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Genome-wide analysis of mobile element insertions in human genomes

By Yiwei Niu, Xueyi Teng, Yirong Shi, Yanyan Li, Yiheng Tang, Peng Zhang, Huaxia Luo, Quan Kang, The Han100K Initiative, Tao Xu, Shunmin He

Posted 24 Jan 2021
bioRxiv DOI: 10.1101/2021.01.22.427873

Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36,699 non-reference MEIs constructed from 5,675 genomes, comprising 2,998 Chinese samples (~26.2X, NyuWa) and 2,677 samples from the 1000 Genomes Project (~7.4X, 1KGP). We discovered that LINE-1 insertions were highly enriched at centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.

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