Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma
Identifieur interne : 002B39 ( Main/Merge ); précédent : 002B38; suivant : 002B40Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma
Auteurs : Anneleen Decock [Belgique] ; Maté Ongenaert [Belgique] ; Robrecht Cannoodt [Belgique] ; Kimberly Verniers [Belgique] ; Bram De Wilde [Belgique] ; Geneviève Laureys [Belgique] ; Nadine Van Roy [Belgique] ; Ana P. Berbegall [Espagne] ; Julie Bienertova-Vasku [République tchèque] ; Nick Bown [Royaume-Uni] ; Nathalie Clément [France] ; Valérie Combaret [France] ; Michelle Haber [Australie] ; Claire Hoyoux [Belgique] ; Jayne Murray [Australie] ; Rosa Noguera [Espagne] ; Gaelle Pierron [France] ; Gudrun Schleiermacher [France] ; Johannes H. Schulte [Allemagne] ; Ray L. Stallings [Irlande (pays)] ; Deborah A. Tweddle [Royaume-Uni] ; Katleen De Preter [Belgique] ; Frank Speleman [Belgique] ; Jo Vandesompele [Belgique]Source :
- Oncotarget [ 1949-2553 ] ; 2015.
Descripteurs français
- KwdFr :
- ADN tumoral (génétique), Biologie informatique, Cellules cancéreuses en culture, Femelle, Humains, Ilots CpG (génétique), Marqueurs biologiques (analyse), Mâle, Méthylation de l'ADN, Neuroblastome (diagnostic), Neuroblastome (génétique), Nourrisson, Pronostic, Réaction de polymérisation en chaine en temps réel, Sites de fixation, Stade de la tumeur, Études de cohortes.
- MESH :
- analyse : Marqueurs biologiques.
- diagnostic : Neuroblastome.
- génétique : ADN tumoral, Ilots CpG, Neuroblastome.
- Biologie informatique, Cellules cancéreuses en culture, Femelle, Humains, Mâle, Méthylation de l'ADN, Nourrisson, Pronostic, Réaction de polymérisation en chaine en temps réel, Sites de fixation, Stade de la tumeur, Études de cohortes.
English descriptors
- KwdEn :
- Binding Sites, Biomarkers (analysis), Cohort Studies, Computational Biology, CpG Islands (genetics), DNA Methylation, DNA, Neoplasm (genetics), Female, Humans, Infant, Male, Neoplasm Staging, Neuroblastoma (diagnosis), Neuroblastoma (genetics), Prognosis, Real-Time Polymerase Chain Reaction, Tumor Cells, Cultured.
- MESH :
- chemical , analysis : Biomarkers.
- diagnosis : Neuroblastoma.
- genetics : CpG Islands, DNA, Neoplasm, Neuroblastoma.
- Binding Sites, Cohort Studies, Computational Biology, DNA Methylation, Female, Humans, Infant, Male, Neoplasm Staging, Prognosis, Real-Time Polymerase Chain Reaction, Tumor Cells, Cultured.
