Concurrent L1 retrotransposition events promote reciprocal translocations in human tumorigenesis

LINE-1 (L1) retrotransposition generates somatic genomic variation in human cancer, but short-read sequencing has limited our understanding of its structural consequences and dynamics. Using long-read sequencing, we analyzed 10 tumors with exceptionally high retrotransposition activity, comprising more than 6000 somatic events. We reveal that L1-mediated reciprocal translocations occur frequently, typically driven by two concurrent L1 retrotransposition events on nonhomologous chromosomes. Using an independent tumor cohort spanning low to high L1 activity, we estimate that retrotransposon-mediated rearrangements arise at a frequency of one event per 60 somatic retrotranspositions. Molecular timing analyses indicate that these events arise early in tumorigenesis, establishing L1 activity as an early driver of chromosomal instability. Our findings demonstrate that L1 contributes substantially to cancer genome evolution in certain tumors.