GoT-ChA: Genotyping of Targeted loci with single-cell Chromatin Accessibility v1

Somatic mutations are crucial for cancer initiation and evolution, and have been identified across a number of healthy tissues in the human body. These mutations can disrupt normal cellular functions, leading to aberrant clonal expansions via acquired fitness advantages or skewed differentiation topologies. GoT-ChA and similar methods (e.g. GoT, TARGET-seq) aim to pair targeted genotyping with single-cell sequencing approaches in order to understand the impact of somatic mutations directly in human patient samples, in both malignant and non-malignant contexts. GoT-ChA is unique in that it is a high-throughput single-cell method that pairs targeted genotyping with chromatin accessibility measurements based on the broadly utilized scATAC-seq platform from 10x Genomics. Previous single-cell genotyping approaches were largely based on scRNA-seq protocols, utilizing expressed and captured mRNA transcripts as sources for genotyping information. This results in a limiting dependence on gene expression and mutation location (due to 3' end bias of most scRNA-seq methods), precluding the usage of such technologies on lowly expressed or inconveniently located loci of interest. GoT-ChA surmounts these limitations via direct utilization of genomic DNA for genotyping, whilst simultaneously assaying chromatin accessibility.