Abstract 5258: Genomic characterization and targeted resequencing of high-risk neuroblastoma (the neuroblastoma TARGET)
Authors: Attiyeh Edward F. , Hogarty Michael D. , Mossé Yaël P. , Diskin Sharon J. , Hakonarson Hakon , Asgharzadeh Shahab , Sposto Richard , London Wendy B. , Gastier-Foster Julie M. , Gerhard Daniela S. , Smith Malcolm A. , Zhang Jinghui , Khan Javed , Seeger Robert C. , Maris John M. 
Published: February 2011

Abstract
Background: Neuroblastoma (NB) is a childhood malignancy of the peripheral nervous system. Although genomic changes (MYCN amplification, 1p LOH, 11q LOH, and hyperdiploidy) are associated with clinical outcome and help define a high-risk group, there are few genes known to be mutated in NB and no genomic aberrations predictive of relapse within this group. The NB TARGET (Therapeutically Applicable Research to Generate Effective Treatments) collaborative research initiative aims to discover novel therapeutic targets and genomic predictors of outcome in an unbiased systematic fashion.
Methods: Whole genome copy number (CN) changes were assayed for using the Illumina HumanHap550 SNP array in 631 highly annotated NB specimens, and genes from regions of recurrent aberration were selected for resequencing. Relative CN was derived from absolute CN (OverUnder), and regions recurrently lost or gained were determined using a statistical test for significance across the sample set (GISTIC).
Results: Low- and intermediate-risk NB cases showed recurrent whole chromosome (WC) gains of chromosomes 2, 7, 12, 13, and 17. In contrast, high-risk cases showed segmental gains in those same chromosomes (2p, 7q, 12q, 13q, and 17q). A similar pattern was found for CN losses: lower-risk cases had WC losses of 3, 4, 9, 11, 14, 19, and 21 (as well as 16) while high-risk cases had segmental losses of 3p, 4p, 9p, 11q, 14q, 19p, 19q, and 21q (as well as 1p and 5p). Candidate genes from within the regions of CN aberration were prioritized, and 117 genes and microRNAs were resequenced in 188 high-risk NB samples. Analysis to date of over 680,000 traces revealed 841 sequence variants that passed strict filtering criteria. Non-silent sequence variants were found in 79/117 genes (range of cases with variants per gene: 1-19). Ongoing resequencing of matched constitutional DNA revealed that 88% of variants were present in the germline, but putative somatic mutations were discovered in several candidate genes at low frequency (ANAPC5 and IGSF21 in 2/188 cases; ETS1, NCAM1, and NRAS in 1/188 cases), suggesting a low frequency of overall somatic mutation in this gene set.
Conclusions: Although the same chromosomes have aberrant CN in both the lower-risk and high-risk groups, the type of aberration (WC vs. segmental) clearly differed, with the high-risk group showing segmental aberrations and the lower-risk group showing WC aberrations for all overlapping regions. This suggests differing mechanisms for genomic rearrangement and reveals potential loci of interest. The low frequency of somatic mutation found by targeted resequencing of genes selected from the large regions of genomic aberration underlines the need for unbiased whole genome sequencing approaches to discover mutated genes in NB.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5258.