Inter- and Intra-Species Comparative Sequencing

随着最近人类基因组测序的完成，其他脊椎动物基因组的测序也占据了中心地位。被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对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，正在考虑进行系统测序的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产生大量的同源序列，用于详细的比较分析。具体地说，来自多个脊椎动物物种的相同目标基因组区域正在大插入克隆中分离，然后进行测序。设计同源杂交探针和从不同物种分离细菌人工染色体(BAC)克隆的有效方法已经被开发和实施。在通过几种映射方法进行表征之后，然后选择BAC的平铺路径并对其进行系统排序。总体而言，与NHGRI基因组技术分部的物理作图科一起，每年产生250Mb的比较测序数据。这一比较序列资源的建立促进了用于多物种序列比较的新计算工具的开发，提供了对其他脊椎动物物种测序中应该进行的适当程度的测序完成的洞察，并揭示了对距离人类不同进化距离的物种进行测序的好处。这些努力正被广泛地集中在启动的ENCODE项目上，该项目旨在识别目标人类基因组1%中的所有功能。事实上，在过去的一年里，NISC的绝大多数测序工作都致力于ENCODE项目。 除了物种间的序列比较外，NISC还通过实施第二条主要的序列产生管道来扩大其产品组合，这条管道旨在为医学研究项目进行物种内(特别是人与人之间)序列比较。在建立和使用基于PCR的测序管道时，NISC再次利用了其独特的环境，即嵌入了更广泛的NIH内部计划，并拥有出色的临床研究基础设施。在目前计划的NISC医学测序项目中，有一项大型工作直接与其他NIH研究所的知名临床研究人员对接，并利用NIH临床中心研究常见人类疾病的分子基础，重点是罕见疾病相关变异的检测和研究。NISC比较测序计划的两条管道应该一起继续产生基因组研究前沿的数据，探索如何使用大规模DNA测序来确定人类基因组的特征，并了解人类健康和疾病的遗传基础。 最后，NISC最近发起了一项重大努力，以确定生活在人类皮肤上的微生物--皮肤微生物群的特征。了解微生物的集合对于了解它们在人类健康和疾病中的作用至关重要，其中绝大多数微生物不能在实验室中培养。NISC将重点放在皮肤上，作为人类微生物组项目的一部分，旨在描述人类皮肤微生物组的特征。

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.