Acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) are prevalent hematopoietic malignancies that are subdivided into distinct disease entities based on clinical, immunophenotypic and genomic features. Cytogenetic analysis (karyotyping and Fluorescent In-Situ Hybridization) together with Multiple Ligation-dependent Probe Amplification (MLPA) and PCR-based methods form the backbone of routine ALL and AML diagnostics. This approach is labor-intensive, time-consuming and costly. New molecular technologies now exist that can detect structural variants (SVs) and copy number alterations in one test.