NHGRI/DIR Genomics Core

NHGRI/DIR 基因组学核心

• 批准号: 10267132
• 负责人: settara chandrasekharappa
• 金额: $ 86.81万
• 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/10267132
• 关键词: Acute Myelocytic Leukemia; Adopted; Attention deficit hyperactivity disorder; Bacterial Artificial Chromosomes; Blood capillaries; CRISPR/Cas technology; Cardiovascular Diseases; Clustered Regularly Interspaced Short Palindromic Repeats; Collection; Coloboma; Colorectal Cancer; Communities; Copy Number Polymorphism; DNA; Data; Data Analyses; Data Set; Diabetes Mellitus; Diagnosis; Diamond-Blackfan anemia; Epilepsy; Evaluation; Eye diseases; Fanconi' s Anemia; Fever; Gap Junctions; Gaucher Disease; Genome; Genomic Segment; Genomics; Genotype; Goals; Haplotypes; Head and Neck Cancer; Holoprosencephaly; Human; Human Cell Line; Infection; Inherited; Institutes; Kidney Diseases; Learning; Leber' s amaurosis; Ligation; Linkage Disequilibrium; Loss of Heterozygosity; Malignant Neoplasms; Methylation; Microsatellite Instability; Mining; Mosaicism; Mus; Mutagenesis; National Human Genome Research Institute; Oculocutaneous Albinism; Parents; Parkinson Disease; Patients; Problem Solving; Process; Research Personnel; Resources; Running; SNP genotyping; Sampling; Scleroderma; Services; Smith Magenis syndrome; Software Tools; Speed; Syndrome; Technology; Testing; Time; Turner' s Syndrome; Variant; Zebrafish; bone marrow failure syndrome; congenic; congenital heart disorder; data access; deafness; identity by descent; induced pluripotent stem cell; insertion/deletion mutation; interest; large datasets; malignant breast neoplasm; mutant; mutation screening; new technology; novel; physical mapping; population stratification; programs; tool; zinc finger nuclease technology

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 regions of interest. The Core adopted ABI technology to find indels generated initially by zinc finger nuclease (ZFN) technology, and later by CRISPR/Cas mutagenesis approach. The Core processed over the last five years 95,000 PCR fragments for zebrafish mutagenesis projects for multiple investigators and the Zebrafish Core. CRISPR/Cas technology is now used increasingly for targeted mutagenesis in mouse and, to some extent, in human cell lines. Currently, services include human and mouse SNP genotyping, mouse, zebrafish and human primer testing and (CRISPR/Cas) mutation screening, mouse speed congenics, human and mouse STRPs, MLPA (Multiplex ligation-dependent probe amplification) for deletions, and fragment analysis for a variety of other applications. Both Illumina and ABI technologies are widely used by a large number of NHGRI investigators. This year, in addition to two programs (NISC and UDP), a total of 15 investigators representing nine branches used the Core genotyping services. Human SNP genotyping was carried out on different BeadArray types using Illumina technology and the Core generated 1.9 billion genotypes in FY2020. The genotyping data is used for studies related to Diamond-Blackfan anemia, Fanconi anemia, cancer, inherited bone marrow failure syndromes, Smith-Magenis syndrome, cardiovascular diseases, scleroderma, diabetes, kidney disease, Gaucher disease/Parkinson's disease, Congenital Heart Disease study, Turner syndrome, ADHD, eye diseases, deafness, and microsatellite instability, among others. The data was analyzed for identity by descent, copy number variation, deletion intervals, methylation status, parent-of-origin of deletions, mosaicism, 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 five years (FY2015-FY2020), the number of samples we processed for NISC were 4,032, 2,256, 2,712, 2,688, 1,728 and 1,920. The genotyping samples processed for NISC belong to multiple investigators from other institutes, indicating the Genomics Core serves a larger scientific community than just NHGRI. In FY2018, two large SNP genotyping projects were completed: 5,056 DNA samples genotyped for cardiovascular disease studies from the Rotimi lab, and 4,118 DNA samples were processed for the scleroderma studies from the Kastner lab. A kidney disease project involving 768 DNA samples was also completed in FY2019. In the coming year, the Shaw lab and the Rotimi anticipates the Core to process a similar project for 800 DNA samples each. Samples run on SNP and methylation arrays (3,032 samples) represent about 47% of the total 6,413 DNA samples processed by the Core this year, which is higher to that of last year (32%). The remaining 68% of samples were processed using ABI technology. The Genomics Core has processed a large number of zebrafish DNA samples (5,492, 14,619, 35,539, 28,986, 34,714, 20,198, 7,593, 3,137 and 95) for the past nine years (FY2012-2020). Since the realization of the efficacy of CRISPR/Cas technology around 2012, there was a surge in the processing of zebrafish samples while a huge number of mutants were being generated. The fact that the efforts of investigators are focused now on characterization of these mutants, and that the Burgess lab and the Zebrafish Core are performing some of their own genotyping, probably explains the decrease in samples processed by the Genomics Core this year. However, The Zebrafish Core has initiated newer projects, and it is anticipated that the Genomics Core will receive more samples in the coming months. Also, Also, the CRISPR technology is being extended to an increasing number of mouse mutagenesis projects, and the genotyping of the founder mice will be performed at the Genomics Core. The Core has been assisting investigators with data analysis and access to software/tools, such as GoldenHelix, Nexus, and GenomeStudio. The 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 been providing significant data analysis support over the years. The services are related to 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 iPSC, acute myeloid leukemia, Smith-Magenis syndrome, Febrile Infection-Related Epilepsy Syndrome, eye diseases coloboma and Leber Congenital Amaurosis (LCA), ADHD, Congenital Heart Disease, Holoprosencephaly, kidney disease, Turner syndrome, Oculocutaneous albinism, breast and colorectal cancers, and Fanconi anemia. In addition to performing analysis, the core also helps with troubleshooting or problem solving any issues investigators may have in handling their data. 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. The Core acquired a QuantStudio that will enable genotyping a smaller number of SNPs in a large number of samples, a service that was hither to unavailable in the Core.

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。Core采用ABI技术来寻找最初通过锌指核酸酶（ZFN）技术生成的插入缺失，后来通过CRISPR/Cas突变方法生成。在过去的五年里，该中心为多名研究人员和斑马鱼核心处理了95，000个斑马鱼诱变项目的PCR片段。CRISPR/Cas技术现在越来越多地用于小鼠的靶向诱变，并在一定程度上用于人类细胞系。目前，服务包括人类和小鼠SNP基因分型，小鼠，斑马鱼和人类引物测试和（CRISPR/Cas）突变筛查，小鼠速度同源性，人类和小鼠STRP，MLPA（多重连接依赖探针扩增）缺失，以及各种其他应用的片段分析。 Illumina和ABI技术都被大量的NHGRI研究人员广泛使用。今年，除了两个项目（NISC和UDP）外，共有15名代表9个分支的研究人员使用了核心基因分型服务。使用Illumina技术对不同BeadArray类型进行人类SNP基因分型，Core于2020财政年度产生19亿个基因型。 基因分型数据用于与Diamond-Blackfan贫血、Fanconi贫血、癌症、遗传性骨髓衰竭综合征、Smith-Magenis综合征、心血管疾病、硬皮病、糖尿病、肾病、戈谢病/帕金森病、先天性心脏病研究、特纳综合征、ADHD、眼病、耳聋和微卫星不稳定性等相关的研究。通过血统、拷贝数变异、缺失间隔、甲基化状态、缺失的起源亲本、镶嵌性分析数据的同一性，并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。在过去五年（2015财政年度至2020财政年度），我们为NISC处理的样本数量分别为4，032、2，256、2，712、2，688、1，728和1，920。为NISC处理的基因分型样本属于来自其他研究所的多个研究人员，表明基因组学核心服务于更大的科学界，而不仅仅是NHGRI。在2018财年，完成了两个大型SNP基因分型项目：Rotimi实验室的5，056份DNA样本用于心血管疾病研究，Kastner实验室的4，118份DNA样本用于硬皮病研究。一项涉及768份DNA样本的肾病项目亦于2019财政年度完成。在接下来的一年里，肖实验室和罗蒂米预计核心将分别处理800个DNA样本的类似项目。 在SNP和甲基化阵列上运行的样本（3，032个样本）约占今年核心处理的6，413个DNA样本的47%，高于去年（32%）。其余68%的样本使用ABI技术进行处理。Genomics Core在过去九年（2012 -2020财年）处理了大量斑马鱼DNA样本（5，492、14，619、35，539、28，986、34，714、20，198、7，593、3，137和95）。自2012年左右CRISPR/Cas技术的有效性实现以来，斑马鱼样本的处理激增，同时产生了大量的突变体。 事实上，研究人员的努力现在集中在这些突变体的表征上，并且伯吉斯实验室和斑马鱼核心正在进行一些自己的基因分型，这可能解释了基因组学核心今年处理的样本减少的原因。 然而，斑马鱼核心已经启动了更新的项目，预计基因组学核心将在未来几个月内收到更多的样本。此外，CRISPR技术正在扩展到越来越多的小鼠诱变项目中，创始小鼠的基因分型将在Genomics Core进行。 核心一直在协助研究者进行数据分析和访问软件/工具，如GoldenHacker、Nexus和GenomeStudio。核心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。多年来，核心一直在提供重要的数据分析支持。这些服务涉及拷贝数变异、连锁不平衡分析、群体分层和关联研究。还对诊断患有范科尼贫血和头颈癌的患者的DNA样本中检测缺失、重复、杂合性丢失以及描绘染色体镶嵌现象迹象的区域进行了分析。其他研究包括与iPSC、急性骨髓性白血病、Smith-Magenis综合征、发热性惊厥相关癫痫综合征、眼病缺损和Leber先天性黑蒙（LCA）、ADHD、先天性心脏病、前脑全裂、肾病、特纳综合征、眼皮肤白化病、乳腺癌和结肠直肠癌以及范可尼贫血的处理相关的变化。除了执行分析外，核心还有助于解决调查人员在处理数据时可能遇到的任何问题。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。核心收购了QuantStudio，可以在大量样本中对较少数量的SNP进行基因分型，这是一项在核心中不可用的服务。