Whole-genome sequencing (WGS) was performed on bulk mononuclear cells (MNCs) from 2 patients (Pat1 and Pat17).
In Pat1, both diagnostic (Pat1_Relapse_Diag_MNC) and relapse (Pat1_Relapse_Relapse_MNC) samples underwent WGS. For Pat17, only the diagnostic sample (Pat17_Remission_Diag_MNC) was sequenced.
Sequence reads were aligned to GRCh37, and mutation calling was carried out using Genomon2 (https://genomon.readthedocs.io/ja/latest/). Mutations were annotated using ANNOVAR.

Targeted capture DNA sequencing served two purposes. One was to identify driver mutations that could act as markers for tracing clones in samples collected at diagnosis. The other was to compare sensitivity in detecting measurable residual disease (MRD) in samples after transplantation.
The names of the BAM files, along with the corresponding patient ID, patient group, cell population, timepoint at sample collection, and capture probes used for library preparation, are listed in "AlloHSCT_bam files.txt."
For patient group, "Relapse" indicates patients who relapsed, and "Remission" indicates those who maintained remission during the observation period.
Population abbreviations: HSC (Hematopoietic Stem Cells), GMP (Granulocyte Monocyte Progenitors), LMPP (Lymphoid-Primed Multipotent Progenitors), MNC (Mononuclear cells).
Capture probe details: Refer to the Blood paper for the targeted gene list for each panel. For samples comparing sensitivity, the IDT panel was used, while the rest of the panels were employed for mutational screening.






