Analysis of Naturally Occurring Somatic Insertions in the Human Genome

Abstract

Biochemical and genetic experimental systems permit precise definition of enzyme requirements and mechanistic steps in DNA repair. Comparison of these findings to repair events at naturally occurring breakage sites in multicellular organisms is valuable for confirming and extending these insights. However, heterogeneity in any cell population increases with each cell division, and the reliable detection of DNA breakage sites and their repair in vivo has been difficult due to technical limitations. Here, we examine somatic insertional mutations naturally occurring during normal metabolism and cell division in single human colon crypts using a novel whole-genome sequencing method. We find that replication slippage is a dominant mechanism for these events, and insertions larger than 10 bp are uncommon. Mechanistic features of these sites in physiologically normal cell clones, such as single human colon crypts, permits inferences about the DNA breakage repair zone and processing within natural chromatin, thereby permitting comparisons to experimental studies using ex vivo cellular and simplified biochemical systems.