP genotyping services covered a variety of applications, such as scanning focus regions for fine mapping of linked loci, copy number variation, identification of deletion intervals, parent of origin of deletions, and mouse studies (speed congenics, identifying transplant matches, loci for phenotypes). In general, the SNP and STRP genotyping services were used for a variety of genome-wide studies including exploring methylation status. While genotyping was the main activity of the Core for this past year, limited physical mapping and sequencing services, as well as access to DNA panels were also offered. A new DNA panel, Mexican-American (HD 100MEX), was added to the Core resources. We continue to provide access to BAC clones from human, mouse or zebrafish libraries. Sequencing services are limited to running the investigator provided reaction plates. Core personnel completed the initiative to inform NHGRI investigators about the Cores services through attending a meeting with each lab and sought their input. These discussions were productive and helped initiate utilization of the technologies available at the Core for novel applications. For instance, a quick and efficient screening strategy was developed for zinc-finger mediated mutagenesis in zebrafish embryos. Thus, the Core strives to enhance the utilization of available technologies for novel applications. The Core purchased and installed an Illumina iScan which allows faster, more efficient scanning of newer, higher density Illumina SNP chips (2.5M, and 5M SNPs) and the high throughput (Omni_Express) SNP chips. Advancing high-density technologies, which allows scanning multiple samples per chip, and availability in the Core of an efficient scanner, permits the Core now to accept moderately large genotyping projects and complete them in a reasonable length of time.

基因组学核心提供资源，服务和建议，以满足与基因组学研究有关的NHGRI调查人员的需求。基因组核心提供的基因分型服务被大量研究人员广泛使用。 在过去的一年中，有15位调查人员要求100个要求。 大多数请求是针对人类基因组SNP基因分型的。核心处理了50条用1M SNP芯片进行基因分型的请求，共有730个DNA样品。处理了其他广泛的Illumina SNP芯片（370K，550K，610K，1M QUAD，250万四边形和甲基化），使总计达到了当年的8.50m SNP基因型。基因型主要用于使用高密度SNP芯片进行基因组变化（缺失/重复/镶嵌）扫描，但是，数据可用于回答与链接，关联，拷贝数和甲基化变化有关的各种其他问题。我们的研究人员研究了使用基因型数据的多种疾病：多态，微观恐惧症，唇裂和pa裂，全脑脑，无诊断性疾病（UDP），钻石 - 戴蒙德 - 黑甲虫，fanconi anemia，fanconi anemia anemia，nf1。核心也继续提供基于STP的基因分型。尽管有40多个STRP基因分型的要求，但通常用于较少数量的样品。这些STRP基因分型服务涵盖了各种应用，例如扫描焦点区域，用于链接的基因座的精细映射，拷贝数变化，缺失间隔的识别，缺失的原点父母和小鼠研究（速度和eNCENICS，识别移植匹配匹配项，位点，表型）。通常，SNP和SNP基因分型服务用于各种全基因组研究，包括探索甲基化状态。 尽管基因分型是过去一年核心的主要活动，但还提供了有限的物理映射和测序服务以及对DNA面板的访问。将新的DNA面板墨西哥裔美国人（HD 100MEX）添加到核心资源中。我们继续从人，小鼠或斑马鱼库中提供BAC克隆的访问权限。测序服务仅限于运行调查员提供的反应板。 核心人员完成了该计划，以通过参加每个实验室会议并寻求他们的意见来告知NHGRI调查人员有关核心服务的信息。这些讨论是有效的，并有助于启动利用新颖应用的核心中可用的技术。例如，为斑马鱼胚胎中的锌指介导的诱变制定了快速有效的筛选策略。因此，核心致力于增强对新应用的可用技术的利用。核心购买并安装了Illumina iscan，该Inlumina ISCan可以更快，更有效地扫描更新，更高的Illumina SNP芯片（2.5m和5m SNP）和高吞吐量（Omni_express）SNP芯片。促进高密度技术，该技术允许每个芯片扫描多个样品，并在有效的扫描仪的核心中供应，允许该核心现在接受中等大型的基因分型项目，并在合理的时间内完成它们。