Characterizing mobile element insertions in 5675 genomes
Yiwei Niu, Xueyi Teng, Honghong Zhou, Yirong Shi, Yanyan Li, Yiheng Tang, Peng Zhang, Huaxia Luo, Quan Kang, Tao Xu, Shunmin He
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.
附件下载：
Characterizing mobile element insertions in 5675 genomes, Nucleic Acids Res, 25 Feb 2022
Nucleic Acids Research, 25 February, 2022, DOI：https://doi.org/10.1093/nar/gkac128
Characterizing mobile element insertions in 5675 genomes
Yiwei Niu, Xueyi Teng, Honghong Zhou, Yirong Shi, Yanyan Li, Yiheng Tang, Peng Zhang, Huaxia Luo, Quan Kang, Tao Xu, Shunmin He
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.
文章链接：https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac128/6536893
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