Abstract 1692: Genomic changes in relapsed neuroblastoma

Abstract

Abstract Neuroblastoma (NB) is an aggressive pediatric malignancy originating from the sympathetic nervous system. Despite recent improvements in multimodal treatment, survival for children diagnosed with high-risk NB, remains below 50% at 5 years from treatment. Although an initial response to treatment is seen in a majority of patients, a significant portion will subsequently relapse with lesions resistant to standard therapy and for NB patients with relapsed or refractory metastatic disease, survival is below 10%. Genetic risk factors previously identified in primary neuroblastoma include MYCN-amplification, 11q-deletion, 1p-deletion and 17q gain and activating ALK mutations. However, treatment resistant tumors will likely have novel genetic aberrations differing from those present at time of diagnosis. To investigate the genetic mechanisms linked to recurrent disease, alterations between five triplet samples of primary tumor, relapsed/refractory tumor and constitutional DNA was investigated through whole genome sequencing. Sequencing was performed using Illumina instrumentation for an average coverage of at least 60X and 30X for tumor samples and normal tissue respectively. Read trimming, mapping to hg19 and variant calling were performed using the CLC Genomics Workbench software while copy number profiles were prepared through the CANVAS software. Systematic filtering was performed using the Ingenuity variant analysis tool. Variants with allele frequency above 3% in common population based cohorts were discarded as well as excluding all synonymous variants or variants in non-coding regions except those affecting canonical splice sites. A median of 21 and 59 non-silent somatic variants were detected in diagnostic and in relapsed samples respectively, while the median number of segmental alterations were 31 in diagnostic samples and 35 in relapse samples. Genes with recurrent alterations that emerged in relapse samples includes CCND1, CDK5RAP1, POLR2A, LSAMP, C3 and CARNS1. One patient showed only one single alteration common between primary and relapse; a t(11;17) resulting 11q-deletion and 17q-gain. The paired tumors did both have CCND1-gain although with different breakpoints and 6p-gain but of different parental alleles. In addition, in one patient an ARID1B mutation was detected in primary tumor but lost in the relapsed sample where an ARID1A mutation had emerged, which could indicate parallel evolution. Gene set analysis of variants in relapsed samples showed no significant functional enrichment differing from primary tumors where cell projection, Rap1-signaling and neuron part showed enrichment. In this study we investigated the genomes of primary and relapsed NB for five patients. We show that mutation load is higher in relapsed NB and includes alterations of previously linked to NB such as ATRX, TERT and CCND1 but lacked alterations in ALK, RAS or other genes of the RAS/MAPK pathway. Citation Format: Susanne Fransson, Angela Martinez Monleon, Anna Djos, Susanne Reinsbach, Rose-Marie Sjoberg, Per Sikora, Per Kogner, Tommy Martinsson. Genomic changes in relapsed neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1692.