Summary
Mutation accumulation varies across a genome by chromosomal location, nucleotide identity, surrounding sequence, and chromatin context1–5. Nevertheless, while mutagens, replication machinery, and repair processes exhibit identifiable mutation signatures, at the tissue scale the aggregate manifestation of these processes has been difficult to measure. The challenge in observing tissue-wide somatic mutation patterns is that prior to clonal expansion, most mutations are relatively rare6–9. This challenge has meant that somatic mutation detection in humans has largely been limited to in vitro expanded stem cells10–13 or clonal expansions that occur in vivo14–17. Here we describe a new method called FERMI (Fast Extremely Rare Mutation Identification), which comprehensively captures and quantifies rare mutations at single DNA molecule resolution, that exist at frequencies as rare as 10−4. Using this method, we observed that mutations are highly prevalent in human peripheral blood cells, with virtually every position mutated across fewer than 105 cells. Our results revealed an unanticipated degree of similarity in somatic mutation patterns across individuals, where most assayed substitutions are found to occur at conserved frequencies across nearly all individuals spanning a nine-decade age range. We observe substantial bias in changes for many positions, including substitution to only a single base across all assayed individuals. These observed mutational patterns existed both within non-conserved, non-coding and non-repetitive regions of the genome and within the coding regions of oncogenes implicated in hematopoietic malignancies. Finally, we identify individuals who deviate from typical mutational patterns in a reproducible manner that resembles a mild mismatch repair deficiency, suggesting that variance from typical somatic mutation rates may be relatively common. This study provides an unprecedented characterization of mutations in terminally differentiated somatic cells and demonstrates that somatic mutations in such cells are significantly more frequent and deterministic than previously believed.