NHGRI/DIR Genomics Core

基因组学核心提供资源、服务和建议，以满足NHGRI研究人员与基因组学研究相关的需求。基因组学核心提供的基因分型服务得到了广泛使用，并得到了大量研究人员的支持。过去一年里，有15名调查人员提出了&gt；100项请求。大多数请求是关于人类基因组SNP基因分型的。核心中心使用100万个SNP芯片处理了50个基因分型请求，总共处理了730个DNA样本。加工了广泛的其他Illumina SNP芯片(370K、550K、610K、1MQuad、2.5MQuad和甲基化)，使全年的SNP基因类型总数达到8.50亿个。基因类型主要用于使用高密度SNP芯片扫描基因组变化(缺失/复制/嵌合体)，然而，这些数据有助于回答与连锁、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利用了基因数据的各种疾病：多指、小眼球、唇腭裂、无前脑畸形、未诊断疾病(UDP)、钻石-布莱克凡贫血、范可尼贫血、NF1等。Core还继续提供基于STRP的基因分型。尽管有40多项STRP基因分型请求，但这些请求通常针对的样本数量较少。这些STRP基因分型服务涵盖了各种应用，例如扫描焦点区域以精细定位连锁基因座、拷贝数变化、确定缺失间隔、缺失起源的亲本、以及小鼠研究(速度遗传、识别移植配对、表型基因座)。总的来说，SNP和STRP基因分型服务被用于各种全基因组研究，包括探索甲基化状态。 虽然基因分型是过去一年核心的主要活动，但也提供了有限的实物测绘和测序服务，以及进入DNA小组的机会。核心资源中增加了一个新的DNA小组，墨西哥裔美国人(HD 100MEX)。我们继续提供对人类、小鼠或斑马鱼文库中的BAC克隆的访问。测序服务仅限于运行调查员提供的反应平板。 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。这些讨论富有成效，有助于启动利用核心现有技术进行新的应用。例如，开发了一种快速有效的斑马鱼胚胎锌指诱变筛选策略。因此，核心努力加强对现有技术的利用，以实现新的应用。Core购买并安装了Illumina iScan，它可以更快、更高效地扫描更新的、更高密度的Illumina SNP芯片(250万和500万个SNP)和高吞吐量(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，并且Core拥有高效的扫描仪，这使得Core现在可以接受中等规模的基因分型项目，并在合理的时间长度内完成这些项目。

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.