Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]

We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detection of multiple mutations within single-cells from genomic and coding DNA in parallel with whole transcriptome analysis, providing a powerful tool to link transcriptional and genetic tumor heterogeneity. Single cell whole transcriptome sequencing of Lineage-CD34+ HSPC (Hematopoietic Stem and Progenitor Cells) from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq reveals distinct molecular signatures associated with the presence of somatic mutations in single cells as well as distinct transcriptional profiles of WT cells from patient samples as compared with normal controls. We isolated single HSPCs from patients with myeloproliferative neoplasms and normal controls using full-length TARGET-seq, a novel method for parallel mutational analysis and whole transcriptome sequencing from the same single cell. We analyzed a cohort of patients with different combinations of JAK2 V617F, TET2 and EZH2 mutations, and performed differential expression analysis between mutant and WT cells from the same patient as well as cells obtained from normal donors. We also analyzed molecular signatures corresponding to every combination of mutations found in single cell as well as molecular signatures of WT cells from patient samples as compared to WT cells from normal controls.