Somatic repetitive element insertions Define New Biomarkers in Pan-cancer genome
Xia, L.; Tu, K.; Wang, H.; Liu, X.; Liu, Y.; Zhang, Q.; Feng, Z.; Yu, C.; Li, M.; Huang, Y.; Wang, J.; Wei, R.; Zeng, T.; Pi, X.; Ling, C.; Zhang, Q.; Qiao, Y.; Hou, S.; Zhang, Z.; Wei, A.; Liao, H.; Liu, J.; Wu, Z.; Wang, Z.; Li, A.; Li, W.; Xie, D.
Show abstract
Repetitive elements insertions (REIs), including tandem repeat insertions (TRIs) and transposable element insertions (TEIs), constitute >90% of large-scale (>50bp) somatic insertions and are linked to diseases and cancer biomarkers. However, the genomic landscape of large-scale REIs in pan-cancer has not been well-characterized due to short-read sequencing limitations. Here, we detected somatic REIs in 325 cancer genomes across 12 cancer types using long-read whole-genome sequencing and customized algorithms. The diverse sequence patterns of somatic TRIs and the insertion mechanisms of somatic TEIs were characterized across different cancer types. We identified 152 high-frequency somatic TRIs, with 10 showing pan-cancer characteristics, including TRIs in SHROOM2, PALMD, and the enhancer of PTPRZ1. The MHC class II gene cluster exhibited the highest somatic TEI abundance, affecting [~]40% tumors. Adenocarcinomas and squamous cell carcinomas exhibited differing TEI distributions within this region. Our study highlights REIs as important but under-explored markers for personalized cancer diagnosis and immunotherapy.
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