Single-cell proteogenomic analysis of clonal evolution in PDX models of AML treated with IDH inhibitors

Method:BM samples were thawed, pooled when necessary, and sorted for live human CD45+ cells by FACS. The sorted cells were immediately processed for library preparation. For surface protein sequencing, cells were stained with the TotalSeq™-D Heme Oncology Cocktail (BioLegend, RRID:AB_2890849), containing antibodies targeting 42 unique surface antigens and 3 isotype control antibodies, plus an additional TotalSeq™-D0392 anti-human CD15 antibody (BioLegend, RRID:AB_2904344). After staining, cells were washed and processed using the Tapestri platform. The DNA sequencing panel targeted 127 amplicons across 20 genes commonly mutated in human AML. Variant calling was performed using MissionBio’s Tapestri pipeline v2.