DNTR-seq of HCT116 cells

We developed ASCENT (Absolute single-cell copynumber evaluation and subclone topology) to analyse scWGS data. We process HCT116 cells with our pipeline and show that we can correctly identify and adjust copy numbers for cycling cells, and sorted multiplets. On a patient sample (deposited on EGA) we show that by low-resolution segmentation we accurately identify breakpoints, down to 100.000 paired end reads per cell, and that by refining breakpoints after clustering, we can detect 140kb segments. We implement a way of haplotyping per clone segments and identify copy-neutral LOH, thereby getting a more accurate clonal evolution.