title: Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients.
abstract: Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using targeted next-generation sequencing coupled with the use of a dPCR platform. t(9;22) genomic breakpoints were successfully mapped in samples from 32 of 32 patients with early stage disease. Disease quantification by DNA-based dPCR was performed using the Fluidigm BioMark platform on 46 follow-up samples from 6 of the 32 patients, including 36 samples that were in deep molecular remission. dPCR detected persistent disease in 81% of molecular-remission samples, outperforming both RT-dPCR (25%) and DNA-based quantitative PCR (19%). We conclude that dPCR for BCR-ABL1 DNA is the most sensitive available method of residual-disease detection in chronic myeloid leukemia and may prove useful in the management of tyrosine kinase inhibitor withdrawal.
authors: Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom. Electronic address: m.alikian@imperial.ac.uk.
authors: Mary
authors: M
authors: Alikian
authors: Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom.
authors: Peter
authors: P
authors: Ellery
authors: Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Martin
authors: M
authors: Forbes
authors: Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Gareth
authors: G
authors: Gerrard
authors: Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Dalia
authors: D
authors: Kasperaviciute
authors: Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Alona
authors: A
authors: Sosinsky
authors: Clinical Genome Informatics Facility, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Michael
authors: M
authors: Mueller
authors: Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom.
authors: Alexandra S
authors: AS
authors: Whale
authors: Clinical Haematology, Imperial College Healthcare National Health Institute Trust, London, United Kingdom.
authors: Dragana
authors: D
authors: Milojkovic
authors: Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Jane
authors: J
authors: Apperley
authors: Molecular & Cell Biology, LGC Limited, Queens Road, Teddington, United Kingdom.
authors: Jim F
authors: JF
authors: Huggett
authors: Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Letizia
authors: L
authors: Foroni
authors: Imperial Molecular Pathology, Imperial Healthcare Trust, Hammersmith Hospital, London, United Kingdom; Centre for Haematology, Faculty of Medicine, Imperial College London, London, United Kingdom.
authors: Alistair G
authors: AG
authors: Reid
mesh_terms: D016044:Fusion Proteins, bcr-abl / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D015464:Leukemia, Myelogenous, Chronic, BCR-ABL Positive / Q000188:drug therapy / Q000235:genetics* / Q000473:pathology; D018365:Neoplasm, Residual; D016133:Polymerase Chain Reaction / Q000379:methods*; D057285:Precision Medicine / Q000379:methods; D012680:Sensitivity and Specificity
chemical_list: C581634:BCR-ABL1 fusion protein, human; D016044:Fusion Proteins, bcr-abl