Population-Scale DNA Sequencing Maps How Somatic Mutations Drive Aging and Cancer Risk

Somatic mutations accumulate in normal tissues throughout life, and clones carrying driver mutations gradually colonize tissues as we age. While this process is central to cancer initiation and may contribute to aging-related diseases, studying it has been difficult because most clones are microscopic and prior methods were low-throughput or limited to a few tissue types.

This study introduces a substantially improved version of NanoSeq, a duplex sequencing technology that reads both strands of each original DNA molecule to eliminate sequencing errors. Two new fragmentation approaches—sonication with exonuclease blunting, and optimized enzymatic fragmentation—allow NanoSeq to work with whole-exome and targeted capture panels while maintaining error rates below 5 × 10⁻⁹ errors per base pair. This is roughly 20-fold lower than standard duplex methods and two orders of magnitude below the actual mutation burden of adult cells, enabling single-molecule mutation detection. The protocol also demonstrated robustness on formalin-fixed, damaged DNA where standard duplex sequencing failed.

Targeted NanoSeq was applied to 1,042 non-invasive oral epithelium swabs and 371 blood samples from a UK twin cohort. In oral epithelium, the researchers identified 46 genes under positive selection, more than double what had previously been reported for this tissue, and detected over 62,000 individual driver mutations. They also found statistically significant evidence of negative selection in essential genes—a rarely observed phenomenon in somatic tissue studies. High-resolution selection maps spanning coding and non-coding regions were generated for multiple genes, effectively performing in vivo saturation mutagenesis at population scale.

Multivariate regression models were used to disentangle how known cancer risk factors—age, tobacco use, and alcohol consumption—independently alter mutation acquisition rates and the selective advantage of driver clones. Age was the dominant driver of mutation burden in blood, with linear accumulation confirmed across donors. Tobacco and alcohol exposure were associated with both increased mutagenesis and altered clonal selection in oral epithelium, providing mechanistic insight into their roles as carcinogens.

The twin cohort design also allows future work to dissect heritable versus environmental contributions to somatic mutation landscapes. Together, these findings establish targeted NanoSeq as a scalable, epidemiological-grade tool for studying somatic evolution, early cancer prevention strategies, and the contribution of clonal mutations to aging biology.