Heterogeneous Prognostic Impact of 9q+ Deletions in Patients with Chronic Myelogenous Leukemia.
Authors: Kreil Sebastian , Waghorn Katherine , Pfirrmann Markus , Reiter Andreas , Hehlmann Rudiger , Hochhaus Andreas , Cross Nicholas C.P. 
Published: October 2019

Abstract
Deletions at the ABL-BCR reciprocal breakpoint on the derivative chromosome 9 are seen in 10–15% of patients with CML and have been associated with a poor prognosis, at least for cases treated with hydroxyurea or interferon alpha (IFN). Studies to date have used different fluorescent-in-situ-hybridization (FISH) probe sets to determine deletion status and thus the results are not always directly comparable. Furthermore, information concerning the extent of deletions is limited and no studies have been performed in the context of a prospective randomised controlled clinical trial. To provide more accurate information about deletion status, we developed a rapid DNA-based screen based on multiplex ligation-dependent probe amplification (MLPA). Der(9) deletions were detected at dilutions of 60% or more MC3 cell DNA in non-deleted DNA, indicating that the method was suitable for analysis of samples with up to 40% normal cells. We then investigated 348 chronic phase (CP) patients that were treated with IFN based therapies in three consecutive prospective controlled German studies. The median duration of IFN-based treatment was 17 months (range, 1–115) with a median observation time of seven years (range, 0.3–16); 160 patients (46%) were alive at the date of analysis. Therapy subsequent to IFN included allogeneic stem cell transplantation (SCT; n=130) or imatinib mesylate (IM; n=62). DNA extracted at diagnosis was tested by MLPA and 9q+ deletions, defined as the loss of at least two consecutive markers, were found in 59/348 (17%) patients. Of these 59 deletions, 21 spanned the ABL-BCR breakpoint and 38 were either upstream only (n=20) or downstream only (n=18) of the breakpoint. Analysis of the baseline parameters age, spleen size, leukocyte count, % eosinophils, basophils and blasts in peripheral blood, platelets, hemoglobin, and prognostic scores according to Hasford and Sokal did not reveal any significant difference between patients with and without deletions. There was no significant difference in overall survival between patients with or without deletions and also no difference in survival when patients were censored at SCT in CP or IM treatment. Patients with large ABL-BCR deletions had a poorer survival compared to all other cases (5.7 vs 8.8 years; p=0.0025) but this fell below the level of significance using censored survival (p=0.08). Patients with low risk Sokal or Hasford scores with breakpoint spanning deletions had a significantly worse prognosis than other cases (p=0.01 and p=0.04, respectively). Patients with ABL-BCR deletions also showed a trend towards a less favourable survival after allogeneic SCT in CP-CML (p=0.06). Surprisingly, patients with deletions that did not span the breakpoint showed a superior outcome (p=0.02). Univariate analysis of baseline data revealed that patients with either ABL or BCR deletions only were younger, presented with more circulating blasts and a larger spleen at diagnosis. Patients with large deletions spanning the breakpoint had fewer additional chromosomal abnormalities. In conclusion, MLPA is a reliable technique for detection of der(9) deletions in CML. Our analysis indicates that only those deletions that span the reciprocal ABL-BCR breakpoint are associated with adverse prognosis but the effect is relatively weak.