Genome-wide massively parallel sequencing to characterize genomic rearrangements in neuroblastoma: from unbalanced translocations to chromothripsis

Neuroblastoma (NB) is a cancer of the peripheral sympathetic nervous system observed in early childhood. Structural chromosome aberrations are emblematic of aggressive tumors. In the present paper, we investigated somatic rearrangements in two NB cell lines and two primary tumors using paired-end sequencing of mate-pair libraries. In cell lines, this approach allowed characterization of inter-chromosomal rearrangements corresponding to unbalanced translocations previously detected by spectral karyotyping and array-CGH. Our approach also revealed a large number of intra-chromosomal rearrangements. In one cell line, mate-pair analysis unexpectedly revealed a huge number of somatically acquired rearrangements between two regions of chromosomes 2p and 3p. This observation was compatible with the recently described phenomenon of chromothripsis and prompted us to investigated two primary NB tumors presenting with shattering of one or two specific chromosomes, previously detected by array-CGH. Mate-pair analysis confirmed the geographic localization of the rearrangements within one or two chromosomes and documented their diversity, consistent with the model of massive genomic rearrangements in a single cellular catastrophe. Using complementary experiments, we characterized 51 rearrangements in the four samples at the base pair resolution that revealed 59 breakpoints. Interestingly, in a subset of cases complex rearrangements were observed with templated insertion of fragments of nearby sequences. A detailed inspection of the breakpoints revealed frequent microhomologies at the junction points, both in cell lines and tumors. Altogether, our data suggest that both nonhomologous end-joining-mediated repair and replicative processes may account for genomic rearrangements in NB.