Platform comparisons for identification of breast cancers with a BRCA-like copy number profile

Breast Cancer Research and Treatment

Volumn 139, Issue 2, 2013, Pages 317-327

  Schouten, Philip C ^a   Van Dyk, Ewald ^a   Braaf, Linde M ^a   Mulder, Lennart ^a   Lips, Esther H ^a   De Ronde, Jorma J ^a   Holtman, Laura ^a   Wesseling, Jelle ^a   Hauptmann, Michael ^a   Wessels, Lodewyk F A ^a,b   Linn, Sabine C ^a   Nederlof, Petra M ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

BRCA1; BRCA2; Chemotherapy benefit; Classification; Clinical genetics; Copy number profile

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BREAST CANCER; CLASSIFICATION ALGORITHM; COMPARATIVE GENE MAPPING; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DATA ANALYSIS; HOMOLOGOUS RECOMBINATION; HUMAN; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SUPPORT VECTOR MACHINE; TUMOR SUPPRESSOR GENE;

BRCA1 PROTEIN; BRCA2 PROTEIN; BREAST NEOPLASMS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; FEMALE; HUMANS; MEDICAL INFORMATICS; NEOPLASM STAGING; SENSITIVITY AND SPECIFICITY;

EID: 84878750494     PISSN: 01676806     EISSN: 15737217     Source Type: Journal    
DOI: 10.1007/s10549-013-2558-2     Document Type: Article

References (35)

