Inter- and Intra-Species Comparative Sequencing

随着人类基因组测序的完成，其他脊椎动物基因组的测序已经成为中心舞台。广泛研究的模式生物的测序（例如，小鼠、大鼠和斑马鱼）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。不太清楚的是其他候选基因组被考虑用于系统测序的相对价值，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，我们正在从多种脊椎动物中产生大量的正向同源序列，以进行详细的比较分析。具体而言，来自多个脊椎动物物种的相同靶向基因组区域在大插入克隆中分离，然后测序。已经开发并实施了用于设计正向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。通过几种映射方法进行表征后，选择BAC的平铺路径并进行系统测序。总的来说，每年与NHGRI基因组技术分支的物理作图部分一起生成>250 Mb的比较测序数据。该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，提供了关于在其他脊椎动物物种的测序中应该追求的适当程度的测序完成的见解，并揭示了从一系列不同进化距离的物种测序的益处。这些努力正在广泛地集中在已启动的ENCODE项目上，该项目旨在确定目标1%人类基因组中的所有功能。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。 除了物种间序列比较之外，NISC还通过实施第二个主要的序列生产管道来扩大其产品组合，该管道旨在为医学研究项目进行物种内（特别是人类间）序列比较。在建立和利用基于PCR的测序管道时，NISC再次利用其独特的环境，即以其出色的临床研究基础设施嵌入更广泛的NIH校内计划。在目前计划的NISC医学测序项目中，有一项巨大的努力是直接与其他NIH研究所的成熟临床研究人员进行交流，并利用NIH临床中心研究常见人类疾病的分子基础，重点是检测和研究罕见疾病相关变异。NISC比较测序计划的两个管道应继续在基因组学研究的前沿产生数据，探索如何使用大规模DNA测序来表征人类基因组并了解人类健康和疾病的遗传基础。

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 capitalize 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.