Finding exclusively deleted or amplified genomic areas in lung adenocarcinomas using a novel chromosomal pattern analysis

BMC Medical Genomics

Volumn 2, Issue , 2009, Pages

  Brot, Philippe ^a,b   Tan, Patrick ^a,d   Alifano, Marco ^c   Camilleri Brot, Sophie ^b   Richardson, Sylvia ^e  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b UNIVERSITÉ PARIS SACLAY   (France)

^c ASSISTANCE PUBLIQUE HÔPITAUX DE PARIS   (France)

^d DUKE NUS MEDICAL SCHOOL   (Singapore)

^e IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER SURVIVAL; CHROMOSOME 11; CHROMOSOME 14; CHROMOSOME 2; CHROMOSOME ABERRATION; COMPARATIVE GENOMIC HYBRIDIZATION; GENE AMPLIFICATION; GENE CLUSTER; GENE DELETION; GENE MAPPING; GENOMICS; HUMAN; KARYOTYPING; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; ONCOGENE; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STATISTICAL MODEL; TUMOR SUPPRESSOR GENE;

EID: 68749097276     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-2-43     Document Type: Article

References (17)

1. Aneuploidy and cancer. H Rajagopalan C Lengauer, Nature 2004 432 338 341 10.1038/nature03099 15549096 (Pubitemid 39551662)
2. Resolving the resolution of array CGH. BP Coe B Ylstra B Carvalho GA Meijer C Macaulay WL Lam, Genomics 2007 89 647 653 10.1016/j.ygeno.2006.12.012 17276656 (Pubitemid 46589944)
3. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. SJ Diskin T Eck J Greshock YP Mosse T Naylor CJ Stoeckert Jr BL Weber JM Maris GR Grant, Genome Res 2006 16 1149 1158 16899652 10.1101/gr.5076506 (Pubitemid 44320402)
4. Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. C Klijn H Holstege J de Ridder X Liu M Reinders J Jonkers L Wessels, Nucleic Acids Res 2008 2 (Pubitemid 351250463)
5. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. R Beroukhim G Getz L Nghiemphu J Barretina T Hsueh D Linhart I Vivanco JC Lee JH Huang S Alexander J Du T Kau RK Thomas K Shah H Soto S Perner J Prensner RM Debiasi F Demichelis C Hatton MA Rubin LA Garraway SF Nelson L Liau PS Mischel TF Cloughesy M Meyerson TA Golub ES Lander IK Mellinghoff WR Sellers, PNAS 2007 104 20007 20012 18077431 10.1073/pnas.0710052104
6. Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. P Brot S Richardson, Bioinformatics 2006 22 911 918 10.1093/bioinformatics/btl035 16455750
7. WinBUGS a Bayesian modelling framework: concepts, structure, and extensibility. DJ Lunn A Thomas N Best D Spiegelhalter, Statistics and Computing 2000 10 325 337 10.1023/A:1008929526011
8. Bayesian measures of model complexity and fit. DJ Spiegelhalter NG Best BP Carlin A van der Linde, J Royal Statist Society Series B 2002 3 583 639 10.1111/1467-9868.00353
9. Discussion on the Paper by Spiegelhalter, Best, Carlin and van der Linde. S Richardson, J Royal Statist Society Series B 2002 3 626 627
10. High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. C Garnis WW Lockwood E Vucic Y Ge L Girard JD Minna AF Gazdar S Lam C MacAulay WL Lam, Int J Cancer 2006 118 1556 1564 10.1002/ijc.21491 16187286 (Pubitemid 43306545)
11. Characterizing the cancer genome in lung adenocarcinoma. BA Weir MS Woo G Getz S Perner L Ding R Beroukhim WM Lin MA Province A Kraja LA Johnson K Shah M Sato RK Thomas JA Barletta IB Borecki S Broderick AC Chang DY Chiang LR Chirieac J Cho Y Fujii AF Gazdar T Giordano H Greulich M Hanna BE Johnson MG Kris A Lash L Lin N Lindeman, Nature 2007 450 893 898 17982442 10.1038/nature06358 (Pubitemid 350231325)
12. High-resolution genomic profiles of human lung cancer. G Tonon KK Wong G Maulik C Brennan B Feng Y Zhang DB Khatry A Protopopov MJ You AJ Aguirre ES Martin Z Yang H Ji L Chin RA Depinho, Proc Natl Acad Sci USA 2005 102 9625 9630 15983384 10.1073/pnas.0504126102 (Pubitemid 40981731)
13. Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. M Soda YL Choi M Enomoto S Takada Y Yamashita S Ishikawa S Fujiwara H Watanabe K Kurashina H Hatanaka M Bando S Ohno Y Ishikawa H Aburatani T Niki Y Sohara Y Sugiyama H Mano, Nature 2007 448 561 566 10.1038/nature05945 17625570 (Pubitemid 47206930)
14. EML4-ALK fusion lung cancer: a rare acquired event. S Perner PL Wagner F Demichelis R Mehra CJ Lafargue BJ Moss S Arbogast A Soltermann W Weder TJ Giordano DG Beer DS Rickman AM Chinnaiyan H Moch MA Rubin, Neoplasia 2008 10 298 302 18320074 (Pubitemid 351328588)
15. Bioconductor: open software development for computational biology and bioinformatics. RC Gentleman VJ Carey DM Bates B Bolstad M Dettling S Dudoit B Ellis L Gautier Y Ge J Gentry K Hornik T Hothorn W Huber S Iacus R Irizarry F Leisch C Li M Maechler AJ Rossini G Sawitzki C Smith G Smyth L Tierney JY Yang J Zhang, Genome Biol 2004 5 10 R80 15461798 10.1186/gb-2004-5-10-r80
16. Cancer genes and the pathways they control. B Vogelstein KW Kinzler, Nat Med 2004 10 789 799 10.1038/nm1087 15286780 (Pubitemid 39070849)
17. Genomic changes defining the genesis, progression, and malignancy potential in solid human tumors: a phenotype/genotype correlation. T Ried K Heselmeyer-Haddad H Blegen E Schröck G Auer, Genes Chromosomes Cancer 1999 3 195 204 10.1002/(SICI)1098-2264(199907)25:3<195::AID-GCC1>3.0.CO;2-8 (Pubitemid 29266688)