Monitoring minimal residual disease (MRD) is crucial for assessing the effectiveness of treatment in acute lymphoblastic and acute myeloid leukemia. Standard MRD targets include mutations in clinically relevant genes (e.g., NPM1, CEBPα) and chromosomal rearrangements that generate fusion transcripts (e.g., AML1-ETO, PML-RARα). However, some patients lack such molecular markers. This protocol provides a platform-independent method for identifying patient-specific chromosomal breakpoints to enable MRD monitoring by PCR. The approach includes chromosomal microdissection, next-generation sequencing (NGS), long-range PCR, and Sanger sequencing. An alternative simplified version using long-read sequencing is also described.