Comparative genomic hybridisation arrays: High-throughput tools to determine targeted therapy in breast cancer

Pathobiology

Volumn 75, Issue 2, 2008, Pages 63-74

  Tan, David S P ^a   Reis Filho, Jorge S ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

Amplification; Breast cancer; Comparative genomic hybridisation; Microarrays; Molecular genetics

Indexed keywords

COMPLEMENTARY DNA;

ANEUPLOIDY; BREAST CANCER; CANCER CELL CULTURE; CANCER RESEARCH; CHROMOSOME TRANSLOCATION; COMPARATIVE GENOMIC HYBRIDIZATION; DATA ANALYSIS; DNA MICROARRAY; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; HETEROZYGOSITY LOSS; HIGH THROUGHPUT SCREENING; HUMAN; MICROARRAY ANALYSIS; ONCOGENE; POLYPLOIDY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; RNA INTERFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

BREAST NEOPLASMS; DNA, NEOPLASM; FEMALE; GENE TARGETING; GENE THERAPY; GENES, NEOPLASM; HUMANS; HYBRIDIZATION, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 44949149181     PISSN: 10152008     EISSN: None     Source Type: Journal    
DOI: 10.1159/000123844     Document Type: Review

References (84)

1. Weinstein IB: Cancer: addiction to oncogenes - the Achilles heal of cancer. Science 2002;297:63-64.
2. Weinstein IB, Joe AK: Mechanisms of disease: oncogene addiction - a rationale for molecular targeting in cancer therapy. Nat Clin Pract Oncol 2006;3:448-457.
3. Hanahan D, Weinberg RA: The hallmarks of cancer. Cell 2000;100:57-70.
4. Weinstein IB: Disorders in cell circuitry during multistage carcinogenesis: the role of homeostasis. Carcinogenesis 2000;21:857-864.
5. Felsher DW, Bishop JM: Reversible tumori-genesis by MYC in hematopoietic lineages. Mol Cell 1999;4:199-207.
6. Kantarjian HM, Giles F, Quintas-Cardama A, Cortes J: Important therapeutic targets in chronic myelogenous leukemia. Clin Cancer Res 2007;13:1089-1097.
7. Lohrisch C, Piccart M: An overview of HER2. Semin Oncol 2001;28:3-11.
8. Hoglund M, Gisselsson D, Sall T, Mitelman F: Coping with complexity: multivariate analysis of tumor karyotypes. Cancer Genet Cytogenet 2002;135:103-109.
9. Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, Gray JW, Waldman F, Pinkel D: Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992;258:818-821.
10. Tan DS, Lambros MB, Natrajan R, Reis-Filho JS: Getting it right: designing microarray (and not 'microawry') comparative genomic hybridization studies for cancer research. Lab Invest 2007;87:737-754.
11. Oostlander AE, Meijer GA, Ylstra B: Microarray-based comparative genomic hybridization and its applications in human genetics. Clin Genet 2004;66:488-495.
12. Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA: BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 2006;34: 445-450.
13. Jong K, Marchiori E, van der Vaart A, Chin SF, Carvalho B, Tijssen M, Eijk PP, van den Ijssel P, Grabsch H, Quirke P, Oudejans JJ, Meijer GA, Caldas C, Ylstra B: Cross-platform array comparative genomic hybridization meta-analysis separates hematopoietic and mesenchymal from epithelial tumors. Oncogene 2007;26:1499-1506.
14. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR: Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006;45:1033-1040.
15. Tanami H, Tsuda H, Okabe S, Iwai T, Sugihara K, Imoto I, Inazawa J: Involvement of cyclin D3 in liver metastasis of colorectal cancer, revealed by genome-wide copy-number analysis. Lab Invest 2005;85:1118-1129.
16. Reis-Filho JS, Simpson PT, Gale T, Lakhani SR: The molecular genetics of breast cancer: the contribution of comparative genomic hybridization. Pathol Res Pract 2005;201:713-725.
17. Reis-Filho JS, Simpson PT, Jones C, Steele D, Mackay A, Iravani M, Fenwick K, Valgeirsson H, Lambros M, Ashworth A, Palacios J, Schmitt F, Lakhani SR: Pleomorphic lobular carcinoma of the breast: role of comprehensive molecular pathology in characterization of an entity. J Pathol 2005;207:1-13.
18. Cheng KW, Lahad JP, Kuo WL, Lapuk A, Yamada K, Auersperg N, Liu J, Smith-McCune K, Lu KH, Fishman D, Gray JW, Mills GB: The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers. Nat Med 2004;10:1251-1256.
19. Reis-Filho JS, Simpson PT, Turner NC, Lambros MB, Jones C, Mackay A, Grigoriadis A, Sarrio D, Savage K, Dexter T, Iravani M, Fenwick K, Weber B, Hardisson D, Schmitt FC, Palacios J, Lakhani SR, Ashworth A: FGFR1 emerges as a potential therapeutic target for lobular breast carcinomas. Clin Cancer Res 2006;12:6652-6662.
