Quantification of somatic mutation flow in individual cell division events by ‘Lineage sequencing’

‘Lineage sequencing’ is a new genome-wide technique that utilizes knowledge of the cell lineage structure to reconstruct mutational events occurring during lineage formation with high resolution, high accuracy, high precision, and minimal bias. By applying ‘lineage sequencing’, we measure the accumulation of SNVs by identifying >90% of SNVs that evolved during lineage formation and mapping these onto cells in the lineage with very high resolution (1 - 4 cell divisions, with little uncertainty in the number of cell divisions in each lineage segment where SNVs were assigned).For proof of concept, we applied lineage sequencing to a human colon cancer cell line with a DNA polymerase epsilon (POLE) proofreading deficiency (HT115) and a human retinal epithelial cell line immortalized by constitutive telomerase expression (RPE1). Cells were cultured under continuous observation to link observed single-cell phenotypes with single-cell mutation data. The high sensitivity, specificity, and resolution of the data provide a unique opportunity for quantitative analysis of variation in mutation rate, spectrum, and correlations among variants.