Exploratory analysis of the copy number alterations in glioblastoma multiforme

PLoS ONE

Volumn 3, Issue 12, 2008, Pages

  Freire, Pablo ^a,b   Vilela, Marco ^a,c   Deus, Helena ^a,c   Kim, Yong Wan ^a   Koul, Dimpy ^a   Colman, Howard ^a   Aldape, Kenneth D ^a   Bogler, Oliver ^a   Yung, W K Alfred ^a   Coombes, Kevin ^a   Mills, Gordon B ^a   Vasconcelos, Ana T ^b   Almeida, Jonas S ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^c INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL JUNCTION; CELL PROLIFERATION; CHROMOSOME ANALYSIS; DATA ANALYSIS SOFTWARE; ENTROPY; GENE COPY NUMBER ALTERATION; GENE MAPPING; GENE MUTATION; GENETIC SCREENING; GLIOBLASTOMA; HUMAN; ONCOGENE; TUMOR SUPPRESSOR GENE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETICS; HUMAN GENOME; METABOLISM; METHODOLOGY; NEOPLASM;

COMPARATIVE GENOMIC HYBRIDIZATION; ENTROPY; GENE DOSAGE; GENE EXPRESSION PROFILING; GENOME, HUMAN; GLIOBLASTOMA; HUMANS; NEOPLASMS;

EID: 58149204044     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0004076     Document Type: Article

References (41)

1. Beckmann MW, Niederacher D, Schnurch HG, Gusterson BA, Bender HG (1997) Multistep carcinogenesis of breast cancer and tumour heterogeneity. J Mol Med 75: 429-439.
2. Weir B, Zhao X, Meyerson M (2004) Somatic alterations in the human cancer genome. Cancer Cell 6: 433-438.
3. Santos GC, Zielenska M, Prasad M, Squire JA (2007) Chromosome 6p amplification and cancer progression. J Clin Pathol 60: 1-7.
4. Bretland Farmer J, Moore JES, Walker CE (1905) On the Cytology of Malignant Grows. Proceedings of the Royal Society of London Series B, Containing Papers of a Biological Character 77: 336-353.
5. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, et al. (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23: 41-46.
6. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, et al. (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20: 207-211.
7. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, et al. (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 64: 4744-4748.
8. Coe BP, Ylstra B, Carvalho B, Meijer GA, Macaulay C, et al. (2007) Resolving the resolution of array CGH. Genomics 89: 647-653.
9. Kallioniemi A (2007) CGH microarrays and cancer. Curr Opin Biotechnol.
10. Merlo LM, Pepper JW, Reid BJ, Maley CC (2006) Cancer as an evolutionary and ecological process. Nature Reviews Cancer 6: 924-935.
11. Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, et al. (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A 104: 20007-20012.
12. Venkatraman ES, Olshen AB (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23: 657-663.
13. Picard F, Robin S, Lavielle M, Vaisse C, Daudin JJ (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics 6: 27.
14. Maher EA, Brennan C, Wen PY, Durso L, Ligon KL, et al. (2006) Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities. Cancer Res 66: 11502-11513.
15. Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, et al. (2006) STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res 16: 1149-1158.
16. Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, et al. (2007) Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet 3: e143.
17. Wiedemeyer R, Brennan C, Heffernan TP, Xiao Y, Mahoney J, et al. (2008) Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 13: 355-364.
18. TCGA Research Network (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
19. Louis DN (2006) Molecular pathology of malignant gliomas. Annu Rev Pathol 1: 97-117.
20. Coombes KR, Wang J, Baggerly KA (2007) Microarrays: retracing steps. Nat Med 13: 1276-1277; author reply 1277-1278.
21. Almeida JS, Chen C, Gorlitsky R, Stanislaus R, Aires-de-Sousa M, et al. (2006) Data integration gets 'Sloppy'. Nat Biotechnol 24: 1070-1071.
22. Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, et al. (2004) Detection of large-scale variation in the human genome. Nat Genet 36: 949-951.
23. Reifenberger G, Collins VP (2004) Pathology and molecular genetics of astrocytic gliomas. J Mol Med 82: 656-670.
24. Bagchi A, Papazoglu C, Wu Y, Capurso D, Brodt M, et al. (2007) CHD5 is a tumor suppressor at human 1p36. Cell 128: 459-475.
25. Ichimura K, Vogazianou AP, Liu L, Pearson DM, Backlund LM, et al. (2007) 1p36 is a preferential target of chromosome 1 deletions in astrocytic tumours and homozygously deleted in a subset of glioblastomas. Oncogene.
26. Yano M, Okano HJ, Okano H (2005) Involvement of Hu and heterogeneous nuclear ribonucleoprotein K in neuronal differentiation through p21 mRNA post-transcriptional regulation. J Biol Chem 280: 12690-12699.
27. Connett JM, Badri L, Giordano TJ, Connett WC, Doherty GM (2005) Interferon regulatory factor 1 (IRF-1) and IRF-2 expression in breast cancer tissue microarrays. J Interferon Cytokine Res 25: 587-594.
28. Di Marcotullio L, Ferretti E, Greco A, De Smaele E, Po A, et al. (2006) Numb is a suppressor of Hedgehog signalling and targets Gli1 for Itch-dependent ubiquitination. Nat Cell Biol 8: 1415-1423.
29. Okawa ER, Gotoh T, Manne J, Igarashi J, Fujita T, et al. (2008) Expression and sequence analysis of candidates for the 1p36.31 tumor suppressor gene deleted in neuroblastomas. Oncogene 27: 803-810.
30. Uziel T, Zindy F, Sherr CJ, Roussel MF (2006) The CDK inhibitor p18Ink4c is a tumor suppressor in medulloblastoma. Cell Cycle 5: 363-365.
31. Li F, Munchhof AM, White HA, Mead LE, Krier TR, et al. (2006) Neurofibromin is a novel regulator of RAS-induced signals in primary vascular smooth muscle cells. Hum Mol Genet 15: 1921-1930.
32. Chen J, Lui WO, Vos MD, Clark GJ, Takahashi M, et al. (2003) The t(1;3) breakpoint-spanning genes LSAMP and NORE1 are involved in clear cell renal cell carcinomas. Cancer Cell 4: 405-413.
33. Vandepoele K, Andries V, Van Roy N, Staes K, Vandesompele J, et al. (2008) A constitutional translocation t(1;17)(p36.2;q11.2) in a neuroblastoma patient disrupts the human NBPF1 and ACCN1 genes. PLoS ONE 3: e2207.
34. Inoue C, Bae SK, Takatsuka K, Inoue T, Bessho Y, et al. (2001) Math6, a bHLH gene expressed in the developing nervous system, regulates neuronal versus glial differentiation. Genes Cells 6: 977-986.
35. Bailey JA, Yavor AM, Massa HF, Trask BJ, Eichler EE (2001) Segmental duplications: organization and impact within the current human genome project assembly. Genome Res 11: 1005-1017.
36. McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature.
37. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100: 9440-9445.
38. Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature 453: 56-64.
39. Parzen E (1956) On Consistent Estimates of the Spectral Density of a Stationary Time Series. Proc Natl Acad Sci U S A 42: 154-157.
40. Eilers PH (2003) A perfect smoother. Anal Chem 75: 3631-3636.
41. Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, et al. (2007) The UCSC genome browser database: update 2007. Nucleic Acids Res 35: D668-673.