Abstract 926: Whole genome and transcriptome sequencing defines the spectrum of somatic changes in high-risk neuroblastoma

Abstract

Abstract The NCI's Therapeutically Applicable Research to Generate Effective Targets (TARGET) initiative uses state-of-the-art genome-wide approaches to identify therapeutic targets for pediatric cancers. Applications of 2nd-generation sequencing technologies to the analysis of adult solid tumors and hematopoietic malignancies have led to novel, often clinically relevant insights into these diseases. The objective of this study is to utilize 2nd-generation sequencing approaches on a highly annotated set of ten high-risk neuroblastomas (NBLs). We performed whole genome shotgun sequencing of six stage 4 MYCN-non-amplified and four stage 4 MYCN-amplified NBL TARGET cases and matched peripheral blood, as well as whole transcriptome sequencing (RNA-Seq) of the corresponding tumor RNA. The tumor and normal genomes were sequenced to 30X haploid coverage, and an average 10.3 Gb of aligned sequence was generated for each tumor transcriptome. The level of sequencing redundancy allowed us to achieve at least 10X coverage across 90% of the genome enabling genome-wide detection of sequence and copy number changes in the tumor DNA. We used alignment and de novo assembly approaches to identify somatic and germline SNVs, indels, structural variants, regions of copy number gains and losses, and genome rearrangements. We used RNA-Seq data to determine whether the detected sequence changes were expressed, and to identify transcripts differentially or alternatively expressed between MYCN-amplified and non-amplified cases. Our analysis of tumor and normal genomes identified an average of 1664 candidate somatic mutations per case, the majority of which were SNVs and small indels falling within introns or intergenic sequence. We also detected two candidate germline mutations in the ALK oncogene, one of which was previously characterized in NBL. An average of 10% of candidate somatic mutations in coding sequence was expressed in the transcriptome representing candidate oncogenic events. In addition, we detected and validated using PCR 9 novel genomic rearrangements resulting in expressed products, 5 of which were somatic and 4 of which were germline. We report on two novel somatic gene fusions, between TRIM37 on chromosome 17 and RNF121 on chromosome 11, and between LSAMP and STAG1 on chromosome 3, previously uncharacterized in NBL. The fusions did not recur in our sample set. This work provides an initial genome-wide view of the landscape of somatic changes that occur in high-risk neuroblastoma and highlights novel candidate oncogenic events that may drive the malignancy. Ongoing efforts will catalogue discovered somatic mutation frequencies in a large set of cases and explore the role of germline DNA variations in NBL tumorigenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 926. doi:10.1158/1538-7445.AM2011-926