Integrated Mobile Element Scanning (ME-Scan) method for identifying multiple types of polymorphic mobile element insertions

Abstract

Background: Mobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome. Polymorphic mobile element insertions (pMEIs) are a major source of human genomic variation and are gaining research interest because of their involvement in gene expression regulation, genome integrity, and disease. Results: Building on our previous Mobile Element Scanning (ME-Scan) protocols, we developed an integrated ME-Scan protocol to identify three major active families of human mobile elements, AluYb, L1HS, and SVA. This approach selectively amplifies insertion sites of currently active retrotransposons for Illumina sequencing. By pooling the libraries together, we can identify pMEIs from all three mobile element families in one sequencing run. To demonstrate the utility of the new ME-Scan protocol, we sequenced 12 human parent-offspring trios. Our results showed high sensitivity (> 90%) and accuracy (> 95%) of the protocol for identifying pMEIs in the human genome. In addition, we also tested the feasibility of identifying somatic insertions using the protocol. Conclusions: The integrated ME-Scan protocol is a cost-effective way to identify novel pMEIs in the human genome. In addition, by developing the protocol to detect three mobile element families, we demonstrate the flexibility of the ME-Scan protocol. We present instructions for the library design, a sequencing protocol, and a computational pipeline for downstream analyses as a complete framework that will allow researchers to easily adapt the ME-Scan protocol to their own projects in other genomes.

SeqURE – a new copy-capture based method for sequencing of unknown Retroposition events

“…Moreover, 98% of AluYa5 and AluYb8 insertions can be identified using either one or the other flank. Thus, despite using non-random fragmentation the power of the developed approach is comparable with the methods based on random DNA fragmentation such as ME-Scan [ 17 ]. We prefer DNA digestion by site specific restrictases to random sheering.…”

“…In most cases with standard WGS coverage non targeted methods allow to find insertions present in 25% of cells or more [ 16 ]. Targeted methods of RE insertion detection include enrichment in RE sequences or their unique genomic flanking regions (flanks) prior to sequencing [ 14 , 17 – 22 ]. The enrichment methods are based on either hybridization to RE specific oligos or selective amplification of RE flanks.…”

Polymorphic mobile element insertions contribute to gene expression and alternative splicing in human tissues

“…Less than half of the pMEI loci (8456) were identified both in this project and in the 1KGP. Recent studies have been able to continually annotate new pMEIs as techniques improve and individuals from diverse populations are considered [ 24 , 40 ]. In addition, because of the repetitive nature of MEs, many pMEIs are missed by the current short-read sequencing technology [ 41 ].…”

“…Next, we define an eGene as a tissue-gene pair that was identified in the eQTL analysis with an FDR < 10%, while an eVariant as a tissue-variant pair with an FDR < 10%. Because an eGene can be influenced by multiple variants and an eVariant may have an impact on multiple genes, the numbers of eGenes (24,109) and eVariants (17,230) are smaller than the total number of eQTLs. The number of eQTLs (FDR < 10%) per tissue ranges from 118 to 1609, and the sample size is strongly correlated with the number of detected eQTLs (r 2 = 0.85, Fig.…”

“…The activities of MEs create new insertional mutations in the genome, leading to thousands of polymorphisms among human individuals and populations [22][23][24]. The effects of polymorphic mobile element insertions (pMEIs) on gene expression have been studied in the transformed B lymphocytes cell lines (LCLs) of the 1000 Genomes Project (1KGP) [25][26][27][28] and in human induced pluripotent stem cells [28].…”