Typical numerical alterations in genome identified by array CGH analysis in neuroblastoma tumors

<abstract><sec> <title>Introduction</title> <p>The clinical variability in the course of neuroblastoma (NB) is closely linked to diverse genetic changes acquired by tumor cells. Rapid NB progression is associated with oncogene MYCN amplification (MNA) and segmental chromosomal aberrations (SCA). Alternatively, numerical chromosomal alterations (NCA) have positive impact on treatment. So far, no studies have been undertaken to identify NCA that may group NB patients. Therefore, the aim of the study was to identify NCA typical for NB.</p> </sec><sec> <title>Materials and methods</title> <p>Copy number alterations in NB tumor genome (fresh samples N = 94; formalin-fixed paraffin-embedded specimens N = 66) were analyzed with a pangenomic array CGH technique.</p> </sec><sec> <title>Results</title> <p>The profile with NCA was observed in 72 (45%) cases, NCA+SCA in 37 (23%), normal in 35 (22%) and MNA in 16 (10%). Samples with NCA were characterized by whole chromosome gains: 17, 7, 6 (78%, 65%, 51%, respectively) and copy loss of chromosome 14 (57%). Similarly to NCA, patients with a combined NCA and SCA profile were also characterized by gain of whole chromosome 17 and 7 (35% both) and loss of chromosome 14 (38%), but with lower frequency. In the combined NCA and SCA profiles, typical NB changes such as deletion 1p36 (27%) and gain 17q (41%) were observed, as well as deletion 11q (24%). The same alterations were detected in MNA samples (44%, 44%, 19%, respectively). A difference was found in spanning 11q deletion between MNA and NCA+SCA subgroup, which may suggest new prognostic markers in NB. In MNA subgroup specific NCA was not indicated.</p> </sec><sec> <title>Conclusions</title> <p>The hypothesis that NCA in NB tumors are more frequent in younger children with good prognosis was confirmed. To gain new insights into the pathogenesis of NB and to establish molecular targets for diagnosis and therapy, candidate genes in the altered chromosomal regions must be investigated.</p> </sec></abstract>

Genetic stratification of neuroblastoma for treatment tailoring

Neuroblastoma is the most common extracranial tumor of childhood. The clinical behavior is variable, ranging from spontaneous regression to fatal progression despite aggressive therapy. The most highly statistically significant and clinically relevant factors that are currently used for classification include stage, age, histopathologic category, MYCN oncogene status, chromosome 11q status and DNA ploidy. These genetic markers were analyzed separately by classical methods until recently: mainly fluorescence in situ hybridization or loss of heterozygosity. The development of genome-wide techniques such as comparative genomic hybridization, array comparative genomic hybridization and single nucleotide polymorphism allows the analysis of copy number variations through the whole genome in one step. This enabled the investigators to refine different genetic subtypes for the better comprehension of neuroblastoma tumor behavior and reach the conclusion that these data together with a genomic profile based on gene expression should be included in future treatment stratification.