The BCR-ABL1 fusion, originating from the reciprocal translocation between chromosomes 9 and 22, is a therapeutic target in chronic myeloid leukemia and Philadelphia-positive acute lymphocytic leukemia. Nevertheless, mutations in the kinase domain of BCR-ABL1 can cause resistance to tyrosine kinase inhibitors. Their detection by Sanger sequencing is crucial for further therapeutic decisions and disease monitoring. Aim of the project was the improvement of the amplification of the BCR-ABL1 fusion transcript in order to detect therapy-relevant mutations at low BCR-ABL1/ABL1 ratios (IS values) below 1%. For that purpose a nested PCR is performed and the amplicons generated in the second PCR are sequenced. The selection between the fusion transcript and the wild type ABL1 allele takes place during the first round of PCR. We therefore aimed to raise its sensitivity by testing various primers and polymerases and finally selected the Q5 Hot Start High-Fidelity DNA polymerase (NEB). Furthermore, we optimized reverse transcription with a gene specific primer from the exon boundary 9-10 of the ABL1 gene and the reverse transcriptase SuperScript IV. The method was validated in a series of samples, provided robust amplification for samples with IS values down to 0.00072% and is already routinely used in the laboratory.