Mobster: accurate detection of mobile element insertions in next generation sequencing data.

Djie Tjwan Thung,Kai Ye,Eline P Slagboom,Joep De Ligt,Lisenka Em Vissers,Mark Kroon,Joris A Veltman,Marloes Steehouwer,Jayne Y Hehir-Kwa,Petra De Vries

doi:10.1186/s13059-014-0488-x

Abstract

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.

Highlights

Mobile elements (MEs) or transposable elements are DNA sequences that can be autonomously copied or moved through the genome, yet their highly repetitive sequence structure makes them difficult to detect
These results show a very high sensitivity (99.1%) with as little as 10X coverage for homozygous ME insertion (MEI) events reporting no false positives (Additional file 1: Figures S1-2)
Paired-end WES simulation show a markedly lower sensitivity, ranging from 52.7% to 85.4% at 10X to 160X, respectively. This reflects the difficulty of identifying MEI events in small exonic capture regions, likely influenced by the simulation capturing on target but not near target sites

Summary

Introduction

Mobile elements (MEs) or transposable elements are DNA sequences that can be autonomously copied or moved through the genome, yet their highly repetitive sequence structure makes them difficult to detect. Only a few MEs remain active or ‘hot’ in the human genome, all of which belong to the retrotransposon class and include the autonomous L1 family (6 kb, 500,000 copies), the non-autonomous Alu (300 bp, 1,000,000 copies) and SVA (2 kb, 3,000 copies) families [5,6,7,8]. These ME families continue to change the genomic architecture by inserting into new regions in the DNA, transducing DNA, shuffling exons, and creating processed pseudogenes.

Methods

Results

Conclusion