IDENTIFICATION OF FREQUENT GENOMIC ABNORMALITIES IN ADULT ACUTE MYELOID LEUKEMIA PATIENTS USING SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS

Introduction. Acute myeloid leukemia (AML) is a heterogeneous disease with various chromosomal aberrations. The karyotype at diagnosis provides important prognostic information that influences therapy and outcome of this disease. However, using conventional chromosome banding techniques alone, karyotype abnormalities are detected in only half of all AML cases. Aims.We sought to identify novel genomic regions of interest in normal karyotype AML and to identify novel candidate regions and disease-related genes in patients with complex karyotypes using genome-wide high resolution SNP-array. Patients and Methods. Samples from 57 AML patients with FAB-M0, M1, M2, M3, M4, M5, miscellaneous cytogenetic abnormalities and normal karyotype were examined. Genomic DNA was isolated from mononuclear AML cells and applied to GeneChip® Human Mapping 250K NspI and Genome-Wide Human SNP 6.0 array microarrays (Affymetrix, Santa Clara, CA) following the manufacturer’s instructions. Copy number aberrations were scored using the Hidden Markov Model and the segmentation approach available within the Partek software package as well as by visual inspection. All aberrations were calculated with respect to a set of 270 Hapmap normal individuals and a set of samples obtained from acute leukaemia cases in remission in order to reduce the noise of raw copy number data. When available, in order to exclude inherited copy number variants a comparison to paired constitutional DNA and to paired remission DNA was performed. Fluorescence in situ hybridization, quantitative PCR and nucleotide sequencing were used to confirm genomic alterations. Results. A wide spectrum of different genetic lesions (gains/losses) involving complete chromosome arms (del 16q, i(13q10), del 3p, del 7p, monosomy 9) or submicroscopic genomic intervals were identified in a substantial proportion of cases (55%) without differences in the frequency of losses or gains. Focal genetic alterations were detected at the breakpoints of previously cytogenetically identified chromosomal translocations, such as t(2;3)(p22-23)(q26-27) and t(1;11)(p32;q23). Hemizygous deletions were identified at 2q33.3-q34 involving ERBB4 (verb-a erythroblastic leukemia viral oncogene homolog 4 avian), at 9p21.3- p21.2 (CDKN2A-2B), at 12p13 (ETV6), at 17q12 (NF1) and 21q21.2 (RUNX1). Most frequent alterations affected the oncogene MYC at 8q24.13 - q24.21 (4.33 Mb), the ABC transporters genes ABCA8, ABCA9, ABCA6, ABCA5, ABCA10 at 17q24, PTPRM at 18p11.31-p11.23 and ERG at 21q22. Other recurring genetic lesions were uncommon and were identified only in single cases. Some lesions affected regions with a single gene, such as: ETAA1, FIGN, STK32B, PRAGMIN, PCM1, GLIS3, MRGPRX1, SESN3, BCL2L14 or lacking annotated genes. Marked differences in the combination of copy number anomalies were identified across the different genetic subtypes of AML. Patients with normal karyotype showed no relevant genetic alterations. Conclusions. These data demonstrated that, in contrast to adult acute lymphoblastic leukaemia (ALL), AML is characterized by relatively few recurring copy number alterations, and that spectrum of genetic anomalies is significantly associated with AML disease subtype. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Fondazione del Monte di Bologna e Ravenna, PIO project 2007, Strategico di Ateneo.