Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs

Accurately quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems. We develop a universal method (UMIs) to label individual DNA molecules for analyzing diverse types of rare genetic variants, with frequency as low as 4x10^-5, using short- or long-read sequencing. It enables base-resolution haplotype-resolved quantitative characterization of rare variants. It provides the first quantitative evidence of persistent nonrandom large deletions and insertions following DNA repair of double-strand breaks induced by CRISPR-Cas9 in human pluripotent stem cells.