SNP Array Analysis Reveals Novel Genomic Abnormalities Including Copy Neutral Loss of Heterozygosity in Anaplastic Oligodendrogliomas

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Idbaih, Ahmed ^a,b,c,d   Ducray, François ^e   Dehais, Caroline ^d   Courdy, Célia ^f,g   Carpentier, Catherine ^a,b   de Bernard, Simon ^h   Uro Coste, Emmanuelle ⁱ   Mokhtari, Karima ^d   Jouvet, Anne ^e   Honnorat, Jérôme ^e   Chinot, Olivier ^f   Ramirez, Carole ^j   Beauchesne, Patrick ^k   Benouaich Amiel, Alexandra ^l   Godard, Joël ^m   Eimer, Sandrine ⁿ   Parker, Fabrice ^o   Lechapt Zalcman, Emmanuelle ^p   Colin, Philippe ^q   Loussouarn, Delphine ^r   Faillot, Thierry ^s   Dam Hieu, Phong ^t   Elouadhani Hamdi, Selma ^u   Bauchet, Luc ^v   Langlois, Olivier ^w   Le Guerinel, Caroline ^x   Fontaine, Denys ^y   Vauleon, Elodie ^z   Menei, Philippe ^aa   Fotso, Marie Janette Motsuo ^ab   Desenclos, Christine ^ac   Verelle, Pierre ^ad   Ghiringhelli, François ^ae   Noel, Georges ^af   Labrousse, François ^ag   Carpentier, Antoine ^ah   Dhermain, Frédéric ^ai   Delattre, Jean Yves ^a,b,c,d   Figarella Branger, Dominique ^f,g   Sevestre, Henri ^ac   Michalak, Sophie ^aa   Al Nader, Edmond ^aa   Lacroix, Catherine ^o   Adam, Clovis ^o   Viennet, Gabriel ^aj   Servagi Vernat, Stéphanie ^aj   Loiseau, Hugues ^ak   Quintin Roue, Isabelle ^al   Guillamo, Jean Sébastien ^am   Emery, Evelyne ^am   Kemeny, Jean Louis ^an   Aubriot Lorton, Marie Hélène ^ao   Christo, Christov ^x   Polivka, Marc ^u   Dubois, François ^j   Maurage, Claude Aliain ^j   Gueye, Edouard Marcel ^ap   Rigau, Valérie ^aq   Vignaud, Jean Michel ^k   Campone, Mario ^ar   Frenel, Jean Sébastien ^ar   VandenBos, Fanny ^as   Diebold, Marie Danièle ^at   Chiforeanu, DanChristian ^au   Laguerrière, Annie ^av   Peoc'h, Michel ^aw   Chenard, Marie Pierre ^ax   Cohen Moyal, Elisabeth ^ao   Lubrano, Xavier ^ao   more..

^a SORBONNE UNIVERSITÉ   (France)

^b INSERM   (France)

^c CNRS   (France)

^d PITIÉ SALPÊTRIÈRE HOSPITAL   (France)

^e HÔPITAL NEUROLOGIQUE   (France)

^f TIMONE HOSPITAL   (France)

^g AIX MARSEILLE UNIVERSITY   (France)

^h Altra Bio   (France)

ⁱ CHU RANGUEIL   (France)

^j LILLE UNIVERSITY HOSPITAL   (France)

^k UNIVERSITY HOSPITAL OF NANCY   (France)

^l CHU PURPAN   (France)

^m UNIVERSITY HOSPITAL JEAN MINJOZ   (France)

ⁿ HÔPITAL PELLEGRIN   (France)

^o BICÊTRE HOSPITAL   (France)

^p CHU CÔTE DE NACRE   (France)

^q Clinique de Courlancy   (France)

^r CHU de Nantes   (France)

^s BEAUJON HOSPITAL   (France)

^t SERVICE DE RHUMATOLOGIE   (France)

^u HÔPITAL LARIBOISIÈRE   (France)

^v GUI DE CHAULIAC HOSPITAL   (France)

^w HÔPITAL CHARLES NICOLLE   (France)

^x HENRI MONDOR HOSPITAL   (France)

^y PASTEUR HOSPITAL   (France)

^z CENTRE EUGÈNE MARQUIS   (France)

^aa ANGERS UNIVERSITY HOSPITAL   (France)

^ab HÔPITAL NORD   (France)

^ac AMIENS UNIVERSITY HOSPITAL   (France)

^ad CENTRE JEAN PERRIN   (France)

^ae CENTRE GEORGES FRANÇOIS LECLERC   (France)

^af CENTRE PAUL STRAUSS   (France)

^ag DUPUYTREN UNIVERSITY HOSPITAL   (France)

^ah AVICENNE HOSPITAL   (France)

^ai INSTITUT GUSTAVE ROUSSY   (France)

^aj UNIVERSITY HOSPITAL OF BESANÇON   (France)

