Identification of structural aberrations in cancer by SNP array analysis

Genome Biology

Volumn 8, Issue 7, 2007, Pages

  Heinrichs, Stefan ^a   Look, A Thomas ^a  

^a DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MICROPHTHALMIA ASSOCIATED TRANSCRIPTION FACTOR; MIXED LINEAGE LEUKEMIA PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR EBF1; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR RUNX1; CARCINOGEN;

CANCER RESEARCH; CHROMOSOME ABERRATION; CYTOGENETICS; GENE DELETION; GENE EXPRESSION PROFILING; GENE FREQUENCY; GENE FUNCTION; GENE IDENTIFICATION; GENE MUTATION; GENE STRUCTURE; GENETIC DISORDER; GENETIC HETEROGENEITY; GENOME ANALYSIS; GENOTYPE; HETEROZYGOSITY LOSS; HUMAN; LEUKEMOGENESIS; MICROARRAY ANALYSIS; PROTEIN TARGETING; SHORT SURVEY; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY; DNA MICROARRAY; GENETICS; METHODOLOGY; NEOPLASM; REVIEW;

CARCINOGENS; CHROMOSOME ABERRATIONS; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 39749162981     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-7-219     Document Type: Short Survey

References (26)

1. Ferrando AA Neuberg DS Staunton J Loh ML Huard C Raimondi SC Behm FG Pui CH Downing JR Gilliland DG et al.: Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell 2002, 1:75-87 10.1016/S1535-6108(02)00018-1 12086890
2. van't Veer LJ Dai H van de Vijver MJ He YD Hart AA Mao M Peterse HL van der Kooy K Marton MJ Witteveen AT et al.: Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536 10.1038/415530a 11823860
3. Rosenwald A Wright G Chan WC Connors JM Campo E Fisher RI Gascoyne RD Muller-Hermelink HK Smeland EB Giltnane JM et al.: The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N Engl J Med 2002, 346:1937-1947 10.1056/ NEJMoa012914 12075054
4. Look AT Oncogenic transcription factors in the human acute leukemias. Science 1997, 278:1059-1064 10.1126/science.278.5340.1059 9353180
5. Attiyeh EF London WB Mosse YP Wang Q Winter C Khazi D McGrady PW Seeger RC Look AT Shimada H et al.: Chromosome 1p and 11q deletions and outcome in neuroblastoma. N Engl J Med 2005, 353:2243-2253 10.1056/NEJMoa052399 16306521
6. Kohn EC Lu Y Wang H Yu Q Yu S Hall H Smith DL Meric-Bernstam F Hortobagyi GN Mills GB Molecular therapeutics: Promise and challenges. Semin Oncol 2004, 31(1 Suppl 3):39-53 10.1053/j.seminoncol.2004.01.009 15052542
7. Sawyers CL Making progress through molecular attacks on cancer. Cold Spring Harb Symp Quant Biol 2005, 70:479-482 10.1101/sqb.2005.70.034 16869786
8. Druker BJ Guilhot F O'Brien SG Gathmann I Kantarjian H Gattermann N Deininger MW Silver RT Goldman JM Stone RM et al.: Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N Engl J Med 2006, 355:2408-2417 10.1056/NEJMoa062867 17151364
9. Greulich H Chen TH Feng W Janne PA Alvarez JV Zappaterra M Bulmer SE Frank DA Hahn WC Sellers WR et al.: Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants. PLoS Med 2005, 2:e313 1240052 16187797 10.1371/journal.pmed.0020313
10. Engelman JA Zejnullahu K Mitsudomi T Song Y Hyland C Park JO Lindeman N Gale CM Zhao X Christensen J et al.: MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. Science 2007, 316:1039-1043 10.1126/science.1141478 17463250
11. Lynch TJ Bell DW Sordella R Gurubhagavatula S Okimoto RA Brannigan BW Harris PL Haserlat SM Supko JG Haluska FG et al.: Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004, 350:2129-2139 10.1056/NEJMoa040938 15118073
12. Golub TR Slonim DK Tamayo P Huard C Gaasenbeek M Mesirov JP Coller H Loh ML Downing JR Caligiuri MA et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537 10.1126/science.286.5439.531 10521349
13. Maser RS Choudhury B Campbell PJ Feng B Wong KK Protopopov A O'Neil J Gutierrez A Ivanova E Perna I et al.: Chromosomally unstable mouse tumours have genomic alterations similar to diverse human cancers. Nature 2007, 447:966-971 10.1038/nature05886 17515920
14. Pinkel D Segraves R Sudar D Clark S Poole I Kowbel D Collins C Kuo WL Chen C Zhai Y et al.: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998, 20:207-211 10.1038/2524 9771718
15. Mullighan CG Goorha S Radtke I Miller CB Coustan-Smith E Dalton JD Girtman K Mathew S Ma J Pounds SB et al.: Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 2007, 446:758-764 10.1038/nature05690 17344859
16. Beroukhim R Lin M Park Y Hao K Zhao X Garraway LA Fox EA Hochberg EP Mellinghoff IK Hofer MD et al.: Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol 2006, 2:e41 1458964 16699594 10.1371/journal.pcbi.0020041
17. Redon R Ishikawa S Fitch KR Feuk L Perry GH Andrews TD Fiegler H Shapero MH Carson AR Chen W et al.: Global variation in copy number in the human genome. Nature 2006, 444:444-454 10.1038/nature05329 17122850
18. Armstrong SA Look AT Molecular genetics of acute lymphoblastic leukemia. J Clin Oncol 2005, 23:6306-6315 10.1200/JCO.2005.05.047 16155013
19. Cobaleda C Schebesta A Delogu A Busslinger M Pax5: The guardian of B cell identity and function. Nat Immunol 2007, 8:463-470 10.1038/ni1454 17440452
20. Fero ML Randel E Gurley KE Roberts JM Kemp CJ The murine gene p27Kip1 is haplo-insufficient for tumour suppression. Nature 1998, 396:177-180 10.1038/24179 9823898
21. Ma L Teruya-Feldstein J Behrendt N Chen Z Noda T Hino O Cordon-Cardo C Pandolfi PP et al.: Genetic analysis of Pten and Tsc2 functional interactions in the mouse reveals asymmetrical haploinsufficiency in tumor suppression. Genes Dev 2005, 19:1779-1786 1182340 16027168 10.1101/ gad.1314405
22. George RE Attiyeh EF Li S Moreau LA Neuberg D Li C Fox EA Meyerson M Diller L Fortina P et al.: Genome-wide analysis of neuroblastomas using high-density single nucleotide polymorphism arrays. PLoS ONE 2007, 2:e255 1797488 17327916 10.1371/journal.pone.0000255
23. Teh MT Blaydon D Chaplin T Foot NJ Skoulakis S Raghavan M Harwood CA Proby CM Philpott MP Young BD et al.: Genomewide single nucleotide polymorphism microarray mapping in basal cell carcinomas unveils uniparental disomy as a key somatic event. Cancer Res 2005, 65:8597-8603 10.1158/0008-5472.CAN-05-0842 16204023
24. Garraway LA Widlund HR Rubin MA Getz G Berger AJ Ramaswamy S Beroukhim R Milner DA Granter SR Du J et al.: Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 2005, 436:117-122 10.1038/nature03664 16001072
25. Lin M Wei LJ Sellers WR Lieberfarb M Wong WH Li C dChip-SNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics 2004, 20:1233-1240 10.1093/ bioinformatics/bth069 14871870
26. dChip Software: Analysis and Visualization of Gene Expression and SNP Microarrays http://biosun1.harvard.edu/complab/dchip/