A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells

Mol Cell. 2020 Nov 5;80(3):541-553.e5. doi: 10.1016/j.molcel.2020.09.025. Epub 2020 Oct 16.


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 sequencing (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.

Keywords: cancer genomics; copy number variation; double-strand break; reverse genetic screen; single-cell RNA sequencing; single-cell multi-omics; single-cell whole genome sequencing; whole-genome sequencing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence / genetics
  • Cell Line, Tumor
  • Gene Expression Profiling / methods*
  • Gene Library
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • RNA / genetics
  • RNA, Messenger / genetics
  • Sequence Analysis, DNA / methods
  • Single-Cell Analysis / methods*
  • Whole Genome Sequencing / methods*


  • RNA, Messenger
  • RNA