NHGRI/DIR Bioinformatics and Scientific Programming Core

NHGRI生物信息学和科学编程核心通过提供生物信息学和计算分析方面的专业知识和援助，积极支持NHGRI研究人员正在进行的研究。该核心促进获得专门的软件和硬件，开发可解决基因组研究中各种问题的通用软件解决方案，开发用于有效存档和检索实验和临床数据的数据库解决方案，向整个基因组社区传播新的软件和数据库解决方案，与NHGRI的研究人员在计算密集型项目上合作，并向NHGRI的研究人员和受训人员提供生物信息学方面的教育机会。 2009-2010年完成的科学项目包括开发一个网站和数据库，对人类表型变异的描述、定义和图像进行编目，以便为人类形态提供标准化术语；利用后续途径和本体论分析进行外显子水平的基因表达分析，以评估菌株依赖的基因组因素在过敏原诱导的小鼠呼吸道高反应性中的作用；开发一个基于网络的系统，用于管理癌症风险感知，包括开发在线调查和跟踪诱因的工具；分析由Multiplex Initiative生成的调查报告和网络行为数据，对Magoh基因进行进化分析，整理多中心调查数据以研究葡萄糖脑苷酶突变与帕金森病之间的关联，比较MLV和CATPAC逆转录病毒载体的整合图谱，并分析诱导多能干细胞(IPS)中的逆转录病毒整合位点。 正在进行的科学项目包括使用NextGen序列数据对Mnformopsis基因组进行注释，分析序列痕迹以检测肿瘤样本中假定的癌基因突变，开发基于Web的产前调查并采用传统的纸质调查技术进行基于Web的部署，开发网站和血液学重要突变数据库，描述脊椎动物、无脊椎动物和植物基因组的大外显子的特征；不断更新和改进乳腺癌信息核心(BIC)，开发生物信息学管道以使用Illumina序列标签绘制斑马鱼逆转录病毒整合位点的图谱，分析CHIP-SEQ数据以评估早衰症中染色质结构的变化，通过转录因子结合位点分析和系统发生足迹预测选定斑马鱼基因的基因调节区，将22-MERS从CFTRUTRs定位到人类基因组，允许错配；通过转录因子结合位点分析和系统发育足迹预测人类髓系白血病相关基因的基因调节区，分析CHIP-SEQ数据以比较正常和MMS诱导的DNA损伤样本，开发定制的SQL数据库用于存储和计算大量记录，包括犬类基因、表型、序列、变异、样本数据和系谱数据；开发色素细胞基因信息网站，注释在选定条件下发挥作用的转录因子的假定结合位点，以及分析序列痕迹，以检测斑马鱼分枝项目的突变。

The NHGRI Bioinformatics and Scientific Programming Core actively supports the research being performed by NHGRI investigators by providing expertise and assistance in bioinformatics and computational analysis. The Core facilitates access to specialized software and hardware, develops generalized software solutions that can address a variety of questions in genomic research, develops database solutions for the efficient archiving and retrieval of experimental and clinical data, disseminates new software and database solutions to the genome community at-large, collaborates with NHGRI researchers on computationally-intensive projects, and provides educational opportunities in bioinformatics to NHGRI Investigators and trainees. Scientific projects completed in 2009-2010 include the development of a Web site and database to catalog descriptions, definitions, and images of human phenotypic variations in order to provide standardized terms for human morphology; exon-level gene expression analysis with subsequent pathway and ontological analysis to evaluate role of strain-dependent genomic factors in allergen-induced airway hyper-responsiveness in mice, development of a Web-based system for administering cancer risk perception, including the development of online surveys and tools for tracking incentives; analysis of survey reports and Web behavior data generated by the Multiplex Initiative, evolutionary analysis of the Magoh gene, collation of multi-center survey data to study association between glucocerebrosidase mutations and Parkinsonism, comparison of integration profiles of MLV and CATPAC retroviral vectors, and analysis of retroviral integration sites in induced pluripotent stem (iPS) cells. Ongoing scientific projects include the annotation of the Mnemiopsis genome using NextGen sequence data, analysis of sequence traces to detect mutations in putative oncogenes in tumor samples, development of a Web-based prenatal survey and adaptation of traditional paper-based survey techniques for Web-based deployment, development of a Web site and database of hematologically important mutations, characterization of large exons in vertebrate, invertebrate, and plant genomes; ongoing updates and improvements to the Breast Cancer Information Core (BIC), development of a bioinformatic pipeline to map zebrafish retroviral integration sites using Illumina sequence tags, analysis of ChIP-seq data to assess chromatin structural changes in progeria, prediction of gene regulatory regions in select zebrafish genes by transcription factor binding site analysis and phylogenetic footprinting, mapping of 22-mers from the CFTR UTRs to the human genome, allowing for mismatches; prediction of gene regulatory regions in human myeloid leukemia-related genes by transcription factor binding site analysis and phylogenetic footprinting, analysis of ChIP-seq data to compare normal and MMS-induced DNA damaged samples, development of a customized SQL database for storing and computing on large numbers of records for canine genotypes, phenotypes, sequences, variations, sample data and pedigree data; development of an informational Web site for pigment cell genes, annotation of putative binding sites for transcription factors that function in selected conditions, and analysis of sequence traces to detection mutations for a zebrafish TILLING project.