Fig. 2.

(A) Frequency of high-confidence somatic L1 insertions varies across 5 colorectal, 7 prostate, 8 ovarian, 7 multiple myeloma, and 16 glioblastoma tumors. Three epithelial cancers (colorectal, prostate, and ovarian) show frequent somatic L1 insertions, whereas no insertions are observed in the blood and brain cancers. One colorectal tumor (CR3518) contains 102 L1 insertions, increasing the average somatic event frequency for colorectal tumors from 9 to 28 when this sample is included. (B) The genes affected by somatic TE insertions are significantly enriched for genes with high mutation rates as estimated from the exome sequencing data of 228 additional colorectal tumors (P < 1 × 10⁻¹⁵). The mutation frequency of each gene was adjusted for its total exon size. (Inset) The top 15 genes with nonsilent mutations. (C) The transcript levels of 45 genes with somatic TE insertions in colorectal tumors were compared with those from 28 normal colorectal tissues, and the expression fold changes are shown. Overall, the genes with a TE insertion were significantly down-regulated in tumors (P = 6.3 × 10⁻⁴, background distribution based on randomly sampled gene sets). KCNIP1 appears twice because of two somatic insertions in two different samples. The dashed line marks 50% reduction in expression.