BRIEF COMMUNICATION MLPA is a powerful tool for detecting lymphoblastic transformation in chronic myeloid leukemia and revealing the clonal origin of relapse in pediatric acute lymphoblastic leukemia Don  at Alp  ar a , Danielle de Jong b , Suvi Savola c , HaciAli Yigittop c ,B  ela Kajt  ar a , L  aszl  o Kereskai a ,L  aszl  o Pajor a ,K  aroly Szuhai b, * a Department of Pathology, Faculty of Medicine, University of P ecs, P ecs, Hungary; b Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, the Netherlands; c MRC-Holland, Amsterdam, the Netherlands Copy number alterations (CNAs) at 58 different loci have been investigated in 95 bone marrow or peripheral blood samples from patients with chronic myeloid leukemia (CML) or pediatric acute lymphoblastic leukemia (pALL) using multiplex ligation-dependent probe amplification (MLPA). In all but one case, the CNA profile correctly distinguished patients with CML who were in chronic phase from those in lymphoblast crisis. Within the chronic phase group, we could not separate patients resistant to imatinib therapy from those who were good responders. In our investigation of patients with pALL, a panel of MLPA probes broader than ever before was applied. Paired diagnostic and relapse samples from patients with pALL demonstrated clonally related or inde- pendent dominant clones, suggesting the presence of a pre-leukemic cell group. Identification of the origin of cell populations dominating at relapse will have a great effect on future treatment strategies. In summary, we have demonstrated the versatility of MLPA by using this cost-effective technique for two new applications. Keywords MLPA, chronic myeloid leukemia, acute lymphoblastic leukemia, relapse, clonal origin Crown Copyright ª 2012 Published by Elsevier Inc. All rights reserved. Multiplex ligation-dependent probe amplification (MLPA) was introduced in 2002 (1) and, since then, has been successfully used for analyzing copy number alterations (CNAs) in various malignant hematopoietic disorders (2e8). To our knowledge, the application of MLPA to detect CNAs in chronic myeloid leukemia (CML) has never been published. Previous single nucleotide polymorphism array (SNP array) studies found a significant difference between the average number of CNAs present in early and advanced phases of CML (9). Acute lymphoblastic leukemia (ALL) is the most common cancer in childhood and includes several subtypes defined by genetic aberrations. Recently, it has been shown that cancer- propagating cell populations have a complex, branching-like subclonal structure, at least in the ETV6-RUNX1 þ and BCR- ABL1 þ subgroups (10,11). These cell pools provide units of selection in the evolutionary diversification and progression of disease. In line with these results, when paired diagnostic and relapse samples from patients with high-hyperdiploid ALL were examined, independent clones of genetically diverse pre- leukemic cell populations were found in the majority of cases tested (12). When scrutinizing follow-up samples of patients diagnosed with ETV6-RUNX1 þ ALL, our workgroup could also detect ancestral, pre-leukemic cells during the remission period, in which these cells can comprise a possible source of late relapses (13). In the studies mentioned previously, advanced technologies (i.e., multicolor interphase fluores- cence in situ hybridization [FISH], combined immunopheno- typing and FISH, motorized microscopy, array comparative genomic hybridization (CGH), and SNP array) were applied, each of which requires significant financial investment. The high cost of techniques needed to determine the relationship of clones dominating at presentation and relapse hampers Received March 6, 2012; received in revised form May 10, 2012; accepted May 14, 2012. * Corresponding author. E-mail address: K.Szuhai@lumc.nl 2210-7762/$ - see front matter Crown Copyright ª 2012 Published by Elsevier Inc. All rights reserved. http://dx.doi.org/10.1016/j.cancergen.2012.05.007 Cancer Genetics 205 (2012) 465e469