Database documentation of retrotransposon insertion polymorphisms

Ping Liang¹, Wanxiangfu Tang¹

1Department of Biological Sciences, Brock University, 500 Glenridge Ave, St. Catharines, Ontario, Canada L2S 3A1

TABLE OF CONTENTS

1. Abstract

2. Introduction

3. Documentation of retrotransposon insertion polymorphisms (RIPs)

3.1. Methods for identification of RIPs

3.2. Special issues related to describing RIPs in details

3.3. Database documentation of RIPs

3.3.1. Current status of RIP database documentation

3.3.2. Overview of dbRIP

3.3.3. dbRIP utilities

3.3.4. dbRIP data tracking and data releases

3.3.5. Future development of dbRIP

4. Summary and concluding remarks

5. Acknowledgements

6. References

1. ABSTRACT

Retrotransposons constitute more than 40% 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.