Authors
Seunghyun Wang, Mingyun Bae, Jinhao Wang, Boxun Zhao, Khue Nguyen, Shayna Mallett, Jessica A Switzenberg, Steven J Losh, Corinne E Sexton, Benpeng Miao, Shihua Dong, Xi Zeng, Ziying Wang, Torrin L McDonald, Camille Mumm, Rohini K Gadde, Arnaz Maryam Tariq, Zhuofu Chen, William C Feng, Aidan Burn, Junseok Park, Chong Chu, Hui Shen, Ting Wang, Alexander E Urban, Xiaowei Zhu, Heng Li, Kathleen H Burns, Hye-Jung E Chun, Peter J Park, SMaHT MEI Working Group, Alan P Boyle, Ryan E Mills, Weichen Zhou, Eunjung Alice Lee
Published in
Cell genomics. Pages 101418. Nov 03, 2026. Epub Nov 03, 2026.
Abstract
Mobile element insertions (MEIs) shape the human genome in both germline and somatic tissues. While inherited MEIs are well characterized, identifying somatic MEIs (sMEIs) in non-cancer tissues remains challenging due to their low allelic fraction and repetitive nature. Here, we present an integrative framework for sMEI mapping that leverages modern sequencing technologies and analytical innovations. We first benchmarked sMEI detection methods, demonstrating advantages of long-read and MEI-targeted sequencing for ultra-rare events, and established an effective cross-platform integrative approach using a mixture of well-established cell lines. Haplotype phasing and donor-specific genome assemblies further refined sMEI calls by distinguishing germline and false signals in in silico tumor-normal mixtures. We also developed a source-tracing approach based on sequence variation within MEIs, expanding the catalog of active source elements beyond traditional transduction-based inference. Applying this framework to benchmark donor tissues, we detected rare somatic L1 insertions in all four tissue types examined, revealing structural and source diversity. Our work provides a foundational framework and biological insight into somatic retrotransposition in the human body.
PMID:
42976861
Bibliographic data and abstract were imported from PubMed on 04 Nov 2026.
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