The Detection of Minor Clones with Somatic KIT D816V Mutations Using Droplet Digital PCR in Pediatric De Novo AML: AML-05 Trial from the Japanese Pediatric Leukemia/Lymphoma Study Group

Introduction Recent medical advances and development of comprehensive genetic understanding dramatically improve the clinical outcome of whole pediatric cancers, particularly in pediatric acute lymphoblastic lymphoma. However, approximately 50% of patients have disease relapse, and overall survival (OS) of pediatric acute myeloid leukemia (AML) is less than 70% as of the major therapeutic challenges. AML is caused by various chromosomal aberrations, gene mutations/epigenetic modifications, and deregulated/overregulated gene expressions, leading to increased proliferation and decreased hematopoietic progenitor cell differentiation. AML with RUNX1-RUNX1T1 gene fusions are generally classified as a low-risk group and resulted in favorable prognosis. However approximately 30% of the patients relapsed within 3 years. Conversely, KIT mutations were found in approximately 30% of AML cases with RUNX1-RUNX1T1 and thought to be a risk factor for relapse, particularly when occurring in D816V within KIT exon 17. Recently, droplet digital PCR (ddPCR), a method for measuring target nucleic acid sequence quantity, has been used to determine low-prevalence somatic mutations that were not detectable using Sanger sequencing. It shows the possibility that there are some of Pediatric AML cases which were not detected minor clones with somatic KIT mutation by using ordinary PCR. In this study, we explored KIT D816V mutations including the cases which are not detected by Sanger sequencing and found the prognosis of them by using Japanese pediatric AML cases. Methods We reanalyzed somatic KIT mutations (p.D816V) in the DNA extracted from 335 pediatric AML patients with RUNX1-RUNX1T1 who participated in the Japanese Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML-05 trial using ddPCR . In this trial, we conducted the tests as follows,: PCR mixture containing 10 μL 2x ddPCR Supermix for probes, 900 nM target-specific PCR primers, and 250 nM mutant-specific (FAM) and wild-type-specific (HEX) probes.20 µL of PCR mixture and 70 μL Droplet generation oil were mixed, and droplet generation was performed using a Bio-Rad QX100 Droplet Generator. The droplet emulsion was thermally cycled in the following conditions: denaturing at 95 °C for 10 min, 40 cycles of PCR at 94 °C for 30 s and at 57 °C for 2 min, and a final extension at 98 °C for 10 min. PCR amplification in the droplets was confirmed using Bio-Rad QX200 Droplet Reader. ThresholdThe threshold was determined by comparing the