Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients

Clinical Cancer Research

Volumn 16, Issue 2, 2010, Pages 651-663

  Horlings, Hugo M ^a   Lai, Carmen ^a,c   Nuyten, Dimitry S A ^a   Halfwerk, Hans ^a   Kristel, Petra ^a   Van Beers, Erik ^a   Joosse, Simon A ^a   Klijn, Christiaan ^a   Nederlof, Petra M ^a   Reinders, Marcel J T ^c   Wessels, Lodewyk F A ^a,c   Van De Vijver, Marc J ^b  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b ACADEMIC MEDICAL CENTER   (Netherlands)

^c Delft University of Technology ^*  (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2;

ADULT; ARTICLE; BREAST CANCER; CHROMOSOME ABERRATION; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER ALTERATION; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE MUTATION; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROGNOSIS;

ADULT; AGED; AGED, 80 AND OVER; BREAST NEOPLASMS; CARCINOMA; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MIDDLE AGED; MOLECULAR DIAGNOSTIC TECHNIQUES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, GENETIC; PROGNOSIS;

EID: 74549158222     PISSN: 10780432     EISSN: None     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-09-0709     Document Type: Article

References (43)

1. van't Veer LJ, Dai H, van de Vijver MJ, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002;415:530-6.
2. Wang Y, Klijn JG, Zhang Y, et al. Gene-expression profiles to predict distant metastasis of lymph-node-negative primary breast cancer. Lancet 2005;365:671-9.
3. Hu Z, Fan C, Oh DS, et al. The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 2006;7:96.
4. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature 2000;406:747-52.
5. Sorlie T, Tibshirani R, Parker J, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 2003;100:8418-23.
6. Chang HY, Nuyten DS, Sneddon JB, et al. Robustness, scalability, and integration of a wound-response gene expression signature in predicting breast cancer survival. Proc Natl Acad Sci U S A 2005;102:3738-43.
7. Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 2006;38:1043-8.
8. Sotiriou C, Wirapati P, Loi S, et al. Gene expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 2006;98:262-72.
9. Fan C, Oh DS, Wessels L, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006;355:560-9.
10. Pollack JR, Sorlie T, Perou CM, et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 2002;99:12963-8.
11. Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002;3:415-28.
12. Visvader JE, Lindeman GJ. Transcriptional regulators in mammary gland development and cancer. Int J Biochem Cell Biol 2003;35:1034-51.
13. Hyman E, Kauraniemi P, Hautaniemi S, et al. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 2002;62:6240-5.
14. Monni O, Barlund M, Mousses S, et al. Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer. Proc Natl Acad Sci U S A 2001;98:5711-6.
15. Orsetti B, Nugoli M, Cervera N, et al. Genomic and expression profiling of chromosome 17 in breast cancer reveals complex patterns of alterations and novel candidate genes. Cancer Res 2004;64:6453-60.
16. Orsetti B, Nugoli M, Cervera N, et al. Genetic profiling of chromosome 1 in breast cancer: mapping of regions of gains and losses and identification of candidate genes on 1q. Br J Cancer 2006;95:1439-47.
17. Bergamaschi A, Kim YH, Wang P, et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006;45:1033-40.
18. Chin K, Devries S, Fridlyand J, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006;10:529-41.
19. Chin SF, Wang Y, Thorne NP, et al. Using array-comparative genomic hybridization to define molecular portraits of primary breast cancers. Oncogene 2007;26:1959-70.
20. Chin SF, Teschendorff AE, Marioni JC, et al. High-resolution array-CGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007;8:R215.
21. Fridlyand J, Snijders AM, Ylstra B, et al. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006;6:96.
