Nonfamilial breast cancer subtypes

Methods in Molecular Biology

Volumn 973, Issue , 2013, Pages 279-295

  Ringnér, Markus ^a   Staaf, Johan ^a   Jönsson, Göran ^a  

^a NONE

Author keywords

ACGH; Amplification; Breast cancer; Deletion; Gene expression; Prognosis; Subtypes

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; CLAUDIN; CYTOKERATIN 5; CYTOKERATIN 6; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; FIBROBLAST GROWTH FACTOR RECEPTOR 1; PROGESTERONE RECEPTOR;

ALGORITHM; AMPLICON; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BREAST CANCER; CANCER CLASSIFICATION; CANCER GENETICS; CANCER PROGNOSIS; CHROMOSOME 10P; CHROMOSOME 17Q; CHROMOSOME 3Q; CHROMOSOME 4; CHROMOSOME 5Q; CHROMOSOME ABERRATION; DNA REPAIR; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BREAST; BREAST TUMOR; CLASSIFICATION; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENETICS; METABOLISM; METHODOLOGY; PATHOLOGY; REVIEW;

BREAST; BREAST NEOPLASMS; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; HUMANS;

MLCS; MLOWN;

EID: 84880842987     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-281-0_18     Document Type: Article

References (72)

1. Perou CM, Sorlie T, Eisen MB et al (2000) Molecular portraits of human breast tumours. Nature 406(6797): 747-752
2. Sorlie T, Tibshirani R, Parker J et al (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 100(14): 8418-8423
3. Sorlie T, Perou CM, Tibshirani R et al (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 98(19): 10869-10874
4. Cheang MC, Chia SK, Voduc D et al (2009) Ki67 index, her2 status, and prognosis of patients with luminal b breast cancer. J Natl Cancer Inst 101(10): 736-750
5. Jonsson G, Staaf J, Vallon-Christersson J et al (2010) Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res 12(3): R42
6. Holm K, Hegardt C, Staaf J et al (2010) Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 12(3): R36
7. Parker JS, Mullins M, Cheang MC et al (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J Clin Oncol 27(8): 1160-1167
8. Guedj M, Marisa L, De Reynies A et al (2011) A refined molecular taxonomy of breast cancer. Oncogene 31(9): 1196-1206
9. Farmer P, Bonnefoi H, Becette V et al (2005) Identification of molecular apocrine breast tumours by microarray analysis. Oncogene 24(29): 4660-4671
10. Teschendorff AE, Miremadi A, Pinder SE et al (2007) An immune response gene expression module identifies a good prognosis subtype in estrogen receptor negative breast cancer. Genome Biol 8(8): R157
11. Herschkowitz JI, Simin K, Weigman VJ et al (2007) Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 8(5): R76
12. Prat A, Parker JS, Karginova O et al (2010) Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res 12(5): R68
13. Creighton CJ, Li X, Landis M et al (2009) Residual breast cancers after conventional therapy display mesenchymal as well as tumorinitiating features. Proc Natl Acad Sci USA 106(33): 13820-13825
14. Nielsen TO, Parker JS, Leung S et al (2010) A comparison of pam50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer. Clin Cancer Res 16(21): 5222-5232
15. Sotiriou C, Pusztai L. (2009) Gene-expression signatures in breast cancer. N Engl J Med 360(8): 790-800
16. Desmedt C, Haibe-Kains B, Wirapati P et al (2008) Biological processes associated with breast cancer clinical outcome depend on the molecular subtypes. Clin Cancer Res 14(16): 5158-5165
17. Reyal F, Van Vliet MH, Armstrong NJ et al (2008) 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 10(6): R93
18. Finak G, Bertos N, Pepin F et al (2008) Stromal gene expression predicts clinical outcome in breast cancer. Nat Med 14(5): 518-527
19. Staaf J, Ringner M, Vallon-Christersson J et al (2010) Identification of subtypes in human epidermal growth factor receptor 2-positive breast cancer reveals a gene signature prognostic of outcome. J Clin Oncol 28(11): 1813-1820
20. Pollack JR, Sorlie T, Perou CM et al (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 99(20): 12963-12968
21. Hyman E, Kauraniemi P, Hautaniemi S et al (2002) Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res 62(21): 6240-6245
22. Holland DG, Burleigh A, Git A et al (2011) Znf703 is a common luminal b breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium. EMBO Mol Med 3(3): 167-180
23. Russnes HG, Vollan HK, Lingjaerde OC et al (2010) Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med 2(38): 38ra47
24. Chin K, Devries S, Fridlyand J et al (2006) Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 10(6): 529-541
25. Andre F, Job B, Dessen P et al (2009) Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. Clin Cancer Res 15(2): 441-451
26. Owens MA, Horten BC, Da Silva MM (2004) Her2 amplification ratios by fluorescence in situ hybridization and correlation with immu-nohistochemistry in a cohort of 6556 breast cancer tissues. Clin Breast Cancer 5(1): 63-69
27. Slamon DJ, Clark GM, Wong SG et al (1987) Human breast cancer: correlation of relapse and survival with amplification of the her-2/neu oncogene. Science 235(4785): 177-182
28. Ross JS, Fletcher JA, Linette GP et al (2003) The her-2/neu gene and protein in breast cancer 2003: biomarker and target of therapy. Oncologist 8(4): 307-325
29. Geyer CE, Forster J, Lindquist D et al (2006) Lapatinib plus capecitabine for her2-positive advanced breast cancer. N Engl J Med 355(26): 2733-2743
30. Piccart-Gebhart M.J., Procter M, Leyland-Jones B et al (2005) Trastuzumab after adjuvant chemotherapy in her2-positive breast cancer. N Engl J Med 353(16): 1659-1672
31. Slamon DJ, Leyland-Jones B, Shak S et al (2001) Use of chemotherapy plus a monoclonal antibody against her2 for metastatic breast cancer that overexpresses her2. N Engl J Med 344(11): 783-792
32. Sircoulomb F, Bekhouche I, Finetti P et al (2010) Genome profiling of erbb2-amplified breast cancers. BMC Cancer 10: 539
33. Staaf J, Jonsson G, Ringner M et al (2010) High-resolution genomic and expression analyses of copy number alterations in her2-amplified breast cancer. Breast Cancer Res 12(3): R25
34. Letessier A, Sircoulomb F, Ginestier C et al (2006) Frequency, prognostic impact, and subtype association of 8p12, 8q24, 11q13, 12p13, 17q12, and 20q13 amplifications in breast cancers. BMC Cancer 6: 245
35. Garcia MJ, Pole JC, Chin SF et al (2005) A 1 mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 24(33): 5235-5245
36. Reis-Filho J.S., Simpson PT, Turner NC et al (2006) Fgfr1 emerges as a potential therapeutic target for lobular breast carcinomas. Clin Cancer Res 12(22): 6652-6662
37. Sircoulomb F, Nicolas N, Ferrari A et al (2011) Znf703 gene amplification at 8p12 specifies luminal b breast cancer. EMBO Mol Med 3(3): 153-166
38. Bostner J, Ahnstrom Waltersson M, Fornander T et al (2007) Amplification of ccnd1 and pak1 as predictors of recurrence and tamoxifen resistance in postmenopausal breast cancer. Oncogene 26(49): 6997-7005
39. Holm K, Staaf J, Jonsson G et al (2012) Characterisation of amplification patterns and target genes at chromosome 11q13 in ccnd1-amplified sporadic and familial breast tumours. Breast Cancer Res Treat 133(2): 583-594
40. Hughes-Davies L., Huntsman D, Ruas M et al (2003) Emsy links the brca2 pathway to sporadic breast and ovarian cancer. Cell 115(5): 523-535
41. Karlsson E, Waltersson MA, Bostner J et al (2011) High-resolution genomic analysis of the 11q13 amplicon in breast cancers identifies synergy with 8p12 amplification, involving the mtor targets s6k2 and 4ebp1. Genes Chromosomes Cancer 50(10): 775-787
42. Kwek SS, Roy R, Zhou H et al (2009) Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis. Oncogene 28(17): 1892-1903
43. Albertson DG, Ylstra B, Segraves R et al (2000) Quantitative mapping of amplicon structure by array cgh identifies cyp24 as a candidate oncogene. Nat Genet 25(2): 144-146
44. Bergamaschi A, Kim YH, Wang P et al (2006) Distinct patterns of DNA copy number alteration are associated with different clinicopatho-logical features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 45(11): 1033-1040
45. Staaf J, Jonsson G, Ringner M et al (2007) Normalization of array-cgh data: influence of copy number imbalances. BMC Genomics 8: 382
46. Autio R, Hautaniemi S, Kauraniemi P et al (2003) Cgh-plotter: matlab toolbox for cgh-data analysis. Bioinformatics 19(13): 1714-1715
