Abstract 3185: Whole genome sequencing for precision medicine in high-risk neuroblastoma patients: Translation from research to clinical practice in Sweden
Authors: Susanne M. Fransson, Angela Martinez-Monleon, Susanne Reinsbach, Per Sikora, Rosa-Marie Sjoberg, Per Kogner, Tommy Martinsson
Journal: Cancer Research (2018)

Abstract The overall survival of children presenting high-risk neuroblastoma is about 40 %, implying an urgent need for rapid improvement in treatment options and strategies for this particular patient group. Clinical use of next-generation sequencing provides a comprehensive approach for rapid determination of genomic biomarkers for diagnosis/prognosis, and of foremost importance, to achieve precision treatment based on the patients' specific tumor targets. Whole genome sequencing (WGS) was performed on tumor DNA and constitutional DNA for 30 neuroblastoma patients, both retrospective samples and a subset of patients with progressive disease despite ongoing treatment. Sequencing was performed using Illumina instrumentation for an average coverage of at least 60X and 30X for tumor 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. Remaining variants were assessed manually through the Integrative Genomics Viewer. Somatic variants and CNVs were evaluated through Qiagen Clinical Insight in relation to clinical significance and action-ability. In our present setting the approximate time for handling is 2,5-3 weeks, counting from arrival of material to analyzed data. The analysis includes copy number variations, structural aberrations and mutational screening. These alterations have then been thoroughly evaluated with regards to biological relevance and druggability, looking for drugs either used in existing cancer treatment or in clinical trials. Among the 30 patients, potentially actionable targets were detected in 14 (47%) of the cases; including aberrations in ALK, CDK4/MDM2, CDKN2A, CCND1, ROCK2 or FLT1. Inconclusive results were seen for 16 patients. This included seven patients where no actionable target were detected and nine patients with weak support for targeted treatment. The latter group includes patients with either TERT-rearrangements or alterations in different mitogen-associated kinases. Our results demonstrate the feasibility to incorporate WGS in clinical practice. A logistic and analytic pipeline has been established in order to present the results in a clinically meaningful time frame. Actionable targets that could be relevant in therapy were detected in 14 out of 30 neuroblastoma patients. The result from this study show promising results and we predict that integration of WGS in clinical routine will lead to improved management of the therapeutically most challenged group. Citation Format: Susanne M. Fransson, Angela Martinez-Monleon, Susanne Reinsbach, Per Sikora, Rosa-Marie Sjoberg, Per Kogner, Tommy Martinsson. Whole genome sequencing for precision medicine in high-risk neuroblastoma patients: Translation from research to clinical practice in Sweden [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3185.