基因组所完成“人类多条理多人群自然选择数据库”构建
为了更好地相识人类差别种群的遗传差别和受到的自然选择情形，以及较量差别指标之间的印证关系。克日，永利集团曾长青研究员实验室的程锋等人，通过选择现在SNP（单核苷酸多态性）分型数目最大和种群数最多的HapMap（国际人类基因组单体型图妄想）分型数据作为研究基础，从基因组大片断，功效基因以及单个SNP位点等三个条理来研究人类差别种群的基因组遗传分解和所受自然选择的情形。凭证使用多个差别指标（HET，Win_HET, FST, Win_FST, iHS, ES_HET, ES_FST, P_iHS等）及战略来扫描选择信号，并把它们置于统一个框架下举行较量和验证，以求获得最大的信息。研究效果建设了“人类多条理多人群自然选择数据库”暨阳性自然选择数据库SNP@Evolution (http://bighapmap.big.ac.cn/)供海内外科研使用，自九月下旬相关文章在BMC Evol Biol揭晓以来，SNP@Evolution已受到来自全天下几十个国家和地区，上万次的会见和下载，为该领域的研究职员提供了一个发明选择信号的有用工具。
SNP@Evolution共分为数据盘问和图形盘问界面两个部分。包括了HapMap II期和III期的数据效果。II期共有3,619,226个SNP数据，以及21,859个基因的剖析数据。共有1606个基因组大片断显示选择信号，660个显示分解信号。III期数据共包括1,389,498 SNPs， 21,099个有用基因剖析数据。在11小我私家群中找到了10,138个受选择的基因组片断，以及464个具有强分解的基因组片断。为了利便研究，SNP@Evolution的盘问效果可以链接到其他数据库获取更多信息。
数据库链接:
http://bighapmap.big.ac.cn
文献纪录:
Cheng Feng, Chen Wei, Richards Elliott, Deng Libin, Zeng Changqing. SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evolutionary Biology 2009, 9:221.
原文链接:
http://www.biomedcentral.com/1471-2148/9/221
原文摘要:
Abstract
Background: Positive selection is a driving force that has shaped the modern human. Recent developments in high throughput technologies and corresponding statistics tools have made it possible to conduct whole genome surveys at a population scale, and a variety of measurements, such as heterozygosity (HET), FST, and Tajima's D, have been applied to multiple datasets to identify signals of positive selection. However, great effort has been required to combine various types of data from individual sources, and incompatibility among datasets has been a common problem. SNP@Evolution, a new database which integrates multiple datasets, will greatly assist future work in this area.
Description: As part of our research scanning for evolutionary signals in HapMap Phase II and Phase III datasets, we built SNP@Evolution as a multi-aspect database focused on positive selection. Among its many features, SNP@Evolution provides computed FST and HET of all HapMap SNPs, 5+ HapMap SNPs per qualified gene, and all autosome regions detected from whole genome window scanning. In an attempt to capture multiple selection signals across the genome, selection-signal enrichment strength (ES) values of HET, FST, and P-values of iHS of most annotated genes have been calculated and integrated within one frame for users to search for outliers. Genes with significant ES or P-values (with thresholds of 0.95 and 0.05, respectively) have been highlighted in color. Low diversity chromosome regions have been detected by sliding a 100 kb window in a 10 kb step. To allow this information to be easily disseminated, a graphical user interface (GBrowser) was constructed with the Generic Model Organism Database toolkit.
Conclusion: Available at http://bighapmap.big.ac.cn, SNP@Evolution is a hierarchical database focused on positive selection of the human genome. Based on HapMap Phase II and III data, SNP@Evolution includes 3,619,226/1,389,498 SNPs with their computed HET and FST, as well as qualified genes of 21,859/21,099 with ES values of HET and FST. In at least one HapMap population group, window scanning for selection signals has resulted in 1,606/10,138 large low HET regions. Among Phase II and III geographical groups, 660 and 464 regions show strong differentiation.
