Genomic differences between estrogen receptor (ER)-positive and ER-negative human breast carcinoma identified by single nucleotide polymorphism array comparative genome hybridization analysis

Cancer

Volumn 117, Issue 10, 2011, Pages 2024-2034

  Fang, Min ^a,b   Toher, Jessica ^b   Morgan, Martin ^a   Davison, Jerry ^a   Tannenbaum, Susan ^b   Claffey, Kevin ^b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

acquired uniparental disomy; breast cancer; copy number; estrogen receptor negative; loss of heterozygosity; single nucleotide polymorphism comparative genome hybridization

Indexed keywords

BRCA1 PROTEIN; ESTROGEN RECEPTOR;

ADULT; AGED; ARTICLE; BRCA 1 GENE; BREAST CARCINOMA; CHROMOSOME 15Q; CHROMOSOME 1Q; CHROMOSOME 21Q; CHROMOSOME 2P; CHROMOSOME 5Q; CHROMOSOME 8Q; CHROMOSOME DELETION; CHROMOSOME LOSS; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE; GENE MUTATION; GENETIC DIFFERENCE; GENETIC HETEROGENEITY; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ADULT; AGED; AGED, 80 AND OVER; BREAST NEOPLASMS; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC VARIATION; GENOMIC INSTABILITY; HUMANS; LOSS OF HETEROZYGOSITY; MIDDLE AGED; NEOPLASMS, HORMONE-DEPENDENT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECEPTORS, ESTROGEN;

EID: 79955497591     PISSN: 0008543X     EISSN: 10970142     Source Type: Journal    
DOI: 10.1002/cncr.25770     Document Type: Article

References (44)

