Recent advances in single-cell technologies have permitted the investigation of heterogeneous cell populations at previously unattainable resolution. In this thesis single-cell approaches are applied to resolve the molecular mechanisms driving disease in mouse haematopoietic stem cells (HSCs), using JAK2 V617F mutant myeloproliferative neoplasms (MPNs) as a model. This study utilises single-cell gene expression and functional assays to identify a subset of JAK2 V617F mutant HSCs that display defective self-renewal. This defect is rescued by crossing JAK2 V617F mice with mice lacking TET2, the most commonly co-mutated gene in patients with MPN. Single-cell gene expression profiling of JAK2 V617F-mutant HSCs revealed reduced expression of specific self-renewal regulator genes, some of which were restored to normal levels in single TET2/JAK2 mutant HSCs. Of these, Bmi1 and, to a lesser extent, Pbx1 and Meis1 overexpression in JAK2-mutant HSCs could improve stem cell self-renewal, allowing development of a disease phenotype in functional assays. Together, these findings refine the molecules involved in clonal expansion of MPNs, and highlight the power of single cell approaches in deconstructing the functional characteristics and molecular network of normal and malignant stem cells.