Zhang Wei, Dolan M Eileen
Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
Curr Bioinform. 2008 Sep 1;3(3):178. doi: 10.2174/157489308785909232.
The International HapMap Project provides a key resource of genotypic data on human samples including lymphoblastoid cell lines derived from individuals of four major world populations of African, European, Japanese and Chinese ancestry. Researchers have utilized this resource to identify genetic elements that correlate with various phenotypes such as risks of common diseases, individual drug response and gene expression variation. However, recent comparative studies have suggested that the currently available HapMap genotypic data may not capture a substantial proportion of rare or untyped SNPs in these populations, implying that the HapMap SNPs may not be sufficient for comprehensive association studies. In this paper, three large-scale deep resequencing projects covering the HapMap samples: ENCODE (Encyclopedia of DNA Elements), SeattleSNPs and NIEHS (National Institute of Environmental Health Sciences) Environmental Genome Project are discussed. Prospectively, once integrated with the HapMap resource, these efforts will greatly benefit the next wave of association studies and data mining using these cell lines.
国际人类基因组单体型图计划提供了关于人类样本的基因型数据的关键资源，这些样本包括来自非洲、欧洲、日本和中国这四个世界主要人群的个体的淋巴母细胞系。研究人员利用这一资源来识别与各种表型相关的遗传元件，如常见疾病风险、个体药物反应和基因表达变异。然而，最近的比较研究表明，目前可用的人类基因组单体型图基因型数据可能并未涵盖这些人群中相当比例的罕见或未分型的单核苷酸多态性（SNP），这意味着人类基因组单体型图的SNP可能不足以进行全面的关联研究。本文讨论了涵盖人类基因组单体型图样本的三个大规模深度重测序项目：DNA元件百科全书（ENCODE）、西雅图SNP和美国国立环境卫生科学研究所（NIEHS）环境基因组计划。前瞻性地看，一旦与人类基因组单体型图资源整合，这些工作将极大地有益于下一波使用这些细胞系的关联研究和数据挖掘。
