Abstract 3108: Copy number variation analysis in neuroblastoma through next generation sequencing data and SNP-microarray

Abstract

Abstract The childhood cancer neuroblastoma show high degree of clinical heterogeneity ranging from aggressive tumors with fatal outcome to cases of spontaneous regression. Analysis of recurrent chromosomal aberrations such as losses of 1p, 11q, gain of 1q, 17q and/or MYCN amplification are currently used for patient stratification and definition of therapeutic strategy. Different analysis techniques for detection of segmental abnormalities include FISH, CGH-microarrays or multiplex ligation-dependent probe amplification (MLPA). However, as next-generation sequencing (NGS) becomes available for clinical use, this could also be used for assessment of copy number alterations simultaneously with mutational analysis. In this study we compare genomic profiles generated through the bioinformatical tool Control-FREEC on Exome sequencing data with profiles generated from Affymetrix 250K or 50K SNP-microarrays on 20 NB tumors of different stages. Exome sequencing was performed by paired-end sequencing on Illumina instrumentation after DNA enrichment with Agilent SureSelect All Exome. The sequencing were performed at three separate occasions with a median raw coverage of 91X, 127X and 340X respectively. Neuroblastoma tumors were normalized with either corresponding constitutional DNA or normal control DNA for NGS data while microarrays were normalized against healthy control DNA. Gross genomic changes were extracted through visual and/or ratio inspection from 20 neuroblastoma tumors. A total of 128 larger segmental aberrations and 63 numerical aneuploidies were detected trough SNP-microarrays. Discrepancies between the two methods were detected in three cases; one segmental loss detected through microarray could not be confirmed by NGS-profiling, one smaller deletion were only detected through NGS-profiling and in one instance both methods indicated 2p-gain but at different positions. Otherwise the results were concordant. Furthermore, through exome sequencing data were we also able to detect ALK mutations in four patients, ATRX-deletions in two patients and chromothripsis of chromosome 5 in one patient. In conclusion, exome sequencing could be used as a new diagnostic tool for neuroblastoma tumors combining mutational screening with detection of common chromosomal and segmental aneuploidies such as 2p-gain, 17q-gain, 11q-deletion as well as MYCN-amplification and alterations of ALK or ATRX. Citation Format: Susanne Fransson, Malin Östenssson, Anna Djos, Niloufar Javanmardi, Per Kogner, Tommy Martinsson. Copy number variation analysis in neuroblastoma through next generation sequencing data and SNP-microarray. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3108. doi:10.1158/1538-7445.AM2014-3108