Abstract
Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in
Url:
PubMed: 26646589
PubMed Central: 4811509
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Berbegall</name><affiliation wicri:level="1"><nlm:aff id="A7"> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Bienertova Vasku, Julie" sort="Bienertova Vasku, Julie" uniqKey="Bienertova Vasku J" first="Julie" last="Bienertova-Vasku">Julie Bienertova-Vasku</name><affiliation wicri:level="3"><nlm:aff id="A8"> Department of Pathological Physiology, Department of Pediatric Oncology, Masaryk University, Černopolní, Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea> Department of Pathological Physiology, Department of Pediatric Oncology, Masaryk University, Černopolní, Brno</wicri:regionArea><placeName><settlement type="city">Brno</settlement><region>Moravie</region></placeName></affiliation></author><author><name sortKey="Bown, Nick" sort="Bown, Nick" uniqKey="Bown N" first="Nick" last="Bown">Nick Bown</name><affiliation wicri:level="1"><nlm:aff id="A9"> Northern Genetics Service, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea> Northern Genetics Service, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne</wicri:regionArea><wicri:noRegion>Newcastle upon Tyne</wicri:noRegion></affiliation></author><author><name sortKey="Clement, Nathalie" sort="Clement, Nathalie" uniqKey="Clement N" first="Nathalie" last="Clément">Nathalie Clément</name><affiliation wicri:level="3"><nlm:aff id="A10"> Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Combaret, Valerie" sort="Combaret, Valerie" uniqKey="Combaret V" first="Valérie" last="Combaret">Valérie Combaret</name><affiliation wicri:level="3"><nlm:aff id="A11"> Centre Léon Bérard, Laboratoire de Recherche Translationnelle, rue Laennec, Lyon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Centre Léon Bérard, Laboratoire de Recherche Translationnelle, rue Laennec, Lyon</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Lyon</settlement></placeName></affiliation></author><author><name sortKey="Haber, Michelle" sort="Haber, Michelle" uniqKey="Haber M" first="Michelle" last="Haber">Michelle Haber</name><affiliation wicri:level="1"><nlm:aff id="A12"> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW</wicri:regionArea><wicri:noRegion>Randwick NSW</wicri:noRegion></affiliation></author><author><name sortKey="Hoyoux, Claire" sort="Hoyoux, Claire" uniqKey="Hoyoux C" first="Claire" last="Hoyoux">Claire Hoyoux</name><affiliation wicri:level="1"><nlm:aff id="A13"> Pediatric Hemato-oncology, CHR Citadelle, Liège, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Pediatric Hemato-oncology, CHR Citadelle, Liège</wicri:regionArea><wicri:noRegion>Liège</wicri:noRegion></affiliation></author><author><name sortKey="Murray, Jayne" sort="Murray, Jayne" uniqKey="Murray J" first="Jayne" last="Murray">Jayne Murray</name><affiliation wicri:level="1"><nlm:aff id="A12"> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW</wicri:regionArea><wicri:noRegion>Randwick NSW</wicri:noRegion></affiliation></author><author><name sortKey="Noguera, Rosa" sort="Noguera, Rosa" uniqKey="Noguera R" first="Rosa" last="Noguera">Rosa Noguera</name><affiliation wicri:level="1"><nlm:aff id="A7"> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Pierron, Gaelle" sort="Pierron, Gaelle" uniqKey="Pierron G" first="Gaelle" last="Pierron">Gaelle Pierron</name><affiliation wicri:level="3"><nlm:aff id="A14"> Unité de Génétique Somatique, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Unité de Génétique Somatique, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schleiermacher, Gudrun" sort="Schleiermacher, Gudrun" uniqKey="Schleiermacher G" first="Gudrun" last="Schleiermacher">Gudrun Schleiermacher</name><affiliation wicri:level="3"><nlm:aff id="A15"> U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schulte, Johannes H" sort="Schulte, Johannes H" uniqKey="Schulte J" first="Johannes H." last="Schulte">Johannes H. Schulte</name><affiliation wicri:level="1"><nlm:aff id="A16"> Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, HufelandstraΔe, Essen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea> Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, HufelandstraΔe, Essen</wicri:regionArea><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion></affiliation></author><author><name sortKey="Stallings, Ray L" sort="Stallings, Ray L" uniqKey="Stallings R" first="Ray L." last="Stallings">Ray L. Stallings</name><affiliation wicri:level="1"><nlm:aff