High-depth Whole Genome Sequencing of Single Human Colon Crypts Uncovers New View on Crypt Clonality

It is generally accepted that each colon crypt is monoclonal and is populated by a single stem cell lineage after early human life. It has been impossible to profile somatic mutations genome-wide because high-depth and high-quality whole genome sequencing (WGS) of single cells is unachievable without tissue culture or whole genome amplification (WGA). Therefore, the cell-to-cell heterogeneity in each individual remains mostly unknown. Applying our novel WGA-free WGS method to obtain >30X post-alignment depth, we comprehensively profiled somatic mutations in 71 single human colon crypts with matched bulk controls from 14 individuals. Analysis reveals that colon crypts are commonly of multiple lineages in human adults. Our study is the first to demonstrate that an appropriately designed WGS approach can determine cell- to-cell heterogeneity in natural cell clones. The much higher sensitivity of WGS than the previous methods in lineage tracing can unlock the complex stem cell dynamics in the colon crypt.