Liang Ping, Tang Wanxiangfu
Department of Biological Sciences, Brock University, 500 Glenridge Ave, St. Catharines, Ontario, Canada L2S 3A1.
Front Biosci (Elite Ed). 2012 Jan 1;4(4):1542-55. doi: 10.2741/479.
Retrotransposons constitute more than 40 percent of the human genome with L1, Alu, SVA, and HERVs known to remain active in transposition. Retrotransposition contribute to genetic diversity in the form of retrotransposon insertion polymorphism (RIP) that is defined as the presence or absence of a retrotransposon insertion among human populations at a specific genomic location. So far close to 5000 cases of RIPs have been identified with more than 50 cases associated with disease. A large number of new RIPs are being and to be identified from newly available personal genomes data, making RIPs an important source of genetic variations/mutations that deserve proper documentation. In this review, we discuss the special characteristics of RIPs and the challenges in their compiling and annotating, and we examine the current status of database documentation of RIPs and describe in details the design, data schema, and utilities of dbRIP, which is currently the only database dedicated to the documentation of retrotransposon insertion polymorphism. Some future perspectives and outstanding issues associated with documentation of RIPs are also presented.
逆转录转座子占人类基因组的40%以上，已知L1、Alu、SVA和HERV在转座过程中仍保持活跃。逆转录转座以逆转录转座子插入多态性（RIP）的形式促进遗传多样性，RIP被定义为在特定基因组位置的人群中存在或不存在逆转录转座子插入。到目前为止，已鉴定出近5000例RIP，其中50多例与疾病相关。从新获得的个人基因组数据中正在并将鉴定出大量新的RIP，这使得RIP成为遗传变异/突变的重要来源，值得进行适当记录。在本综述中，我们讨论了RIP的特殊特征及其编译和注释中的挑战，我们研究了RIP数据库记录的现状，并详细描述了dbRIP的设计、数据模式和实用程序，dbRIP是目前唯一专门用于记录逆转录转座子插入多态性的数据库。还介绍了与RIP记录相关的一些未来展望和突出问题。
