title: MYCN amplicon junctions as tumor-specific targets for minimal residual disease detection in neuroblastoma.
abstract: The MYCN gene is frequently amplified in unfavorable neuroblastoma tumors. Therefore, this study aimed at characterizing the novel junctions connecting the amplified DNA segments (amplicons) and obtaining tumor-specific PCR fragments for use in detecting minimal residual disease (MRD). High-density SNP arrays were used to map the end-points of the MYCN amplicons in a subset of neuroblastoma tumors. Primers were designed to give rise to a tumor-specific PCR product and were examined for MRD in the blood and bone marrow using quantitative PCR. Tumor-specific junction fragments were detected in all cases, confirming a head-to-tail tandem orientation of the amplicons and revealing microhomology at the amplicon junctions, thus suggesting a rolling circle caused by microhomology-mediated break-induced replication (MMBIR) as a possible mechanism initiating the MYCN amplification. We also evaluated the use of these junctions as tumor-specific targets for detecting MRD and observed that tumor DNA could be readily detected and quantified in either blood or bone marrow at a sensitivity of 1/106 tumor/control DNA. This study provides new information on the mechanisms of oncogene amplification and envisages means of rapidly obtaining highly sensitive PCR-based tools for tumor/patient-specific monitoring of treatment response and the early detection of relapse in patients with neuroblastoma.
authors.affiliation: Department of Clinical Genetics, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, SE-41345 Gothenburg, Sweden.
authors.forename: Hanna
authors.initials: H
authors.lastname: Kryh
authors.forename: Jonas
authors.initials: J
authors.lastname: Abrahamsson
authors.forename: Elsa
authors.initials: E
authors.lastname: Jegerås
authors.forename: Rose-Marie
authors.initials: RM
authors.lastname: Sjöberg
authors.forename: Irene
authors.initials: I
authors.lastname: Devenney
authors.forename: Per
authors.initials: P
authors.lastname: Kogner
authors.forename: Tommy
authors.initials: T
authors.lastname: Martinsson
mesh_terms: D001483:Base Sequence; D014408:Biomarkers, Tumor / Q000235:genetics*; D001853:Bone Marrow / Q000378:metabolism; D045744:Cell Line, Tumor; D004247:DNA / Q000097:blood; D005784:Gene Amplification / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D000071447:N-Myc Proto-Oncogene Protein; D018365:Neoplasm, Residual; D009447:Neuroblastoma / Q000175:diagnosis* / Q000235:genetics; D009687:Nuclear Proteins / Q000235:genetics*; D015513:Oncogene Proteins / Q000235:genetics*; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
chemical_list: D014408:Biomarkers, Tumor; C459801:MYCN protein, human; D000071447:N-Myc Proto-Oncogene Protein; D009687:Nuclear Proteins; D015513:Oncogene Proteins; D004247:DNA