1. Hanahan D, Weinberg RA,. The hallmarks of cancer. Cell. 2000; 100: 57-70. (Pubitemid 30046295)
2. Albertson DG,. Profiling breast cancer by array CGH. Breast Cancer Res Treat. 2003; 78: 289-298. (Pubitemid 36543209)
3. van Beers EH, Nederlof PM,. Array-CGH and breast cancer [serial online]. Breast Cancer Res. 2006; 8: 210.
4. Climent J, Dimitrow P, Fridlyand J, et al. Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer. Cancer Res. 2007; 67: 818-826. (Pubitemid 46192223)
5. Kallioniemi A, Kallioniemi OP, Sudar D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992; 258: 818-821.
6. Pinkel D, Albertson DG,. Array comparative genomic hybridization and its applications in cancer. Nat Genet. 2005; 37 (suppl): S11-S17. (Pubitemid 40770398)
7. Loo LW, Grove DI, Williams EM, et al. Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res. 2004; 64: 8541-8549. (Pubitemid 39552066)
8. Brommesson S, Jonsson G, Strand C, et al. Tiling array-CGH for the assessment of genomic similarities among synchronous unilateral and bilateral invasive breast cancer tumor pairs [serial online]. BMC Clin Pathol. 2008; 8: 6.
9. 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: 441-451.
10. Hagenkord JM, Monzon FA, Kash SF, Lilleberg S, Xie Q, Kant JA,. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. J Mol Diagn. 2010; 12: 184-196.
11. Maciejewski JP, Tiu RV, O'Keefe C,. Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Br J Haematol. 2009; 146: 479-488.
12. Fridlyand J, Snijders AM, Ylstra B, et al. Breast tumor copy number aberration phenotypes and genomic instability [serial online]. BMC Cancer. 2006; 6: 96.
13. Melchor L, Honrado E, Huang J, et al. Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer. Clin Cancer Res. 2007; 13: 7305-7313.
14. Loo LW, Ton C, Wang YW, et al. Differential patterns of allelic loss in estrogen receptor-positive infiltrating lobular and ductal breast cancer. Genes Chromosomes Cancer. 2008; 47: 1049-1066.
15. Waddell N, Arnold J, Cocciardi S, et al. Subtypes of familial breast tumours revealed by expression and copy number profiling. Breast Cancer Res Treat. 2010; 123: 661-677.
16. Richardson AL, Wang ZC, De Nicolo A, et al. X chromosomal abnormalities in basal-like human breast cancer. Cancer Cell. 2006; 9: 121-132. (Pubitemid 43202662)
17. Ronski K, Sanders M, Burleson JA, Moyo V, Benn P, Fang M,. Early growth response gene 1 (EGR1) is deleted in estrogen receptor-negative human breast carcinoma. Cancer. 2005; 104: 925-930. (Pubitemid 41170218)
18. Beroukhim R, Getz G, Nghiemphu L, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A. 2007; 104: 20007-20012.
19. Hupe P, Stransky N, Thiery J-P, Radvanyl F, Barillot E,. GLAD: Gain and Loss Analysis of DNA. R Statistical Package, Version 2.10.0. Paris, France: Institut Curie Bioinformatics Unit; 2010.
20. Smyth GK,. Limma: linear models for microarray data. In:, Gentleman VC, Dudoit S, Irizarry R, Huber W, eds. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. New York: Springer; 2005: 397-420.
21. Climent J, Garcia JL, Mao JH, Arsuaga J, Perez-Losada J,. Characterization of breast cancer by array comparative genomic hybridization. Biochem Cell Biol. 2007; 85: 497-508. (Pubitemid 47518044)
22. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits of human breast tumours. Nature. 2000; 406: 747-752.
23. Sorlie T, Perou CM, Tibshirani R, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001; 98: 10869-10874. (Pubitemid 32878711)
24. Melchor L, Benitez J,. An integrative hypothesis about the origin and development of sporadic and familial breast cancer subtypes. Carcinogenesis. 2008; 29: 1475-1482.
25. Wang ZC, Lin M, Wei LJ, et al. Loss of heterozygosity and its correlation with expression profiles in subclasses of invasive breast cancers. Cancer Res. 2004; 64: 64-71. (Pubitemid 38114083)
26. Chin K, DeVries S, Fridlyand J, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006; 10: 529-541. (Pubitemid 44854748)
27. Carlson JA, Ross JS, Slominski A, et al. Molecular diagnostics in melanoma. J Am Acad Dermatol. 2005; 52: 743-775. (Pubitemid 40614638)
28. University of Santa Cruz (UCSC). UCSC Genome Bioinformatics. Accessed June 15, 2010.
29. Downing TE, Oktay MH, Fazzari MJ, Montagna C,. Prognostic and predictive value of 16p12.1 and 16q22.1 copy number changes in human breast cancer. Cancer Genet Cytogenet. 2010; 198: 52-61.
30. Hansen LL, Yilmaz M, Overgaard J, Andersen J, Kruse TA,. Allelic loss of 16q23.2-24.2 is an independent marker of good prognosis in primary breast cancer. Cancer Res. 1998; 58: 2166-2169. (Pubitemid 28232903)
31. Nordgard SH, Johansen FE, Alnaes GI, et al. Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients. Genes Chromosomes Cancer. 2008; 47: 680-696. (Pubitemid 351847581)
32. Natrajan R, Lambros MB, Geyer FC, et al. Loss of 16q in high grade breast cancer is associated with estrogen receptor status: evidence for progression in tumors with a luminal phenotype? Genes Chromosomes Cancer. 2009; 48: 351-365.
33. Wennmalm K, Calza S, Ploner A, et al. Gene expression in 16q is associated with survival and differs between Sorlie breast cancer subtypes. Genes Chromosomes Cancer. 2007; 46: 87-97. (Pubitemid 44772875)
34. Farabegoli F, Hermsen MA, Ceccarelli C, et al. Simultaneous chromosome 1q gain and 16q loss is associated with steroid receptor presence and low proliferation in breast carcinoma. Mod Pathol. 2004; 17: 449-455. (Pubitemid 41646600)
35. van Agthoven T, Sieuwerts AM, Meijer-van Gelder ME, et al. Relevance of breast cancer antiestrogen resistance genes in human breast cancer progression and tamoxifen resistance. J Clin Oncol. 2009; 27: 542-549.
36. Vincent-Salomon A, Lucchesi C, Gruel N, et al. Integrated genomic and transcriptomic analysis of ductal carcinoma in situ of the breast. Clin Cancer Res. 2008; 14: 1956-1965. (Pubitemid 351551104)
37. Dancau AM, Wuth L, Waschow M, et al. PPFIA1 and CCND1 are frequently coamplified in breast cancer. Genes Chromosomes Cancer. 2010; 49: 1-8.
38. Pierga JY, Reis-Filho JS, Cleator SJ, et al. Microarray-based comparative genomic hybridisation of breast cancer patients receiving neoadjuvant chemotherapy. Br J Cancer. 2007; 96: 341-351. (Pubitemid 46160641)
39. Rebhun JF, Castro AF, Quilliam LA,. Identification of guanine nucleotide exchange factors (GEFs) for the Rap1 GTPase. Regulation of MR-GEF by M-Ras-GTP interaction. J Biol Chem. 2000; 275: 34901-34908.
40. Raghavan M, Lillington DM, Skoulakis S, et al. Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res. 2005; 65: 375-378.
41. Steinemann D, Arning L, Praulich I, et al. Mitotic recombination and compound-heterozygous mutations are predominant NF1-inactivating mechanisms in children with juvenile myelomonocytic leukemia and neurofibromatosis type 1. Haematologica. 2010; 95: 320-323.
42. Loman N, Johannsson O, Bendahl PO, Borg A, Ferno M, Olsson H,. Steroid receptors in hereditary breast carcinomas associated with BRCA1 or BRCA2 mutations or unknown susceptibility genes. Cancer. 1998; 83: 310-319. (Pubitemid 28317811)
43. Paciorkowski AR, Fang M,. Chromosomal microarray interpretation: what is a child neurologist to do? Pediatr Neurol. 2009; 41: 391-398.
44. Li J, Wang K, Li S, Timmermans-Wielenga V, et al. DNA copy number aberrations in breast cancer by array comparative genomic hybridization. Genomics Proteomics Bioinformatics. 2009; 7 (1-2): 13-24.