id="A17"> National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea> National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin</wicri:regionArea><wicri:noRegion>Dublin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A18"> Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea> Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, Dublin</wicri:regionArea><wicri:noRegion>Dublin</wicri:noRegion></affiliation></author><author><name sortKey="Tweddle, Deborah A" sort="Tweddle, Deborah A" uniqKey="Tweddle D" first="Deborah A." last="Tweddle">Deborah A. Tweddle</name><affiliation wicri:level="1"><nlm:aff id="A19"> Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea> Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne</wicri:regionArea><wicri:noRegion>Newcastle upon Tyne</wicri:noRegion></affiliation></author><author><name sortKey="De Preter, Katleen" sort="De Preter, Katleen" uniqKey="De Preter K" first="Katleen" last="De Preter">Katleen De Preter</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3"> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Vandesompele, Jo" sort="Vandesompele, Jo" uniqKey="Vandesompele J" first="Jo" last="Vandesompele">Jo Vandesompele</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3"> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26646589</idno><idno type="pmc">4811509</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811509</idno><idno type="RBID">PMC:4811509</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000570</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000570</idno><idno type="wicri:Area/Pmc/Curation">000570</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000570</idno><idno type="wicri:Area/Pmc/Checkpoint">000E62</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000E62</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">002517</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002517</idno><idno type="wicri:Area/PubMed/Curation">002449</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002449</idno><idno type="wicri:Area/PubMed/Checkpoint">002449</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002449</idno><idno type="wicri:Area/Ncbi/Merge">002E35</idno><idno type="wicri:Area/Ncbi/Curation">002E35</idno><idno type="wicri:Area/Ncbi/Checkpoint">002E35</idno><idno type="wicri:Area/Main/Merge">002B39</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma</title><author><name sortKey="Decock, Anneleen" sort="Decock, Anneleen" uniqKey="Decock A" first="Anneleen" last="Decock">Anneleen Decock</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Ongenaert, Mate" sort="Ongenaert, Mate" uniqKey="Ongenaert M" first="Maté" last="Ongenaert">Maté Ongenaert</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation></author><author><name sortKey="Cannoodt, Robrecht" sort="Cannoodt, Robrecht" uniqKey="Cannoodt R" first="Robrecht" last="Cannoodt">Robrecht Cannoodt</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3"> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A4"> DAMBI, VIB Inflammation Research Center, Technologiepark, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> DAMBI, VIB Inflammation Research Center, Technologiepark, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="4"><nlm:aff id="A5"> Department of Respiratory Medicine, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Department of Respiratory Medicine, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation></author><author><name sortKey="Verniers, Kimberly" sort="Verniers, Kimberly" uniqKey="Verniers K" first="Kimberly" last="Verniers">Kimberly Verniers</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="De Wilde, Bram" sort="De Wilde, Bram" uniqKey="De Wilde B" first="Bram" last="De Wilde">Bram De Wilde</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A6"> Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Laureys, Genevieve" sort="Laureys, Genevieve" uniqKey="Laureys G" first="Geneviève" last="Laureys">Geneviève Laureys</name><affiliation wicri:level="1"><nlm:aff id="A6"> Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Department of Pediatric Hematology and Oncology, Ghent University Hospital, De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Van Roy, Nadine" sort="Van Roy, Nadine" uniqKey="Van Roy N" first="Nadine" last="Van Roy">Nadine Van Roy</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Berbegall, Ana P" sort="Berbegall, Ana P" uniqKey="Berbegall A" first="Ana P." last="Berbegall">Ana P. Berbegall</name><affiliation wicri:level="1"><nlm:aff id="A7"> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Bienertova