The new aspect of our work is to reveal that Ph-like alterations are common among patients with Ph-ALL experiencing relapse after hematopoietic cell transplantation (HCT), despite acquisition of MRD-negative complete responses prior to transplant. This is also the central finding of our work. Therefore, the anticipated benefits of HCT appear diminished among this patient subset; such patients may be better served with efforts to further increase MRD depth prior to HCT, or alternative therapies.