Inter- and Intra-Species Comparative Sequencing

随着人类基因组序列的完成，其他脊椎动物基因组的测序已经占据了中心位置。广泛研究的模式生物（如小鼠、大鼠和斑马鱼）的测序为未来的实验和脊椎动物生物学的重要见解提供了宝贵的资源。不太清楚的是其他候选基因组的相对价值，特别是关于它们对人类基因组序列的注释和解释的潜在贡献。为了研究这些问题，我们正在从多个脊椎动物中生成大块的同源序列，以进行详细的比较分析。具体来说，从多个脊椎动物物种中分离出相同的目标基因组区域，然后对其进行测序。已经开发并实现了设计同源杂交探针和分离不同种类细菌人工染色体（BAC）克隆的有效方法。通过几种映射方法进行表征，然后选择bac的平铺路径并进行系统测序。与NHGRI基因组技术处的物理制图科合作，每年总共产生bb50 250 Mb的比较测序数据。该比较序列资源的建立促进了多物种序列比较新计算工具的开发，为其他脊椎动物物种的测序提供了合适的测序完成度，并揭示了从与人类不同进化距离的物种进行测序的好处。这些努力主要集中在已启动的ENCODE项目上，该项目旨在确定人类基因组中1%的所有功能。事实上，在过去的一年中，NISC的大部分测序工作都致力于ENCODE项目。

With the recent completion of the human genome sequence, the sequencing of other vertebrate genomes has taken center stage. The sequencing of widely studied model organisms (e.g., mouse, rat, and zebrafish) is providing a valuable resource for future experimentation and important insights into vertebrate biology. Less clear is the relative value of other candidate genomes being considered for systematic sequencing, especially with regard to their potential contribution to the annotation and interpretation of the human genome sequence. To investigate such issues, we are generating large blocks of orthologous sequence from multiple vertebrates for detailed comparative analyses. Specifically, the same targeted genomic regions from multiple vertebrate specie are being isolated in large-insert clones and then sequenced. Efficient methods for designing orthologous hybridization probes and isolating bacterial artificial chromosome (BAC) clones from the different species have been developed and implemented. Following characterization by several mapping methods, tiling paths of BACs are then selected and systematically sequenced. In total, >250 Mb of comparative sequencing data is being generated each year, in conjunction with the Physical Mapping Section of the NHGRI Genome Technology Branch. The establishment of this comparative sequence resource is facilitating the development of new computational tools for multi-species sequence comparisons, providing insight about the appropriate degrees of sequencing finishing that should be pursued in the sequencing of other vertebrate species, and revealing the benefits of sequencing species from a range of different evolutionary distances from human. These efforts are being extensively focused on the launched ENCODE project, which aims to identify all functional in a targeted 1% of the human genome. Indeed, the great majority of NISC sequencing over the past year has been dedicated to the ENCODE project. In addition to its inter-species sequence comparisons, NISC is broadening its portfolio by implementing a second major sequence-production pipeline one designed for performing intra-species (specifically, inter-human) sequence comparisons for medical research projects. In establishing and utilizing a PCR-based sequencing pipeline, NISC is once again capitalizing on its unique circumstance of being embedded within the broader NIH Intramural Program with its outstanding clinical research infrastructure. Among the currently planned NISC medical sequencing projects is a large effort that directly interfaces with well-established clinical researchers at other NIH Institutes and utilizes the NIH Clinical Center to study the molecular basis for common human diseases, with an emphasis on the detection and study of rare disease-associated variants. Together, the two pipelines of the NISC Comparative Sequencing Program should continue to produce data at the cutting edge of genomics research, exploring how large-scale DNA sequencing can be used to characterize the human genome and to understand the genetic basis for human health and disease. Finally, NISC has recently launched a major effort to characterize the microbes living on human skin-- the skin microbiome. Understanding the collection of microbes, the great majority of which cannot be cultured in the laboratory, is critical for understanding their role in human health and disease. With a focus on the skin, NISC aims to characterize the human skin microbiome as part of the Human Microbiome Project.