To address how genetic variation alters gene expression in complex cell mixtures, we developed Direct Nuclear Tagmentation and RNA-sequencing (DNTR-seq), which enables whole genome and mRNA sequencing jointly in single cells. DNTR-seq readily identified minor subclones within leukemia patients. In a large-scale DNA damage screen, DNTR-seq was used to detect regions under purifying selection, and identified genes where mRNA abundance was resistant to copy number alteration, suggesting strong genetic compensation. mRNA-seq quality equals RNA-only methods, and the low positional bias of genomic libraries allowed detection of sub-megabase aberrations at ultra-low coverage. Each cell library is individually addressable and can be re-sequenced at increased depth, allowing multi-tiered study designs. Additionally, the direct tagmentation protocol enables coverage-independent estimation of ploidy, which can be used to identify cell singlets. Thus, DNTR-seq directly links each cell?s state to its corresponding genome at scale, enabling routine analysis of heterogeneous tumors and other complex tissues. SOURCE: Vasilios Zachariadis (vasilios.zachariadis@ki.se) - BioClinicum J6:30 Karolinska Institutet

Pluto Bioinformatics

GSE144296: A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells