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• Clonal selection after gene therapy in sickle cell disease

  While gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD), the occurrence of myeloid malignancies in clinical trials has prompted concern. To interrogate potential mechanisms underlying increased cancer risk, we used hematopoietic stem cell (HSC) clonal tracking by whole genome sequencing (WGS) to map the somatic mutation and clonal landscape of 2,592 gene modified as well as unmodified single stem and progenitor cells from six SCD patients undergoing gene therapy (7-26 years old, average 12.7× depth). Pre-GT phylogenetic trees in SCD were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified. However, an increased frequency of driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) were seen in both genetically modified and unmodified cells suggested positive selection of mutant clones during gene therapy. This work sheds light on the mutation landscape and HSC clonal dynamics in gene therapy for SCD and highlights enhanced fitness of some HSCs harboring pre-existing driver mutations following gene therapy. Future studies should define the long-term fate of mutant clones including any contribution to expansions associated with myeloid neoplasms.

  Dataset EGAD00001010913

• Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls

  Study EGAS00001005069

• Cell-free DNA cleavages analysis (human)

  Cell-free DNA cleavages analysis (human)

  Study EGAS00001006701

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A90560A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 585 samples; filetype=bam

  Dataset EGAD00001004733

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95660A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 1522 samples; filetype=bam

  Dataset EGAD00001004750

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95632B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 626 samples; filetype=bam

  Dataset EGAD00001004748

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95670B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 636 samples; filetype=bam

  Dataset EGAD00001004754

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A75617A

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 692 samples; filetype=bam

  Dataset EGAD00001004727

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A73044B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 2057 samples; filetype=bam

  Dataset EGAD00001004720

• Whole genome sequencing of single cells identifies stochastic aneuploidies, genome replication, states, and clonal repertoires for library A95724B

  Transposase-based amplification-free single-cell genome direct library preparation in nanowell chips; 561 samples; filetype=bam

  Dataset EGAD00001004757