Detailed Characterization of Alterations of Chromosomes 7, 9, and 10 in Glioblastomas as Assessed by Single-Nucleotide Polymorphism Arrays Inês Crespo,

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Detailed Characterization of Alterations of Chromosomes 7, 9, and 10 in Glioblastomas as Assessed by Single-Nucleotide Polymorphism Arrays Inês Crespo, Ana Luísa Vital, Ana Belen Nieto, Olinda Rebelo, Hermínio Tão, Maria Celeste Lopes, Catarina Resende Oliveira, Pim J. French, Alberto Orfao, María Dolores Tabernero The Journal of Molecular Diagnostics Volume 13, Issue 6, Pages 634-647 (November 2011) DOI: 10.1016/j.jmoldx.2011.06.003 Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Frequency of CN gains (red areas) and losses (blue areas) along the tumor cell genome of 35 glioblastomas. A: An overview of the frequency of CN changes detected for each individual chromosome is shown. B: A heat map representation of the CN changes detected for chromosomes 7, 9, and 10 is displayed for each case analyzed. The intensity of colors is directly proportional to the frequency of genetic gains (red color) or losses (blue color) identified for each specific chromosomal region. Cutoff values for chromosome gains and losses were defined at CN values of 2.50 or greater and 1.30 or less, respectively. The Journal of Molecular Diagnostics 2011 13, 634-647DOI: (10.1016/j.jmoldx.2011.06.003) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Detailed characterization of the amplified 7p11.2 chromosomal segments (n = 10, A) and the deleted chromosome 9p21.3 sequences (n = 22, B) in glioblastomas. Note that the EGFR gene extends from 55,086,725 bp to 55,275,031 bp from pter positions (Entrez Gene, GeneID1956); in the 500K SNP array, the SNPs assayed in this region of chromosome 7p11.2 extended from the 55,062,691-bp to the 55,236,410-bp positions. Regarding del(9p21) no single gene was systematically deleted; however, both CDKN2A and CDKN2B were lost in all except one case. The Journal of Molecular Diagnostics 2011 13, 634-647DOI: (10.1016/j.jmoldx.2011.06.003) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 Overall survival curves of glioblastoma patients (n = 35) from our patients (A–C) and our patients plus cases from five other series (154 total cases) from the literature (D–F), according to the different cytogenetic patterns of alteration detected for chromosomes 7, 9, and 10 (A and D) and the presence of EGFR amplification in the whole series (B and E) and among patients older than 60 years (C and F). Cytogenetic patterns by SNP array studies corresponded to the following profiles: pattern 1, EGFR amplification; pattern 2, +7/del(9p) or cnLOH 9/−10 or del(10p) with del(10q); pattern 3, +7/without monosomy 10; pattern 4, +7/−10/absence of del(9p21.3); and pattern 5, +7 and + 9. The Journal of Molecular Diagnostics 2011 13, 634-647DOI: (10.1016/j.jmoldx.2011.06.003) Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions