Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas

International Journal of Cancer

Volumn 130, Issue 11, 2012, Pages 2599-2606

  Fieuw, Annelies ^a   Kumps, Candy ^a   Schramm, Alexander ^b   Pattyn, Filip ^a   Menten, Björn ^a   Antonacci, Francesca ^c   Sudmant, Peter ^c   Schulte, Johannes H ^b   Van Roy, N ^a   Vergult, Sarah ^a   Buckley, Patrick G ^d,e   De Paepe, A ^a   Noguera, Rosa ^f   Versteeg, Rogier ^g   Stallings, Raymond ^d   Eggert, Angelika ^b   Vandesompele, Jo ^a   De Preter, K ^a   Speleman, Frank ^a  

^a GHENT UNIVERSITY HOSPITAL   (Belgium)

^b UNIVERSITY HOSPITAL ESSEN   (Germany)

^c UNIVERSITY OF WASHINGTON   (United States)

^d OUR LADY S CHILDREN S HOSPITAL   (Ireland)

^e ROYAL COLLEGE OF SURGEONS IN IRELAND   (Ireland)

^f UNIVERSITY OF VALENCIA   (Spain)

^g UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

array CGH; chromosome 1; deletion; neuroblastoma

Indexed keywords

MICRORNA;

ARTICLE; CANCER CELL CULTURE; CANCER LOCALIZATION; CANCER STAGING; CHROMOSOME 1Q; CHROMOSOME DELETION; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; EGL NINE HOMOLOG 1 GENE; FUMARATE HYDRATASE GENE; GENE IDENTIFICATION; GENE LOCATION; GENETIC ASSOCIATION; GENETIC CONSERVATION; GENETIC GAIN; GENETIC RISK; HUMAN; HUMAN CELL; HUMAN TISSUE; INFANT; MOLECULAR PATHOLOGY; MYCN GENE; NEUROBLASTOMA; ONCOGENE; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; TUMOR SUPPRESSOR GENE;

CELL LINE, TUMOR; CHROMOSOME DELETION; CHROMOSOMES, HUMAN, PAIR 11; COMPARATIVE GENOMIC HYBRIDIZATION; FUMARATE HYDRATASE; GENE DOSAGE; HUMANS; NEUROBLASTOMA; NUCLEAR PROTEINS; ONCOGENE PROTEINS; PROCOLLAGEN-PROLINE DIOXYGENASE;

EID: 84859158885     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.26317     Document Type: Article

References (31)