22. Andre F, Job B, Dessen P, et al. Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res 2009;15:441-51.
23. Adler AS, Lin M, Horlings H, et al. Genetic regulators of large-scale transcriptional signatures in cancer. Nat Genet 2006;38:421-30.
24. Adelaide J, Finetti P, Bekhouche I, et al. Integrated profiling of basal and luminal breast cancers. Cancer Res 2007;67:11565-75.
25. Lai C, Horlings HH, van de Vijver MM, et al. SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets. BMC Bioinformatics 2007;8:422.
26. van de Vijver MJ, He YD, van't Veer LJ, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999-2009.
27. Nuyten DS, Hastie T, Chi JT, Chang HY, van d V. Combining biological gene expression signatures in predicting outcome in breast cancer: an alternative to supervised classification. Eur J Cancer 2008;44:2319-29.
28. Balaton AL, Coindre JM, Collin F, et al. [Recommendations for the immunohistochemical evaluation of hormone receptors on paraffin sections of breast cancer. Study Group on Hormone Receptors using Immunohistochemistry FNCLCC/AFAQAP. National Federation of Centres to Combat Cancer/French Association for Quality Assurance in Pathology]Recommandations pour l'evaluation immunohistochimique des recepteurs hormonaux sur coupes en paraffine dans les carcinomes mammaires. Groupe d'Etude des Recepteurs Hormonaux par Immunohistochimie FNCLCC/AFAQAP. Federation Nationale des Centres de Lutte Contre le Cancer Association Francaise d'Assuransce de Qualite en Pathologie. Ann Pathol 1996;16:144-8.
29. van d V, Bilous M, Hanna W, et al. Chromogenic in situ hybridisation for the assessment of HER2 status in breast cancer: an international validation ring study. Breast Cancer Res 2007;9:R68.
30. Raap AK, van der Burg MJ, Knijnenburg J, et al. Array comparative genomic hybridization with cyanin cis-platinum-labeled DNAs. Biotechniques 2004;37:130-4.
31. Geisler S, Lonning PE, Aas T, et al. Influence of TP53 gene alterations and c-erbB-2 expression on the response to treatment with doxorubicin in locally advanced breast cancer. Cancer Res 2001;61:2505-12.
32. Berns K, Horlings HM, Hennessy BT, et al. A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer. Cancer Cell 2007;12:395-402.
33. Joosse SA, van Beers EH, Nederlof PM. Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 2007;7:43.
34. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001;98:5116-21.
35. Naderi A, Teschendorff AE, Barbosa-Morais NL, et al. A geneexpression signature to predict survival in breast cancer across independent data sets. Oncogene 2007;26:1507-16.
36. Stein D, Wu J, Fuqua SA, et al. The SH2 domain protein GRB-7 is co-amplified, overexpressed and in a tight complex with HER2 in breast cancer. EMBO J 1994;13:1331-40.
37. Haibe-Kains B, Desmedt C, Piette F, et al. Comparison of prognostic gene expression signatures for breast cancer. BMC Genomics 2008;9:394.
38. Reyal F, van Vliet MH, Armstrong NJ, et al. A comprehensive analysis of prognostic signatures reveals the high predictive capacity of the proliferation, immune response and RNA splicing modules in breast cancer. Breast Cancer Res 2008;10:R93.
39. Loo LW, Grove DI, Williams EM, et al. Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 2004;64:8541-9.
40. Nessling M, Richter K, Schwaenen C, et al. Candidate genes in breast cancer revealed by microarray-based comparative genomic hybridization of archived tissue. Cancer Res 2005;65:439-47.
41. Holst F, Stahl PR, Ruiz C, et al. Estrogen receptor α (ESR1) gene amplification is frequent in breast cancer. Nat Genet 2007;39:655-60.
42. Horlings HM, Bergamaschi A, Nordgard SH, et al. ESR1 gene amplification in breast cancer: a common phenomenon? Nat Genet 2008;40:807-8.
43. Hu G, Chong RA, Yang Q, et al. MTDH activation by 8q22 genomic gain promotes chemoresistance and metastasis of poor-prognosis breast cancer. Cancer Cell 2009;15:9-20.