NCM 2021: Detection of cell-free DNA in acute lymphoblastic leukemia patients to identify CNS disease and monitor response to therapy

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer: 6,000 people are diagnosed every year, and half of those are children. It results from the rapid expansion of immature lymphoid cells in the blood and this can be fatal in as little as three weeks. Thankfully, 90% of children and 40% of adults can be cured; however, if the patient has a relapse, the prognosis is only 30% survival. Minimal residual disease (MRD) is the best prognostic indicator of whether the disease will return. MRDs are lymphoblasts that are left in the patient’s blood after chemotherapy. Another clinical concern with this disease is the infiltration of ALL cells into the central nervous system (CNS), which is a significant cause of mortality. Current diagnosis methods rely on the presence of lymphoblasts in the patient sample and may not be sensitive enough or the lymphoblasts may not be present in the sample. Jessica’s group wanted to know how they could detect ALL in patients without leukemia cells in the sample. Cell-free DNA is secreted from normal and cancer cells so that cancer at a distant location can be detected via its cell-free DNA in the patient’s blood. Every T cell and B cell has a unique sequence in its genome related to its receptor; the receptor can be sequenced to provide a unique barcode, making it possible to track leukemic clones. Jessica’s group have developed a simple Nanopore sequencing workflow: cell-free DNA is extracted from a patient sample, PCR amplification is applied to the region of interest, ready for nanopore sequencing and data analysis using MinKnow, Minimap2 and Featurecount. Nanopore sequencing identified patients with MRD and the response of clones to therapy could be tracked over time. The technique was also used to identify patients with leukemia-associated cell-free DNA in the spinal fluid. This was the first time that cell-free DNA has been used to monitor CNS disease in ALL patients; Jessica states ‘it was exciting that we could actually even detect this’.