1. Brodeur GM,. Neuroblastoma: biological insights into a clinical enigma. Nat Rev Cancer 2003; 3: 203-16.
2. Van Roy N, De Preter K, Hoebeeck J, Van Maerken T, Pattyn F, Mestdagh P, Vermeulen J, Vandesompele J, Speleman F,. The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Med 2009; 1: 74.
3. Piccaluga PP, Rondoni M, Paolini S, Rosti G, Martinelli G, Baccarani M,. Imatinib mesylate in the treatment of hematologic malignancies. Expert Opin Biol Ther 2007; 7: 1597-611.
4. Tsao MS, Sakurada A, Cutz JC, Zhu CQ, Kamel-Reid S, Squire J, Lorimer I, Zhang T, Liu N, Daneshmand M, Marrano P, da Cunha Santos G, et al. Erlotinib in lung cancer-molecular and clinical predictors of outcome. N Engl J Med 2005; 353: 133-44.
5. Van Maerken T, Speleman F, Vermeulen J, Lambertz I, De Clercq S, De Smet E, Yigit N, Coppens V, Philippe J, De Paepe A, Marine JC, Vandesompele J,. Small-molecule MDM2 antagonists as a new therapy concept for neuroblastoma. Cancer Res 2006; 66: 9646-55.
6. Heidorn SJ, Milagre C, Whittaker S, Nourry A, Niculescu-Duvas I, Dhomen N, Hussain J, Reis-Filho JS, Springer CJ, Pritchard C, Marais R,. Kinase-dead BRAF and oncogenic RAS cooperate to drive tumor progression through CRAF. Cell 2010; 140: 209-21.
7. Cohn SL, Pearson ADJ, London WB, Monclair T, Ambros PF, Brodeur GM, Faldum A, Hero B, Iehara T, Machin D, Mosseri V, Simon T, et al. The international neuroblastoma risk group (INRG) classification system: an INRG task force report. J Clin Oncol 2009; 27: 289-97.
8. Michels E, Vandesompele J, De Preter K, Hoebeeck J, Vermeulen J, Schramm A, Molenaar JJ, Menten B, Marques B, Stallings RL, Combaret V, Devalck C, et al. ArrayCGH-based classification of neuroblastoma into genomic subgroups. Gene Chromosome Cancer 2007; 46: 1098-108.
9. Vandesompele J, Baudis M, De Preter K, Van Roy N, Ambros P, Bown N, Brinkschmidt C, Christiansen H, Combaret V, Lastowska M, Nicholson J, O'Meara A, et al. Unequivocal delineation of clinicogenetic subgroups and development of a new model for improved outcome prediction in neuroblastoma. J Clin Oncol 2005; 23: 2280-99.
10. Janoueix-Lerosey I, Schleiermacher G, Michels E, Mosseri V, Ribeiro A, Lequin D, Vermeulen J, Couturier J, Peuchmaur M, Valent A, Plantaz D, Rubie H, et al. Overall genomic pattern is a predictor of outcome in neuroblastoma. J Clin Oncol 2009; 27: 1026-33.
11. Olshen AB, Venkatraman ES, Lucito R, Wigler M,. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004; 5: 557-72.
12. van de Wiel MA, Brosens R, Eilers PH, Kumps C, Meijer GA, Menten B, Sistermans E, Speleman F, Timmerman ME, Ylstra B,. Smoothing waves in array CGH tumor profiles. Bioinformatics 2009; 25: 1099-104.
13. Menten B, Pattyn F, De Preter K, Robbrecht P, Michels E, Buysse K, Mortier G, De Paepe A, van Vooren S, Vermeesch J, Moreau Y, De Moor B, et al. arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays. BMC Bioinform 2005; 6: 124.
14. Van Roy N, Laureys G, Van Gele M, Opdenakker G, Miura R, van der Drift P, Chan A, Versteeg R, Speleman F,. Analysis of 1;17 translocation breakpoints in neuroblastoma: implications for mapping of neuroblastoma genes. Eur J Cancer 1997; 33: 1974-8.
15. Van Limbergen H, Poppe B, Michaux L, Herens C, Brown J, Noens L, Berneman Z, De Bock R, De Paepe A, Speleman F,. Identification of cytogenetic subclasses and recurring chromosomal aberrations in AML and MDS with complex karyotypes using M-FISH. Genes Chromosomes Cancer 2002; 33: 60-72.
16. Mestdagh P, Bostrom AK, Impens F, Fredlund E, Van Peer G, De Antonellis P, von Stedingk K, Ghesquiere B, Schulte S, Dews M, Thomas-Tikhonenko A, Schulte JH, et al. The miR-17-92 microRNA cluster regulates multiple components of the TGF-beta pathway in neuroblastoma. Mol Cell 2010; 40: 762-73.
17. Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J,. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 2008; 36: e143.
18. Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, Speleman F, Vandesompele J,. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009; 10: R64.
19. Krumsiek J, Arnold R, Rattei T,. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007; 23: 1026-8.
20. Buckley PG, Alcock L, Bryan K, Bray I, Schulte JH, Schramm A, Eggert A, Mestdagh P, De Preter K, Vandesompele J, Speleman F, Stallings RL,. Chromosomal and microRNA expression patterns reveal biologically distinct subgroups of 11q- neuroblastoma. Clin Cancer Res 2010; 16: 2971-8.
21. Caren H, Kryh H, Nethander M, Sjoberg RM, Trager C, Nilsson S, Abrahamsson J, Kogner P, Martinsson T,. High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset. Proc Natl Acad Sci USA 2010; 107: 4323-8.
22. Mosse YP, Diskin SJ, Wasserman N, Rinaldi K, Attiyeh EF, Cole K, Jagannathan J, Bhambhani K, Winter C, Maris JM,. Neuroblastomas have distinct genomic DNA profiles that predict clinical phenotype and regional gene expression. Genes Chromosomes Cancer 2007; 46: 936-49.
23. Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, Eichler EE,. Diversity of human copy number variation and multicopy genes. Science 2010; 330: 641-6.
24. Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O, Sahinalp SC, Gibbs RA, et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 2009; 41: 1061-7.
25. Chen R, Morgan AA, Dudley J, Deshpande T, Li L, Kodama K, Chiang AP, Butte AJ,. FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. Genome Biol 2008; 9: R170.
26. Refae MA, Wong N, Patenaude F, Begin LR, Foulkes WD,. Hereditary leiomyomatosis and renal cell cancer: an unusual and aggressive form of hereditary renal carcinoma. Nat Clin Pract Oncol 2007; 4: 256-61.
27. Bordoli MR, Stiehl DP, Borsig L, Kristiansen G, Hausladen S, Schraml P, Wenger RH, Camenisch G,. Prolyl-4-hydroxylase PHD2- and hypoxia-inducible factor 2-dependent regulation of amphiregulin contributes to breast tumorigenesis. Oncogene 2011; 30: 548-60.
28. Ladroue C, Carcenac R, Leporrier M, Gad S, Le Hello C, Galateau-Salle F, Feunteun J, Pouyssegur J, Richard S, Gardie B,. PHD2 mutation and congenital erythrocytosis with paraganglioma. N Engl J Med 2008; 359: 2685-92.
29. Van Vlierberghe P, Palomero T, Khiabanian H, Van der Meulen J, Castillo M, Van Roy N, De Moerloose B, Philippe J, Gonzalez-Garcia S, Toribio ML, Taghon T, Zuurbier L, et al. PHF6 mutations in T-cell acute lymphoblastic leukemia. Nat Genet 2010; 42: 338-42.
30. Sjoblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006; 314: 268-74.
31. Pollard PJ, Briere JJ, Alam NA, Barwell J, Barclay E, Wortham NC, Hunt T, Mitchell M, Olpin S, Moat SJ, Hargreaves IP, Heales SJ, et al. Accumulation of Krebs cycle intermediates and over-expression of HIF1alpha in tumours which result from germline FH and SDH mutations. Hum Mol Genet 2005; 14: 2231-9.