Massively parallel assessment of human variants with base editor screens

Cell. 2021 Feb 18;184(4):1064-1080.e20. doi: 10.1016/j.cell.2021.01.012.


Understanding the functional consequences of single-nucleotide variants is critical to uncovering the genetic underpinnings of diseases, but technologies to characterize variants are limiting. Here, we leverage CRISPR-Cas9 cytosine base editors in pooled screens to scalably assay variants at endogenous loci in mammalian cells. We benchmark the performance of base editors in positive and negative selection screens, identifying known loss-of-function mutations in BRCA1 and BRCA2 with high precision. To demonstrate the utility of base editor screens to probe small molecule-protein interactions, we screen against BH3 mimetics and PARP inhibitors, identifying point mutations that confer drug sensitivity or resistance. We also create a library of single guide RNAs (sgRNAs) predicted to generate 52,034 ClinVar variants in 3,584 genes and conduct screens in the presence of cellular stressors, identifying loss-of-function variants in numerous DNA damage repair genes. We anticipate that this screening approach will be broadly useful to readily and scalably functionalize genetic variants.

Keywords: CRISPR; ClinVar; DNA damage; PARPi; apoptosis; base editing; genetic screens.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alleles
  • BRCA1 Protein / genetics
  • BRCA2 Protein / genetics
  • Base Sequence
  • Catalytic Domain
  • Cell Line, Tumor
  • Gene Editing*
  • Genetic Variation*
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Loss of Function Mutation
  • Mutagenesis / genetics
  • Myeloid Cell Leukemia Sequence 1 Protein / genetics
  • Point Mutation / genetics
  • Poly(ADP-ribose) Polymerases / chemistry
  • Poly(ADP-ribose) Polymerases / genetics
  • Reproducibility of Results
  • Selection, Genetic
  • bcl-X Protein / genetics


  • BCL2L1 protein, human
  • BRCA1 Protein
  • BRCA2 Protein
  • MCL1 protein, human
  • Myeloid Cell Leukemia Sequence 1 Protein
  • bcl-X Protein
  • Poly(ADP-ribose) Polymerases