Characterizing mobile element insertions in 5675 genomes. Issue 5 (25th February 2022)

• Record Type: Journal Article
• Authors: Niu, Yiwei; Teng, Xueyi; Zhou, Honghong; Shi, Yirong; Li, Yanyan; Tang, Yiheng; Zhang, Peng; Luo, Huaxia; Kang, Quan; Xu, Tao; He, Shunmin
• Is Part Of: Nucleic acids research. Volume 50:Issue 5(2022)
• Page Start: 2493
• Page End: 2508
• Publication Date: 2022-02-25
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkac128
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: 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 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in 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.