^ak BORDEAUX UNIVERSITY HOSPITAL   (France)

^al BREST UNIVERSITY HOSPITAL   (France)

^am CAEN UNIVERSITY HOSPITAL   (France)

^an UNIVERSITY HOSPITAL OF CLERMONT FERRAND   (France)

^ao CHU Bicêtre ^*

^ap LIMOGES UNIVERSITY HOSPITAL   (France)

^aq MONTPELLIER UNIVERSITY HOSPITAL   (France)

^ar NANTES UNIVERSITY HOSPITAL   (France)

^as UNIVERSITY HOSPITAL OF NICE   (France)

^at REIMS UNIVERSITY HOSPITAL   (France)

^au RENNES UNIVERSITY HOSPITAL   (France)

^av ROUEN UNIVERSITY HOSPITAL   (France)

^aw UNIVERSITY HOSPITAL OF SAINT ETIENNE   (France)

^ax UNIVERSITY HOSPITAL OF STRASBOURG   (France)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A;

ADULT; AGED; ARTICLE; BLOOD SAMPLING; CANCER CLASSIFICATION; CANCER TISSUE; CDKN2A GENE; CHROMOSOME 19Q; CHROMOSOME 1P; CHROMOSOME ANALYSIS; CHROMOSOME DELETION; CONTROLLED STUDY; COPY NEUTRAL LOSS OF HETEROZYGOSITY; FEMALE; FUBP1 GENE; GENE; GENE AMPLIFICATION; GENE DISRUPTION; GENE DOSAGE; GENE EXPRESSION REGULATION; GENE LOCUS; GENE SILENCING; GENOME ANALYSIS; HETEROZYGOSITY; HISTOPATHOLOGY; HOMOZYGOTE; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MOLECULAR PATHOLOGY; OLIGODENDROGLIOMA; PROSPECTIVE STUDY; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; AGED; BRAIN NEOPLASMS; FEMALE; GENE DELETION; GENES, P16; HUMANS; LOSS OF HETEROZYGOSITY; MALE; MIDDLE AGED; MUTATION; OLIGODENDROGLIOMA; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84867391511     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045950     Document Type: Article

References (31)

