Acknowledgements: This work was supported by the Bill and Melinda Gates Foundation (INV-002189 and INV-038816, D.G.K.). M.S.C. was supported by a Wellcome Clinical PhD Fellowship. Work conducted by D.A.W. and colleagues was supported by National Institutes of Health grant R01HL (137848) and NHLBI Cure Sickle grant (OT2HL 154815). Investigators at the Sanger Institute were supported by a core grant from the Wellcome Trust. This research was funded in part by the Wellcome Trust (206194 and 108413/A/15/D). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. J.N. is supported by a Cancer Research UK Fellowship. Work in the D.G.K. laboratory is supported by a European Research Council Starting Grant (ERC-2016-STG-715371) and a Cancer Research UK Programme Foundation Award (DCRPGF\100008). The authors thank the IT Support team of the Cancer, Ageing and Somatic mutation programme at the Sanger Institute for their support and V. Sankaran and L. Naldini for helpful discussion. The authors also thank the patients for donating the samples that have been used in this study.Gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms
