title: Whole-genome sequencing identifies patient-specific DNA minimal residual disease markers in neuroblastoma.
abstract: PCR-based detection of minimal residual disease (MRD) in neuroblastoma is currently based on RNA markers; however, expression of these targets can vary, and only paired-like homeobox 2b has no background expression. We investigated whether chromosomal breakpoints, identified by whole-genome sequencing (WGS), can be used as patient-specific DNA MRD markers. WGS data were used to develop large numbers of real-time PCRs specific for tumors of eight patients. These PCRs were used to quantify chromosomal breakpoints in primary tumor and bone marrow samples. Finally, the DNA breakpoints with the highest abundance were compared with a panel of RNA markers. By WGS we identified 42 chromosomal breakpoints in tumor samples from eight patients and developed specific quantitative real-time PCRs for each breakpoint. The tumor-specific breakpoints were all present in bone marrow at diagnosis. For one patient slight clonal selection was observed in response to treatment. Positivity of DNA MRD markers preceded disease progression in four of five patients; in one patient the RNA markers remained negative. For 16 of 22 samples MRD levels determined by RNA and DNA were comparable and in 6 of 22 samples higher MRD levels were detected by DNA markers. DNA breakpoints used as MRD targets in neuroblastoma are reliable and stable markers. In addition, this technique might be applicable for detecting tumor cells in other types of cancer.
authors.affiliation: Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Landsteiner Laboratory, Department of Pediatric Oncology, Emma Children's Hospital, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Esther M
authors.initials: EM
authors.lastname: van Wezel
authors.affiliation: Department of Oncogenomics, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Danny
authors.initials: D
authors.lastname: Zwijnenburg
authors.affiliation: Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Lily
authors.initials: L
authors.lastname: Zappeij-Kannegieter
authors.affiliation: Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Bus
authors.affiliation: Department of Pediatric Oncology, Sophia Children's Hospital, Erasmus Medical Center, Rotterdam, the Netherlands.
authors.forename: Max M
authors.initials: MM
authors.lastname: van Noesel
authors.affiliation: Department of Oncogenomics, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Jan J
authors.initials: JJ
authors.lastname: Molenaar
authors.affiliation: Department of Oncogenomics, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Rogier
authors.initials: R
authors.lastname: Versteeg
authors.affiliation: Department of Biostatistics, Leiden University Medical Center, Leiden, the Netherlands; Dutch Childhood Oncology Group, The Hague, the Netherlands.
authors.forename: Marta
authors.initials: M
authors.lastname: Fiocco
authors.affiliation: Landsteiner Laboratory, Department of Pediatric Oncology, Emma Children's Hospital, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Huib N
authors.initials: HN
authors.lastname: Caron
authors.affiliation: Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: C Ellen
authors.initials: CE
authors.lastname: van der Schoot
authors.affiliation: Department of Oncogenomics, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Koster
authors.affiliation: Landsteiner Laboratory, Department of Pediatric Oncology, Emma Children's Hospital, Academical Medical Center, University of Amsterdam, Amsterdam, the Netherlands. Electronic address: g.a.tytgat@amc.uva.nl.
authors.forename: Godelieve A M
authors.initials: GA
authors.lastname: Tytgat
mesh_terms: D000970:Antineoplastic Agents / Q000627:therapeutic use; D014408:Biomarkers, Tumor / Q000235:genetics*; D001853:Bone Marrow / Q000378:metabolism / Q000473:pathology; D002648:Child; D002675:Child, Preschool; D056905:Chromosome Breakpoints; D005260:Female; D005819:Genetic Markers; D015894:Genome, Human; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007223:Infant; D008297:Male; D009367:Neoplasm Staging; D018365:Neoplasm, Residual / Q000188:drug therapy / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D009447:Neuroblastoma / Q000188:drug therapy / Q000235:genetics* / Q000401:mortality / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D016019:Survival Analysis
chemical_list: D000970:Antineoplastic Agents; D014408:Biomarkers, Tumor; D005819:Genetic Markers