Vasku, Julie" sort="Bienertova Vasku, Julie" uniqKey="Bienertova Vasku J" first="Julie" last="Bienertova-Vasku">Julie Bienertova-Vasku</name><affiliation wicri:level="3"><nlm:aff id="A8"> Department of Pathological Physiology, Department of Pediatric Oncology, Masaryk University, Černopolní, Brno, Czech Republic</nlm:aff><country xml:lang="fr">République tchèque</country><wicri:regionArea> Department of Pathological Physiology, Department of Pediatric Oncology, Masaryk University, Černopolní, Brno</wicri:regionArea><placeName><settlement type="city">Brno</settlement><region>Moravie</region></placeName></affiliation></author><author><name sortKey="Bown, Nick" sort="Bown, Nick" uniqKey="Bown N" first="Nick" last="Bown">Nick Bown</name><affiliation wicri:level="1"><nlm:aff id="A9"> Northern Genetics Service, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea> Northern Genetics Service, Institute of Genetic Medicine, Central Parkway, Newcastle upon Tyne</wicri:regionArea><wicri:noRegion>Newcastle upon Tyne</wicri:noRegion></affiliation></author><author><name sortKey="Clement, Nathalie" sort="Clement, Nathalie" uniqKey="Clement N" first="Nathalie" last="Clément">Nathalie Clément</name><affiliation wicri:level="3"><nlm:aff id="A10"> Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Combaret, Valerie" sort="Combaret, Valerie" uniqKey="Combaret V" first="Valérie" last="Combaret">Valérie Combaret</name><affiliation wicri:level="3"><nlm:aff id="A11"> Centre Léon Bérard, Laboratoire de Recherche Translationnelle, rue Laennec, Lyon, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Centre Léon Bérard, Laboratoire de Recherche Translationnelle, rue Laennec, Lyon</wicri:regionArea><placeName><region type="region">Auvergne-Rhône-Alpes</region><region type="old region">Rhône-Alpes</region><settlement type="city">Lyon</settlement></placeName></affiliation></author><author><name sortKey="Haber, Michelle" sort="Haber, Michelle" uniqKey="Haber M" first="Michelle" last="Haber">Michelle Haber</name><affiliation wicri:level="1"><nlm:aff id="A12"> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW</wicri:regionArea><wicri:noRegion>Randwick NSW</wicri:noRegion></affiliation></author><author><name sortKey="Hoyoux, Claire" sort="Hoyoux, Claire" uniqKey="Hoyoux C" first="Claire" last="Hoyoux">Claire Hoyoux</name><affiliation wicri:level="1"><nlm:aff id="A13"> Pediatric Hemato-oncology, CHR Citadelle, Liège, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Pediatric Hemato-oncology, CHR Citadelle, Liège</wicri:regionArea><wicri:noRegion>Liège</wicri:noRegion></affiliation></author><author><name sortKey="Murray, Jayne" sort="Murray, Jayne" uniqKey="Murray J" first="Jayne" last="Murray">Jayne Murray</name><affiliation wicri:level="1"><nlm:aff id="A12"> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea> Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Randwick NSW</wicri:regionArea><wicri:noRegion>Randwick NSW</wicri:noRegion></affiliation></author><author><name sortKey="Noguera, Rosa" sort="Noguera, Rosa" uniqKey="Noguera R" first="Rosa" last="Noguera">Rosa Noguera</name><affiliation wicri:level="1"><nlm:aff id="A7"> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia, Spain</nlm:aff><country xml:lang="fr">Espagne</country><wicri:regionArea> Department of Pathology, Medical School, University of Valencia, and Health Research Institute INCLIVA, Blasco Ibañez, Valencia</wicri:regionArea><wicri:noRegion>Valencia</wicri:noRegion></affiliation></author><author><name sortKey="Pierron, Gaelle" sort="Pierron, Gaelle" uniqKey="Pierron G" first="Gaelle" last="Pierron">Gaelle Pierron</name><affiliation wicri:level="3"><nlm:aff id="A14"> Unité de Génétique Somatique, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> Unité de Génétique Somatique, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schleiermacher, Gudrun" sort="Schleiermacher, Gudrun" uniqKey="Schleiermacher G" first="Gudrun" last="Schleiermacher">Gudrun Schleiermacher</name><affiliation wicri:level="3"><nlm:aff id="A15"> U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea> U830 INSERM, Recherche Translationelle en Oncologie Pédiatrique (RTOP) and Department of Pediatric Oncology, Institut Curie, rue d'Ulm, Paris</wicri:regionArea><placeName><region type="region">Île-de-France</region><region type="old region">Île-de-France</region><settlement type="city">Paris</settlement></placeName></affiliation></author><author><name sortKey="Schulte, Johannes H" sort="Schulte, Johannes H" uniqKey="Schulte