Abstract B49: Genome-wide analysis of liquid biopsies reveals a novel layer of tumorheterogeneity in neuroblastoma

Abstract

Abstract Purpose: For 60% of high risk neuroblastoma patients this tumor is still a deadly disease. Even though great progress has been achieved over the last decades concerning molecular classifiers and drug targets, most of the results are based on single biopsies of bulky tumors. However, recent data show that neuroblastoma tumors are frequently inhomogeneous and that driver mutations are frequently not, or only in a sub-clone, detectable in the primary tumor. To bypass intra-tumor heterogeneity and the frequently insufficient tumor tissue, alternative strategies need to be evaluated to overcome these limitations. Isolating cell-free tumor DNA from more easily accessible patient biomaterial sources could surmount these challenges. We investigated the feasibility in neuroblastoma patients of cell-free peripheral blood (PB) and bone marrow (BM) plasma for tumor genome analyses. Experimental Design: Cell-free DNA, isolated from 126 plasma samples from 24 stage M neuroblastoma patients and ultrahigh-density SNP array (UHD SNP) data from 19 samples were compared with UHD SNP array and I-FISH data from the corresponding tumor or enriched disseminated tumor cells from bone marrow (BM-DTCs) samples. Results: Genomic aberrations were retrieved from 14/19 cfDNA samples. MYCN amplification or other amplified sequences and all typical segmental chromosomal aberrations (SCA) besides atypical aberrations and micro-deletions or small gains could be unambiguously identified. Most genomic aberrations detected in cell-free tumor DNA from our patient cohort were identical to aberrations detected in other tumor cell sources from the same patient. While genomic aberrations detected in cell-free tumor DNA from BM plasma or BM-DTCs were completely identical (3/3), discordances were detected between BM and PB plasma samples obtained at the same time point and tumor tissue (1/1) sources. Conclusions: Cell-free tumor DNA may serve as an additional source for tumor genome analyses, not only in cases for which biopsy or surgical interventions carry a high risk for the patient, but especially to detect additional genetically distinct tumor clones frequently not visible in the primary tumor. Our findings contradict the widely accepted view that all bodily fluids yield an identical picture of tumor genetics. Comparing datasets from different intra-patient locations will produce a more complete representation of tumor heterogeneity, thus improving our understanding of tumor dynamics and progression in individual patients. Citation Format: Sophia C. Huetter, Diana S. Walder, Clemens Brunner, Reza M. Abbasi, Fikret Rifatbegovic, Caroline Hutter, Ruth Ladenstein, Inge M. Ambros, Peter F. Ambros. Genome-wide analysis of liquid biopsies reveals a novel layer of tumorheterogeneity in neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr B49.