Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for “personalized monitoring” of residual disease in chronic myeloid leukemia patients
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Cosimo Cumbo1,*, Luciana Impera1,*, Crescenzio Francesco Minervini1, Paola Orsini1, Luisa Anelli1, Antonella Zagaria1, Nicoletta Coccaro1, Giuseppina Tota1, Angela Minervini1, Paola Casieri1, Claudia Brunetti1, Antonella Russo Rossi1, Elisa Parciante1, Giorgina Specchia1 and Francesco Albano1
1Department of Emergency and Organ Transplantation, Hematology Section, University of Bari, 70124 Bari, Italy
*These authors contributed equally to this work
Francesco Albano, email: [email protected]
Keywords: genomic BCR-ABL1 breakpoint; chronic myeloid leukemia; FISH; MinION sequencing; droplet digital PCR
Received: November 13, 2017 Accepted: January 02, 2018 Published: January 05, 2018
For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts. Several studies reported that a DNA-based assay enhances the sensitivity of detection of the BCR-ABL1 genomic rearrangement, even if its characterization results difficult. We developed a DNA-based method for detecting and quantifying residual BCR-ABL1 positive leukemic stem cells in CML patients. We propose two alternative approaches: the first one is a fluorescence in situ hybridization (FISH)-based step followed by Sanger sequencing; the second one employs MinION, a single molecule sequencer based on nanopore technology. Finally, after defining the BCR-ABL1 genomic junction, we performed the target CML patient–specific quantification, using droplet digital PCR (ddPCR). FISH and MinION steps, respectively, together with ddPCR analysis, greatly reduce the complexity that has impeded the use of “personalized monitoring” of CML in clinical practice. Our report suggests a feasible pipeline, in terms of costs and reproducibility, aimed at characterizing and quantifying the genomic BCR-ABL1 rearrangement during MRD monitoring in CML patients.
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