While introduction of novel targeted inhibitors has markedly altered the therapeutic options for treating patients with blood cancers, relapses due to acquired resistance after initial response remain a major problem. To delineate drug resistance, we applied a novel single-cell omics approach on samples from patients with progressive leukaemia who failed therapy with a targeted agent. Combining short-read with long-read targeted and whole-transcriptome sequencing identified mutations and alternative transcripts in specific sub-clones of the tumour at relapse. Thus, our single-cell integration of short-read and full-length RNA-seq provides novel insights into how complex tumour heterogeneity evolves upon acquisition of drug resistance.

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