J" first="Johannes H." last="Schulte">Johannes H. Schulte</name><affiliation wicri:level="1"><nlm:aff id="A16"> Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, HufelandstraΔe, Essen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea> Department of Pediatric Oncology and Hematology, University Children's Hospital Essen, HufelandstraΔe, Essen</wicri:regionArea><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion><wicri:noRegion>Essen</wicri:noRegion></affiliation></author><author><name sortKey="Stallings, Ray L" sort="Stallings, Ray L" uniqKey="Stallings R" first="Ray L." last="Stallings">Ray L. Stallings</name><affiliation wicri:level="1"><nlm:aff id="A17"> National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea> National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin</wicri:regionArea><wicri:noRegion>Dublin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A18"> Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, Dublin, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea> Department of Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, York House, Dublin</wicri:regionArea><wicri:noRegion>Dublin</wicri:noRegion></affiliation></author><author><name sortKey="Tweddle, Deborah A" sort="Tweddle, Deborah A" uniqKey="Tweddle D" first="Deborah A." last="Tweddle">Deborah A. Tweddle</name><affiliation wicri:level="1"><nlm:aff id="A19"> Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea> Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Framlington Place, Newcastle upon Tyne</wicri:regionArea><wicri:noRegion>Newcastle upon Tyne</wicri:noRegion></affiliation></author><author><name sortKey="De Preter, Katleen" sort="De Preter, Katleen" uniqKey="De Preter K" first="Katleen" last="De Preter">Katleen De Preter</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3"> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Speleman, Frank" sort="Speleman, Frank" uniqKey="Speleman F" first="Frank" last="Speleman">Frank Speleman</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Vandesompele, Jo" sort="Vandesompele, Jo" uniqKey="Vandesompele J" first="Jo" last="Vandesompele">Jo Vandesompele</name><affiliation wicri:level="4"><nlm:aff id="A1"> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Center for Medical Genetics, Ghent University, De Pintelaan, Ghent</wicri:regionArea><orgName type="university">Université de Gand</orgName><placeName><settlement type="city">Gand</settlement><region>Région flamande</region><region type="district" nuts="2">Province de Flandre-Orientale</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="A2"> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Cancer Research Institute Ghent (CRIG), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="A3"> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea> Bioinformatics Institute Ghent From Nucleotides to Networks (BIG N2N), De Pintelaan, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author></analytic><series><title level="j">Oncotarget</title><idno type="eISSN">1949-2553</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Biomarkers (analysis)</term><term>Cohort Studies</term><term>Computational Biology</term><term>CpG Islands (genetics)</term><term>DNA Methylation</term><term>DNA, Neoplasm (genetics)</term><term>Female</term><term>Humans</term><term>Infant</term><term>Male</term><term>Neoplasm Staging</term><term>Neuroblastoma (diagnosis)</term><term>Neuroblastoma (genetics)</term><term>Prognosis</term><term>Real-Time Polymerase Chain Reaction</term><term>Tumor Cells, Cultured</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN tumoral (génétique)</term><term>Biologie informatique</term><term>Cellules cancéreuses en culture</term><term>Femelle</term><term>Humains</term><term>Ilots CpG (génétique)</term><term>Marqueurs biologiques (analyse)</term><term>Mâle</term><term>Méthylation de l'ADN</term><term>Neuroblastome (diagnostic)</term><term>Neuroblastome (génétique)</term><term>Nourrisson</term><term>Pronostic</term><term>Réaction de polymérisation en chaine en temps réel</term><term>Sites de fixation</term><term>Stade de la tumeur</term><term>Études de cohortes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Biomarkers</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Marqueurs biologiques</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Neuroblastoma</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Neuroblastome</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>CpG Islands</term><term>DNA, Neoplasm</term><term>Neuroblastoma</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN