In this work, we established an approach combining amplified fragment length polymorphism (AFLP) and next-generation sequencing (NGS) techniques to map the malignant genomes of patients with chronic myeloid leukemia (CML), a disease characterized by the presence of reciprocal translocation between chromosomes 9 and 22 t(9;22)(q34;q11), known as the Philadelphia chromosome, resulting in a BCR-ABL1 fusion oncogene. The gene discussed is BCR; the disease is chronic myelogenous leukemia, BCR-ABL1 positive.