Next-generation sequencing (NGS), particularly single-cell sequencing, has revolutionized the
scale and scope of genomic and biomedical research. Recent technological advances in NGS and singlecell
studies have made the deep whole-genome (DNA-seq), whole-epigenome and whole-transcriptome
sequencing (RNA-seq) at single-cell level feasible. NGS at the single-cell level expands our view of
genome, epigenome and transcriptome and allows the genome, epigenome and transcriptome of any
organism to be explored without a priori assumptions and with unprecedented throughput. And it does
so with single-nucleotide resolution. NGS is also a very powerful tool for drug discovery and drug development.
In this review, we describe the current state of single-cell sequencing techniques, which can
provide a new, more powerful and precise approach for analyzing effects of drugs on treated cells and
tissues. Our review discusses single-cell whole genome/exome sequencing (scWGS/scWES), single-cell
transcriptome sequencing (scRNA-seq), single-cell bisulfite sequencing (scBS), and multiple omics of
single-cell sequencing. We also highlight the advantages and challenges of each of these approaches.
Finally, we describe, elaborate and speculate the potential applications of single-cell sequencing for drug
discovery and drug development.