1. Thompson D, Easton D (2004) The genetic epidemiology of breast cancer genes. J Mammary Gland Biol Neoplasia 9(3):221-236
2. Venkitaraman AR (2009) Linking the cellular functions of BRCA genes to cancer pathogenesis and treatment. Annu Rev Pathol 4:461-487
3. Wessels LFA, van Welsem T, Hart AAM, van't Veer LJ, Reinders MJT, Nederlof PM (2002) Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res 62(23):7110-7117
4. van Beers EH, van Welsem T, Wessels LFA, Li Y, Oldenburg RA, Devilee P et al (2005) Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 65(3):822-827
5. Joosse SA, van Beers EH, Tielen IHG, Horlings H, Peterse JL, Hoogerbrugge N 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
6. Joosse SA, Brandwijk KIM, Devilee P, Wesseling J, Hogervorst FBL, Verhoef S et al (2012) Prediction of BRCA2-association in hereditary breast carcinomas using array-CGH. Breast Cancer Res Treat 132(2):379-389
7. Joosse SA, Brandwijk KIM, Mulder L, Wesseling J, Hannemann J, Nederlof PM (2011) Genomic signature of BRCA1 deficiency in sporadic basal-like breast tumors. Genes Chromosom Cancer 50(2):71-81
8. Vollebergh MA, Lips EH, Nederlof PM, Wessels LFA, Schmidt MK, van Beers EH 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(7):1561-1570
9. Linn S, Lips E, Nederlof P, Wessels L, Wesseling J, van de Vijver M, et al (2011) Genomic patterns resembling BRCA-mutated breast cancers and benefit of intensified carboplatin-based chemotherapy in HER2-negative breast cancer. J Clin Oncol 29(suppl; abstr 10505)
10. Costa JL, Meijer G, Ylstra B, Caldas C (2008) Array comparative genomic hybridization copy number profiling: a new tool for translational research in solid malignancies. Semin Radiat Oncol 18(2):98-104
11. Baumbusch LO, Aarøe J, Johansen FE, Hicks J, Sun H, Bruhn L et al (2008) Comparison of the Agilent, ROMA/NimbleGen and Illumina platforms for classification of copy number alterations in human breast tumors. BMC Genomics 9:379
12. Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10:588
13. Hester SD, Reid L, Nowak N, Jones WD, Parker JS, Knudtson K et al (2009) Comparison of comparative genomic hybridization technologies across microarray platforms. J Biomol Technol 20(2):135-151
14. Wicker N, Carles A, Mills IG, Wolf M, Veerakumarasivam A, Edgren H et al (2007) A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 8:84
15. Krijgsman O, Israeli D, Haan JC, van Essen HF, Smeets SJ, Eijk PP et al (2012) CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosom Cancer 51(4):344-352
16. Rodenhuis S, Bontenbal M, Beex LVAM, Wagstaff J, Richel DJ, Nooij MA et al (2003) High-dose chemotherapy with hematopoietic stem-cell rescue for high-risk breast cancer. N Engl J Med 349(1):7-16
17. R Development Core Team. R: a language and environment for statistical computing (Internet) (2012) R Foundation for Statistical Computing, Vienna. http://www.R-project.org/. Accessed 7 May 2013
18. Venkatraman ES, Olshen AB (2007) A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6):657-663
19. Picard F, Lebarbier E, Hoebeke M, Rigaill G, Thiam B, Robin S (2011) Joint segmentation, calling, and normalization of multiple CGH profiles. Biostatistics 12(3):413-428
20. Zhang NR, Siegmund DO (2007) A modified Bayes information criterion with applications to the analysis of comparative genomic hybridization data. Biometrics 63(1):22-32
21. Duin R, Juszczak P, Paclik P, Pekalska E, de Ridder D (2007) A Matlab toolbox for pattern recognition. Delft University of Technology, Delft
22. Coombes KR (2012) ClassDiscovery: classes and methods for "class discovery" with microarrays or proteomics (Internet). http:// bioinformatics.mdanderson.org/main/OOMPA:Overview. Accessed 7 May 2013
23. De Ronde J, Klijn C, Velds A (2010) KCsmart: multi sample aCGH analysis package using kernel convolution. BMC Res Notes 11(3):298
24. Therneau T (2012) A Package for survival analysis in S. R package version 2.37-2. http://CRAN.R-project.org/package=survival. Accessed 7 May 2013
25. Stevenson M (2012) epiR: an R package for the analysis of epidemiological data (Internet). http://CRAN.R-project.org/package=epiR. Accessed 7 May 2013
26. Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99(10):6567-6572
27. Weigelt B, Mackay A, A'hern R, Natrajan R, Tan DSP, Dowsett M et al (2010) Breast cancer molecular profiling with single sample predictors: a retrospective analysis. Lancet Oncol 11(4):339-349
28. Mackay A, Weigelt B, Grigoriadis A, Kreike B, Natrajan R, A'Hern R et al (2011) Microarray-based class discovery for molecular classification of breast cancer: analysis of interobserver agreement. J Natl Cancer Inst 103(8):662-673
29. Colombo P-E, Milanezi F, Weigelt B, Reis-Filho JS (2011) Microarrays in the 2010s: the contribution of microarray-based gene expression profiling to breast cancer classification, prognostication and prediction. Breast Cancer Res 13(3):212
30. Jong K, Marchiori E, van der Vaart A, Chin S-F, Carvalho B, Tijssen M et al (2007) Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 26(10):1499-1506
31. Sargent DJ, Conley BA, Allegra C, Collette L (2005) Clinical trial designs for predictive marker validation in cancer treatment trials. J Clin Oncol 23(9):2020-2027
32. Vollebergh MA, Jonkers J, Linn SC (2012) Genomic instability in breast and ovarian cancers: translation into clinical predictive biomarkers. Cell Mol Life Sci 69(2):223-245
33. Beelen K, Zwart W, Linn SC (2012) Can predictive biomarkers in breast cancer guide adjuvant endocrine therapy? Nat Rev Clin Oncol 9(9):529-541
34. McShane LM, Altman DG, Sauerbrei W, Taube SE, Gion M, Clark GM (2006) REporting recommendations for tumor MARKer prognostic studies (REMARK). Breast Cancer Res Treat 100(2):229-235
35. Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M et al (2010) Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 38(14):e151