Two-dimensional DNA electrophoresis identifies novel CpG islands frequently coamplified with MYCN in neuroblastoma

Background. Amplification of the oncogene MYCN in neuroblastoma has been fo und to correlate with aggressive tumour growth and is used as a predictor o f clinical outcome. The MYCN amplicon is known to involve coamplification o f extensive DNA regions. Therefore it is possible that other genes are coam plified in this amplicon and that they may play a role in the poor outcome of MYCN amplified tumours. Procedure. We have implemented an approach for t he two-dimensional separation of human genomic restriction fragments to det ect and isolate as yet unknown amplified sequences in the MYCN amplicon in neuroblastoma. Using this approach we have recently cloned a novel gene ref erred to as NAG that is frequently coamplified with MYCN in neuroblastoma. Results and Conclusions. We report here the identification and cloning of t wo ad-ditional CpG islands that are amplified in neuroblastoma. One contain s a sequence that is identical to the first intron of DDX1. The other repre sents a novel CpG island that is associated with an as yet unidentified gen e. We show that the novel CpG island is located in close proximity to the M YCN locus on chromosome 2 and is as frequently coamplified with MYCN in neu roblastoma as NAG and DDX1. Med. Pediatr. Oncol. 36:75-79, 2001. (C) 2001 W iley-Liss, Inc.