ALBERT

Description: INTRODUCTION Five to 20% of patients with myeloproliferative neoplasms (MPN), including Essential Thrombocythemia (ET), Polycythemia Vera (PV) and Primary Myelofibrosis (PMF), transform to an aggressive secondary acute myeloid leukemia (sAML). While several studies reported the association of some mutations with the risk of leukemic transformation (Vannucchi AM et al, Leukemia 2013), the mechanisms that contribute to transformation from MPN to sAML remain largely poor characterized. METHODS. We collected annotated samples from 15 chronic-phase (CP) MPN patients (pts), 6 pts with accelerated phase (AP; PB blasts 10-19%) and 12 pts with sAML; for the latter, paired samples (chronic/blast phase-BP) were available. CP and BP samples were separated by a mean of 77 (12 to 216) months interval. We used Illumina whole exome sequencing (WES) to identify copy number variations (CNV) in all samples. In the paired samples set, we also performed long reads genome sequencing by the Oxford Nanopore technology, a uniform process that generates sequences randomly and independently, without classical sources of bias such as GC-content and mappability. Data analysis for CNV detection was performed by a novel devised computational package (Nano-GLADIATOR; Magi A, Bartalucci N et al, Genome Biology, submitted) allowing the analysis of individual samples without the need of paired-analysis. RESULTS. The mean number of CNV detected in CP, AP and BP samples was respectively 130.7±49, 132±42 and 177.4±61 (P=0.03 of BP vs CP). CNV were represented by gain of genomic material in 63.6%, 68.2% and 64.1% of CP, AP and BP. Considering the length of all CNV, expressed as base pairs (bp), we found that 96.8% of CNV in CP were focal alterations spanning 1Mb and 〉30Mb in BP samples were 14.4% (P=0.05) and 2.1% (P=0.04), and corresponding figures in AP were respectively 5.3% (ns vs CP, P=0.05 vs BP) and 0.7% (P=0.04 vs CP). Considering CNV 〉1Mb only, 53.7% were gains in CP compared with 68.1% in AP and 63.6% in BP, while losses were 46.3%, 31.9% and 36.4% respectively. Furthermore, alterations involving all the short (p) and long (q) -arm or the whole chromosome were found in 77% of BP compared to 36% of AP and 11% only of CP samples (P