tumoral</term><term>Ilots CpG</term><term>Neuroblastome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Cohort Studies</term><term>Computational Biology</term><term>DNA Methylation</term><term>Female</term><term>Humans</term><term>Infant</term><term>Male</term><term>Neoplasm Staging</term><term>Prognosis</term><term>Real-Time Polymerase Chain Reaction</term><term>Tumor Cells, Cultured</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie informatique</term><term>Cellules cancéreuses en culture</term><term>Femelle</term><term>Humains</term><term>Mâle</term><term>Méthylation de l'ADN</term><term>Nourrisson</term><term>Pronostic</term><term>Réaction de polymérisation en chaine en temps réel</term><term>Sites de fixation</term><term>Stade de la tumeur</term><term>Études de cohortes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Accurate assessment of neuroblastoma outcome prediction remains challenging. Therefore, this study aims at establishing novel prognostic tumor DNA methylation biomarkers. In total, 396 low- and high-risk primary tumors were analyzed, of which 87 were profiled using methyl-CpG-binding domain (MBD) sequencing for differential methylation analysis between prognostic patient groups. Subsequently, methylation-specific PCR (MSP) assays were developed for 78 top-ranking differentially methylated regions and tested on two independent cohorts of 132 and 177 samples, respectively. Further, a new statistical framework was used to identify a robust set of MSP assays of which the methylation score (i.e. the percentage of methylated assays) allows accurate outcome prediction. Survival analyses were performed on the individual target level, as well as on the combined multimarker signature. As a result of the differential DNA methylation assessment by MBD sequencing, 58 of the 78 MSP assays were designed in regions previously unexplored in neuroblastoma, and 36 are located in non-promoter or non-coding regions. In total, 5 individual MSP assays (located in <italic>CCDC177</italic>, <italic>NXPH1</italic>, <italic>lnc-MRPL3-2, lnc-TREX1-1</italic> and one on a region from chromosome 8 with no further annotation) predict event-free survival and 4 additional assays (located in <italic>SPRED3</italic>, <italic>TNFAIP2</italic>, <italic>NPM2</italic> and <italic>CYYR1</italic>) also predict overall survival. Furthermore, a robust 58-marker methylation signature predicting overall and event-free survival was established. In conclusion, this study encompasses the largest DNA methylation biomarker study in neuroblastoma so far. We identified and independently validated several novel prognostic biomarkers, as well as a prognostic 58-marker methylation signature.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cohn, Sl" uniqKey="Cohn S">SL Cohn</name></author><author><name sortKey="Pearson, Adj" uniqKey="Pearson A">ADJ Pearson</name></author><author><name sortKey="London, Wb" uniqKey="London W">WB London</name></author><author><name sortKey="Monclair, T" uniqKey="Monclair T">T Monclair</name></author><author><name sortKey="Ambros, Pf" uniqKey="Ambros P">PF Ambros</name></author><author><name sortKey="Brodeur, Gm" uniqKey="Brodeur G">GM Brodeur</name></author><author><name sortKey="Faldum, A" uniqKey="Faldum A">A Faldum</name></author><author><name sortKey="Hero, B" uniqKey="Hero B">B Hero</name></author><author><name sortKey="Iehara, T" uniqKey="Iehara T">T Iehara</name></author><author><name sortKey="Machin, D" uniqKey="Machin D">D 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Kleinberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="London, Wb" uniqKey="London W">WB London</name></author><author><name sortKey="Castleberry, Rp" uniqKey="Castleberry R">RP Castleberry</name></author><author><name sortKey="Matthay, Kk" uniqKey="Matthay K">KK Matthay</name></author><author><name sortKey="Look, At" uniqKey="Look A">AT Look</name></author><author><name sortKey="Seeger, Rc" uniqKey="Seeger R">RC Seeger</name></author><author><name sortKey="Shimada, H" uniqKey="Shimada H">H Shimada</name></author><author><name sortKey="Thorner, P" uniqKey="Thorner P">P Thorner</name></author><author><name sortKey="Brodeur, Gm" uniqKey="Brodeur G">GM Brodeur</name></author><author><name sortKey="Maris, Jm" uniqKey="Maris J">JM Maris</name></author><author><name sortKey="Reynolds, Cp" uniqKey="Reynolds C">CP Reynolds</name></author><author><name sortKey="Cohn, Sl" uniqKey="Cohn S">SL 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