Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Vollebergh, Marieke A ^a   Klijn, Christiaan ^a   Schouten, Philip C ^a   Wesseling, Jelle ^a   Israeli, Danielle ^b   Ylstra, Bauke ^b   Wessels, Lodewyk F A ^a,c   Jonkers, Jos ^a   Linn, Sabine C ^a  

^a ANTONI VAN LEEUWENHOEK HOSPITAL   (Netherlands)

^b VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^c Department of Bioinformatics and Statistics Netherlands Cancer Institute Antoni Van Leeuwenhoek Hospital ^*  (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARRAY COMPARATIVE GENOMIC HYBRIDIZATION; ARTICLE; BIOINFORMATICS; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA EXTRACTION; DNA HYBRIDIZATION; GENETIC HETEROGENEITY; GENOMIC INSTABILITY; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; LYMPH NODE METASTASIS; NUCLEOTIDE SEQUENCE; TRIPLE NEGATIVE BREAST CANCER; BREAST TUMOR; CLINICAL TRIAL; CLUSTER ANALYSIS; FEMALE; GENETICS; GENOMICS; LYMPH NODE; METABOLISM; MULTICENTER STUDY; PATHOLOGY; PROGNOSIS;

BREAST NEOPLASMS; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; FEMALE; GENETIC HETEROGENEITY; GENOMIC INSTABILITY; GENOMICS; HUMANS; LYMPH NODES; LYMPHATIC METASTASIS; PROGNOSIS; TRIPLE NEGATIVE BREAST NEOPLASMS;

EID: 84905376653     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103177     Document Type: Article

References (34)

1. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100: 57-70. (Pubitemid 30046295)
2. Hanahan D,Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144: 646-74.
3. Weigelt B, Peterse JL, van't Veer LJ (2005) Breast cancer metastasis: markers and models. Nat.Rev.Cancer 5: 591-602. (Pubitemid 41081385)
4. Kuukasjarvi T, Karhu R, Tanner M, Kahkonen M, Schaffer A, et al. (1997) Genetic heterogeneity and clonal evolution underlying development of asynchronous metastasis in human breast cancer. Cancer Res 57: 1597-1604. (Pubitemid 27175581)
5. Nishizaki T, DeVries S, Chew K, Goodson WH III, Ljung BM, et al. (1997) Genetic alterations in primary breast cancers and their metastases: direct comparison using modified comparative genomic hybridization. Genes Chromosomes. Cancer 19: 267-272. (Pubitemid 27330238)
6. Cavalli LR, Urban CA, Dai D, de Assis S, Tavares DC, et al. (2003) Genetic and epigenetic alterations in sentinel lymph nodes metastatic lesions compared to their corresponding primary breast tumors. Cancer Genet. Cytogenet. 146: 33-40. (Pubitemid 37117432)
7. Torres L, Ribeiro FR, Pandis N, Andersen JA, Heim S, et al. (2007) Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases. Breast Cancer Res Treat. 102: 143-155. (Pubitemid 46452166)
8. Friedrich K, Weber T, Scheithauer J, Meyer W, Haroske G, et al. (2008) Chromosomal genotype in breast cancer progression: comparison of primary and secondary manifestations. Cell Oncol 30: 39-50. (Pubitemid 351161037)
9. Wang C, Iakovlev VV, Wong V, Leung S, Warren K, et al. (2009) Genomic alterations in primary breast cancers compared with their sentinel and more distal lymph node metastases: an aCGH study. Genes Chromosomes.Cancer 48: 1091-1101.
10. Desouki MM, Liao S, Huang H, Conroy J, Nowak NJ, et al. (2011) Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach. J Cancer Res Clin Oncol 137: 795-809.
11. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, et al. (2008) Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl.Acad.Sci.U.S.A 105: 16224-16229.
12. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, et al. (2000) Molecular portraits of human breast tumours. Nature 406: 747-752.
13. Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc.Natl.Acad.Sci.U S A 98: 10869-10874. (Pubitemid 32878711)
14. Smeets SJ, Harjes U, van Wieringen WN, Sie D, Brakenhoff RH, et al. (2011) To DNA or not to DNA? That is the question, when it comes to molecular subtyping for the clinic! Clin Cancer Res 17: 4959-4964.
15. Melchor L, Honrado E, Garcia MJ, Alvarez S, Palacios J, et al. (2008) Distinct genomic aberration patterns are found in familial breast cancer associated with different immunohistochemical subtypes. Oncogene 27: 3165-3175. (Pubitemid 351693170)
16. Stefansson OA, Jonasson JG, Johannsson OT, Olafsdottir K, Steinarsdottir M, et al. (2009) Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes. Breast Cancer Res. 11: R47.
17. Holstege H, van Beers E, Velds A, Liu X, Joosse SA, et al. (2010) Cross-species comparison of aCGH data from mouse and human B. BMC Cancer 10: 455.
18. Smid M, Hoes M, Sieuwerts AM, Sleijfer S, Zhang Y, et al. (2011) Patterns and incidence of chromosomal instability and their prognostic relevance in breast cancer subtypes. Breast Cancer Res.Treat. 128: 23-30.
19. Rodenhuis S, Bontenbal M, Beex LV, Wagstaff J, Richel DJ, et al. (2003) High-dose chemotherapy with hematopoietic stem-cell rescue for high-risk breast cancer. N Engl J Med 349: 7-16. (Pubitemid 36765098)
20. Van De Vijver MJ, Peterse JL, Mooi WJ, Wisman P, Lomans J, et al. (1988) Neu-protein overexpression in breast cancer. Association with comedo-type ductal carcinoma in situ and limited prognostic value in stage II breast cancer. N Engl J Med 319: 1239-1245. (Pubitemid 18267063)
21. van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FB, et al. (2006) A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 94: 333-337. (Pubitemid 43151556)
22. Buffart TE, Israeli D, Tijssen M, Vosse SJ, Mrsic A, et al. (2008) Across array comparative genomic hybridization: a strategy to reduce reference channel hybridizations. Genes Chromosomes.Cancer 47: 994-1004.
23. Schouten PC, van Dyk E, Braaf LM, Mulder L, Lips EH, et al. (2013) Platform comparisons for identification of breast cancers with a BRCA-like copy number profile. Breast Cancer Res Treat 139: 317-327
24. Klijn C, Holstege H, de Ridder J, Liu X, Reinders M, et al. (2008) Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data. Nucleic Acids Res 36: e13.
25. de Ronde JJ, Klijn C, Velds A, Holstege H, Reinders MJ, et al. (2010) KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data. BMC.Res Notes 3: 298.
26. Weigelt B, Glas AM, Wessels LF, Witteveen AT, Peterse JL, et al. (2003) Gene expression profiles of primary breast tumors maintained in distant metastases. Proc.Natl.Acad.Sci.U.S.A 100: 15901-15905. (Pubitemid 38021087)
27. Falck AK, Ferno M, Bendahl PO, Ryden L (2010) Does analysis of biomarkers in tumor cells in lymph node metastases give additional prognostic information in primary breast cancer? World J Surg. 34: 1434-1441.
28. Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, et al. (2010) Inferring tumor progression from genomic heterogeneity. Genome Res 20: 68-80.
29. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94.
30. Turner NC, Reis-Filho JS (2006) Basal-like breast cancer and the BRCA1 phenotype. Oncogene 25: 5846-5853. (Pubitemid 44453440)
31. Lips EH, Mulder L, Hannemann J, Laddach N, Vrancken Peeters MT, et al. (2011) Indicators of homologous recombination deficiency in breast cancer and association with response to neoadjuvant chemotherapy. Ann.Oncol. 22: 870-876.
32. Vollebergh MA, Lips EH, Nederlof PM, Wessels LF, Schmidt MK, et al. (2011) An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients. Ann.Oncol. 22: 1561-1570.
33. Holstege H, Horlings HM, Velds A, Langerod A, Borresen-Dale AL, 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.
34. Drost R, Bouwman P, Rottenberg S, Boon U, Schut E, et al. (2011) BRCA1 RING function is essential for tumor suppression but dispensable for therapy resistance. Cancer Cell 20: 797-809.