47. Hupe P, Stransky N, Thiery JP et al (2004) Analysis of array cgh data: from signal ratio to gain and loss of DNA regions. Bioinformatics 20(18): 3413-3422
48. Venkatraman ES, Olshen A.B. (2007) A faster circular binary segmentation algorithm for the analysis of array cgh data. Bioinformatics 23(6): 657-663
49. Peiffer DA, Le JM, Steemers FJ et al (2006) High-resolution genomic profiling of chromosomal aberrations using infinium wholegenome genotyping. Genome Res 16(9): 1136-1148
50. Assie G, Laframboise T, Platzer P et al (2008) Snp arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. Am J Hum Genet 82(4): 903-915
51. Popova T, Manie E, Stoppa-Lyonnet D et al (2009) Genome alteration print (gap): a tool to visualize and mine complex cancer genomic profiles obtained by snp arrays. Genome Biol 10(11): R128
52. Van Loo P., Nordgard SH, Lingjaerde OC et al (2010) Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA 107(39): 16910-16915
53. Beroukhim R, Getz G, Nghiemphu L et al (2007) Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci USA 104(50): 20007-20012
54. Mermel CH, Schumacher SE, Hill B et al (2011) Gistic2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 12(4): R41
55. Hicks J, Krasnitz A, Lakshmi B et al (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16(12): 1465-1479
56. Chin SF, Teschendorff AE, Marioni JC et al (2007) High-resolution acgh and expression profiling identifies a novel genomic subtype of er negative breast cancer. Genome Biol 8(10): R215
57. Jonsson G, Naylor TL, Vallon-Christersson J et al (2005) Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 65(17): 7612-7621
58. Joosse SA, Van Beers EH, Tielen IH et al (2009) Prediction of brca1-association in hereditary non-brca1/2 breast carcinomas with array-cgh. Breast Cancer Res Treat 116(3): 479-489
59. Holstege H, Horlings HM, Velds A et al (2010) Brca1-mutated and basal-like breast cancers have similar acgh profiles and a high incidence of protein truncating tp53 mutations. BMC Cancer 10: 654
60. Cortesi L, Turchetti D, Bertoni C et al (2000) Comparison between genotype and phenotype identifies a high-risk population carrying brca1 mutations. Genes Chromosomes Cancer 27(2): 130-135
61. Lakhani SR, Gusterson BA, Jacquemier J et al (2000) The pathology of familial breast cancer: histological features of cancers in families not attributable to mutations in brca1 or brca2. Clin Cancer Res 6(3): 782-789
62. Lakhani SR, Jacquemier J, Sloane JP et al (1998) Multifactorial analysis of differences between sporadic breast cancers and cancers involving brca1 and brca2 mutations. J Natl Cancer Inst 90(15): 1138-1145
63. Stefansson OA, Jonasson JG, Olafsdottir K et al (2011) Cpg island hypermethylation of brca1 and loss of prb as co-occurring events in basal/triple-negative breast cancer. Epigenetics 6(5): 638-649
64. Joosse SA, Brandwijk KI, Mulder L et al (2011) Genomic signature of brca1 deficiency in sporadic basal-like breast tumors. Genes Chromosomes Cancer 50(2): 71-81
65. Saal LH, Gruvberger-Saal SK, Persson C et al (2008) Recurrent gross mutations of the pten tumor suppressor gene in breast cancers with deficient dsb repair. Nat Genet 40(1): 102-107
66. Smid M, Hoes M, Sieuwerts AM et al (2011) Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes. Breast Cancer Res Treat 128(1): 23-30
67. Thompson PA, Brewster AM, Kim-Anh D et al (2011) Selective genomic copy number imbalances and probability of recurrence in earlystage breast cancer. PLoS One 6(8): e23543
68. Borg A, Tandon AK, Sigurdsson H et al (1990) Her-2/neu amplification predicts poor survival in node-positive breast cancer. Cancer Res 50(14): 4332-4337
69. Carter SL, Eklund AC, Kohane IS et al (2006) A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 38(9): 1043-1048
70. Farmer H, Mccabe N, Lord CJ et al (2005) Targeting the DNA repair defect in brca mutant cells as a therapeutic strategy. Nature 434(7035): 917-921
71. Fong PC, Boss DS, Yap TA et al (2009) Inhibition of poly(adp-ribose) polymerase in tumors from brca mutation carriers. N Engl J Med 361(2): 123-134
72. Silver DP, Richardson AL, Eklund AC et al (2010) Efficacy of neoadjuvant cisplatin in triple-negative breast cancer. J Clin Oncol 28(7): 1145-1153