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相关的NHGRI调查人员的需求。Genomics Core提供的基因分型服务被大量研究者广泛使用。 去年，15名调查员提出了100多项请求。 大多数请求是人类基因组SNP基因分型。该中心处理了50个使用1 M SNP芯片进行基因分型的请求，共730个DNA样本。处理了各种其他Illumina SNP芯片（370 K，550 K，610 K，1 M Quad，2.5M Quad和甲基化），使今年的SNP基因型总数达到850 M。基因型主要用于使用高密度SNP芯片扫描基因组变化（缺失/重复/嵌合），然而，该数据可用于回答与连锁、关联、拷贝数和甲基化变化相关的各种其他问题。我们的研究人员研究了利用基因型数据的各种疾病：多指（趾）畸形、小眼畸形、唇腭裂、前脑无裂、未诊断疾病（UDP）、Diamond-Blackfan贫血、Fanconi贫血、NF 1等。核心继续提供基于STRP的基因分型以及。虽然有超过40个STRP基因分型的请求，但这些通常用于较少数量的样本。这些STRP基因分型服务涵盖了多种应用，例如扫描焦点区域以精细绘制连锁基因座、拷贝数变异、缺失间隔的鉴定、缺失起源的亲本和小鼠研究（快速同源、鉴定移植匹配、表型基因座）。一般来说，SNP和STRP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。 虽然基因分型是核心小组过去一年的主要活动，但也提供了有限的物理绘图和测序服务，以及获取DNA样本的机会。一个新的DNA面板，墨西哥裔美国人（HD 100 MEX），被添加到核心资源。我们继续提供从人类、小鼠或斑马鱼文库获得BAC克隆的途径。测序服务仅限于运行研究者提供的反应板。 核心人员通过参加与每个实验室的会议并征求他们的意见，完成了向NHGRI调查人员通报核心服务的倡议。这些讨论是富有成效的，并有助于启动利用核心的新应用程序的现有技术。例如，开发了一种用于斑马鱼胚胎中锌指介导的诱变的快速有效的筛选策略。因此，核心努力提高现有技术在新应用中的利用率。核心购买并安装了Illumina iScan，该iScan允许更快，更有效地扫描更新，更高密度的Illumina SNP芯片（2.5M和5 M SNP）和高通量（Omni_Express）SNP芯片。先进的高密度技术，允许每个芯片扫描多个样本，并在核心的有效扫描仪的可用性，允许核心现在接受中等规模的基因分型项目，并在合理的时间内完成它们。