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被大量研究者广泛使用。在过去的一年里，15名调查人员提出了100多万份请求。大多数要求是人类基因组SNP基因分型。Core处理了50个请求，使用1M个SNP芯片对总共730个DNA样本进行基因分型。我们还处理了大量其他Illumina SNP芯片（370K、550K、610K、1M Quad、2.5M Quad和甲基化），使今年的SNP基因型总数达到850M。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/镶嵌），然而，这些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多种疾病，其中利用了基因型数据：多指畸形、小眼症、唇腭裂、前脑畸形、未诊断疾病（UDP）、Diamond-Blackfan贫血、Fanconi贫血、NF1等。Core也继续提供基于STRP的基因分型。尽管有40多个STRP基因分型请求，但这些请求通常用于较少数量的样本。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确定位连锁位点、拷贝数变异、缺失间隔鉴定、缺失起源的亲本以及小鼠研究（速度基因、鉴定移植匹配、表型位点）。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。

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.