Abstract
The aim of this study was to compare next-generation sequencing (NGS) with the traditional fluorescence in situ hybridization (FISH) for detecting segmental chromosomal aberrations (SCAs) such as 1p deletion, 11q deletion and 17q gain, which are well-known predictive markers for adverse outcome in neuroblastoma. The tumor tissue obtained from 35 patients with neuroblastoma was tested by FISH and targeted NGS, which is specially designed to detect copy number alterations across the entire chromosomal region in addition to mutations in 353 cancer-related genes. All chromosomal copy number alterations were analyzed using the copy number variation plot derived from targeted NGS. FISH was performed to detect 1p deletion, 11q deletion and 17q gain. The copy numbers of 1p, 11q, and 17q obtained via NGS were correlated with those acquired via FISH. The SCAs determined by NGS were matched with those by FISH. Most 17q gain of mismatched cases detected by NGS alone showed a subsegmental gain of 17q. FISH revealed 11q deletion and 17q gain in a few tumor cells of two cases, which were not detected by NGS. NGS can be a sensitive complementary and alternative method to the conventional FISH for detecting SCAs.
Highlights
Neuroblastoma (NB) is a pediatric solid tumor and the most common extracranial neoplasm among children aged 1–14 years [1]
We found that 1p deletion was statistically correlated with stage 4 by next-generation sequencing (NGS) and unfavorable International Neuroblastoma Pathology Classification (INPC) histology by fluorescence in situ hybridization (FISH)
Even though the other segmental chromosomal aberrations (SCAs) were not correlated with MYCN amplification, 17q gain was detected in two out of three cases and 11q deletion was not detected in none of three cases, which showed the similar tendency to previous studies [18,19,20,24]
Summary
Neuroblastoma (NB) is a pediatric solid tumor and the most common extracranial neoplasm among children aged 1–14 years [1]. It is derived from the neural crest precursor cells of the sympathetic nervous system. FISH has been an important tool in the molecular diagnosis of various chromosomal abnormalities, including gain, deletions, and translocations, which are detecting by locus-specific probes targeting at specific DNA sequences. NGS has been applied to detect single nucleotide variations and copy number variations of multiple genes as well as gene fusions, which play a significant role in diagnosis, prediction of outcome, and potential targeted cancer therapy of solid tumors [10].
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