1. Central Brain Tumor Registry of the United States (n.d.). Available:http://www.cbtrus.org/. Accessed 2012 Jun 10.
2. Rigau V, Zouaoui S, Mathieu-Daudé H, Darlix A, Maran A, et al. (2011) French brain tumor database: 5-year histological results on 25 756 cases. Brain Pathol 21: 633-644 doi:10.1111/j.1750-3639.2011.00491.x.
3. Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, et al. (2007) The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol 114: 97-109 doi:10.1007/s00401-007-0243-4.
4. Cairncross G, Berkey B, Shaw E, Jenkins R, Scheithauer B, et al. (2006) Phase III trial of chemotherapy plus radiotherapy compared with radiotherapy alone for pure and mixed anaplastic oligodendroglioma: Intergroup Radiation Therapy Oncology Group Trial 9402. J Clin Oncol 24: 2707-2714 doi:10.1200/JCO.2005.04.3414.
5. van den Bent MJ, Carpentier AF, Brandes AA, Sanson M, Taphoorn MJB, et al. (2006) Adjuvant procarbazine, lomustine, and vincristine improves progression-free survival but not overall survival in newly diagnosed anaplastic oligodendrogliomas and oligoastrocytomas: a randomized European Organisation for Research and Treatment of Cancer phase III trial. J Clin Oncol 24: 2715-2722 doi:10.1200/JCO.2005.04.6078.
6. Reifenberger J, Reifenberger G, Liu L, James CD, Wechsler W, et al. (1994) Molecular genetic analysis of oligodendroglial tumors shows preferential allelic deletions on 19q and 1p. Am J Pathol 145: 1175-1190.
7. Cairncross JG, Ueki K, Zlatescu MC, Lisle DK, Finkelstein DM, et al. (1998) Specific genetic predictors of chemotherapeutic response and survival in patients with anaplastic oligodendrogliomas. J Natl Cancer Inst 90: 1473-1479.
8. Jenkins RB, Blair H, Ballman KV, Giannini C, Arusell RM, et al. (2006) A t(1;19)(q10;p10) mediates the combined deletions of 1p and 19q and predicts a better prognosis of patients with oligodendroglioma. Cancer Res 66: 9852-9861 doi:10.1158/0008-5472.CAN-06-1796.
9. Griffin CA, Burger P, Morsberger L, Yonescu R, Swierczynski S, et al. (2006) Identification of der(1;19)(q10;p10) in five oligodendrogliomas suggests mechanism of concurrent 1p and 19q loss. J Neuropathol Exp Neurol 65: 988-994 doi:10.1097/01.jnen.0000235122.98052.8f.
10. Yan H, Parsons DW, Jin G, McLendon R, Rasheed BA, et al. (2009) IDH1 and IDH2 mutations in gliomas. N Engl J Med 360: 765-773 doi:10.1056/NEJMoa0808710.
11. Sanson M, Marie Y, Paris S, Idbaih A, Laffaire J, et al. (2009) Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomas. J Clin Oncol 27: 4150-4154 doi:10.1200/JCO.2009.21.9832.
12. Idbaih A, Crinière E, Marie Y, Rousseau A, Mokhtari K, et al. (2008) Gene amplification is a poor prognostic factor in anaplastic oligodendrogliomas. Neuro-oncology 10: 540-547 doi:10.1215/15228517-2008-022.
13. Bettegowda C, Agrawal N, Jiao Y, Sausen M, Wood LD, et al. (2011) Mutations in CIC and FUBP1 contribute to human oligodendroglioma. Science 333: 1453-1455 doi:10.1126/science.1210557.
14. Sahm F, Koelsche C, Meyer J, Pusch S, Lindenberg K, et al. (2012) CIC and FUBP1 mutations in oligodendrogliomas, oligoastrocytomas and astrocytomas. Acta Neuropathol 123: 853-860 doi:10.1007/s00401-012-0993-5.
15. Yip S, Butterfield YS, Morozova O, Chittaranjan S, Blough MD, et al. (2012) Concurrent CIC mutations, IDH mutations, and 1p/19q loss distinguish oligodendrogliomas from other cancers. J Pathol 226: 7-16 doi:10.1002/path.2995.
16. Home- ClinicalTrials.gov (n.d.). Available:http://www.clinicaltrials.gov/. Accessed 2012 Jun 10.
17. Houillier C, Wang X, Kaloshi G, Mokhtari K, Guillevin R, et al. (2010) IDH1 or IDH2 mutations predict longer survival and response to temozolomide in low-grade gliomas. Neurology 75: 1560-1566 doi:10.1212/WNL.0b013e3181f96282.
18. Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA, (2009) R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics 25: 2621-2623 doi:10.1093/bioinformatics/btp470.
19. Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, et al. (2011) A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics 12: 33-50 doi:10.1093/biostatistics/kxq043.
20. Bengtsson H, Neuvial P, Speed TP, (2010) TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics 11: 245 doi:10.1186/1471-2105-11-245.
21. Sun W, Wright FA, Tang Z, Nordgard SH, Van Loo P, et al. (2009) Integrated study of copy number states and genotype calls using high-density SNP arrays. Nucleic Acids Res 37: 5365-5377 doi:10.1093/nar/gkp493.
22. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I, (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
23. Labussière M, Idbaih A, Wang X-W, Marie Y, Boisselier B, et al. (2010) All the 1p19q codeleted gliomas are mutated on IDH1 or IDH2. Neurology 74: 1886-1890 doi:10.1212/WNL.0b013e3181e1cf3a.
24. Christensen BC, Smith AA, Zheng S, Koestler DC, Houseman EA, et al. (2011) DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma. J Natl Cancer Inst 103: 143-153 doi:10.1093/jnci/djq497.
25. Xu W, Yang H, Liu Y, Yang Y, Wang P, et al. (2011) Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. Cancer Cell 19: 17-30 doi:10.1016/j.ccr.2010.12.014.
26. Turcan S, Rohle D, Goenka A, Walsh LA, Fang F, et al. (2012) IDH1 mutation is sufficient to establish the glioma hypermethylator phenotype. Nature 483: 479-483 doi:10.1038/nature10866.
27. van den Bent MJ, Gravendeel LA, Gorlia T, Kros JM, Lapre L, et al. (2011) A hypermethylated phenotype is a better predictor of survival than MGMT methylation in anaplastic oligodendroglial brain tumors: a report from EORTC study 26951. Clin Cancer Res 17: 7148-7155 doi:10.1158/1078-0432.CCR-11-1274.
28. Makishima H, Maciejewski JP, (2011) Pathogenesis and consequences of uniparental disomy in cancer. Clin Cancer Res 17: 3913-3923 doi:10.1158/1078-0432.CCR-10-2900.
29. Idbaih A, Marie Y, Pierron G, Brennetot C, Hoang-Xuan K, et al. (2005) Two types of chromosome 1p losses with opposite significance in gliomas. Ann Neurol 58: 483-487 doi:10.1002/ana.20607.
30. Jeuken J, Cornelissen S, Boots-Sprenger S, Gijsen S, Wesseling P, (2006) Multiplex ligation-dependent probe amplification: a diagnostic tool for simultaneous identification of different genetic markers in glial tumors. J Mol Diagn 8: 433-443 doi:10.2353/jmoldx.2006.060012.
31. Benetkiewicz M, Idbaih A, Cousin P-Y, Boisselier B, Marie Y, et al. (2009) NOTCH2 is neither rearranged nor mutated in t(1;19) positive oligodendrogliomas. PLoS ONE 4: e4107 doi:10.1371/journal.pone.0004107.