MeX pipeline for analysis of mobile genetic elements in cancer genome

Abstract

Background: Mobile genetic elements (MGEs) comprise a major portion of the human genome and are essential for genetic diversity. These elements are known to have the capability to induce mutations in the human genome. To date, there are several MGE insertions which have been reported to be associated with cancer. We aim to use genome next-generation sequencing data and appropriate bioinformatics tools to accurately identify the insertion sites of MGEs in the human genome.Results: Herein, we introduce the MeX pipeline for the localization and annotation of MGEs in paired-end sequencing data. It requires the reference genome sequence, MGE sequences and paired-end sequencing reads. We evaluated MeX on high depth (>75×) Illumina HiSeq data produced at the Broad Institute (NA12878) against human genome 38-built (including only chromosome 1, 2 and 3) and Alu elements. We could identify 78 reference and 1 non-reference Alu insertions in the NA12878 sample. Upon annotation, it was found that the non-reference Alu element was in the 3' UTR region of the RNF2 gene. Out of 78 reference insertions, 42 were in the intronic region, 7 in the upstream region, 5 in the downstream region, 1 in the 3’ UTR region and the rest were not associated with any gene. MeX showed high performance for the identification and annotation of MGEs in genome samples.Conclusion: This study showed that MeX is a robust and powerful tool for the identification and annotation of MGE insertions. It may also serve as a valuable tool to study the phenotypic changes resulting from transpositional events in cancer genomics.