20. Reis-Filho JS, Pinheiro C, Lambros MB, Milanezi F, Carvalho S, Savage K, Simpson PT, Jones C, Swift S, Mackay A, Reis RM, Hornick JL, Pereira EM, Baltazar F, Fletcher CD, Ashworth A, Lakhani SR, Schmitt FC: EGFR amplification and lack of activating mutations in metaplastic breast carcinomas. J Pathol 2006;209:445-453.
21. Bentley DR: Whole-genome re-sequencing. Curr Opin Genet Dev 2006;16:545-552.
22. Simon R, Radmacher MD, Dobbin K, McShane LM: Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003;95:14-18.
23. Pinkel D, Albertson DG: Array comparative genomic hybridization and its applications in cancer. Nat Genet 2005;37(suppl):S11-S17.
24. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO: Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 1999;23:41-46.
25. Lockwood WW, Chari R, Chi B, Lam WL: Recent advances in array comparative genomic hybridization technologies and their applications in human genetics. Eur J Hum Genet 2006;14:139-148.
26. Johnson NA, Hamoudi RA, Ichimura K, Liu L, Pearson DM, Collins VP, Du MQ: Application of array CGH on archival formalin-fixed paraffin-embedded tissues including small numbers of microdissected cells. Lab Invest 2006;86:968-978.
27. Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C: Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics 2006;87:298-306.
28. Fan JB, Chee MS, Gunderson KL: Highly parallel genomic assays. Nat Rev Genet 2006;7:632-644.
29. Ji H, Kumm J, Zhang M, Farnam K, Salari K, Faham M, Ford JM, Davis RW: Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma. Cancer Res 2006;66:7910-7919.
30. Wang Y, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M: Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res 2005;33:e183.
31. van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FB, Verhoef S, Nederlof PM: A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 2006;94:333-337.
32. Baldwin C, Garnis C, Zhang L, Rosin MP, Lam WL: Multiple microalterations detected at high frequency in oral cancer. Cancer Res 2005;65:7561-7567.
33. Nessling M, Richter K, Schwaenen C, Roerig P, Wrobel G, Wessendorf S, Fritz B, Bentz M, Sinn HP, Radlwimmer B, Lichter P: Candidate genes in breast cancer revealed by microarray-based comparative genomic hybridization of archived tissue. Cancer Res 2005;65:439-447.
34. van Dekken H, Paris PL, Albertson DG, Alers JC, Andaya A, Kowbel D, van der Kwast TH, Pinkel D, Schroder FH, Vissers KJ, Wildhagen MF, Collins C: Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis. Genes Chromosomes Cancer 2004;39:249-256.
35. Harvell JD, Kohler S, Zhu S, Hernandez-Boussard T, Pollack JR, van de Rijn M: High-resolution array-based comparative genomic hybridization for distinguishing paraffin-embedded Spitz nevi and melanomas. Diagn Mol Pathol 2004;13:22-25.
36. Linn SC, West RB, Pollack JR, Zhu S, Hernandez-Boussard T, Nielsen TO, Rubin BP, Patel R, Goldblum JR, Siegmund D, Botstein D, Brown PO, Gilks CB, van de Rijn M: Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans. Am J Pathol 2003;163:2383-2395.
37. Thompson ER, Herbert SC, Forrest SM, Campbell IG: Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue. Hum Mutat 2005;26:384-389.
38. Weiss MM, Hermsen MA, Meijer GA, van Grieken NC, Baak JP, Kuipers EJ, van Diest PJ: Comparative genomic hybridisation. Mol Pathol 1999;52:243-251.
39. Arriola E, Lambros MB, Jones C, Dexter T, Mackay A, Tan DS, Tamber N, Fenwick K, Ashworth A, Dowsett M, Reis-Filho JS: Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation. Lab Invest 2007;87:75-83.
40. Raponi M, Zhang Y, Yu J, Chen G, Lee G, Taylor JM, Macdonald J, Thomas D, Moskaluk C, Wang Y, Beer DG: Gene expression signatures for predicting prognosis of squamous cell and adenocarcinomas of the lung. Cancer Res 2006;66:7466-7472.
41. Pirker C, Raidl M, Steiner E, Elbling L, Holzmann K, Spiegl-Kreinecker S, Aubele M, Grasl-Kraupp B, Marosi C, Micksche M, Berger W: Whole genome amplification for CGH analysis: Linker-adapter PCR as the method of choice for difficult and limited samples. Cytometry A 2004;61:26-34.
42. Tanabe C, Aoyagi K, Sakiyama T, Kohno T, Yanagitani N, Akimoto S, Sakamoto M, Sakamoto H, Yokota J, Ohki M, Terada M, Yoshida T, Sasaki H: Evaluation of a whole-genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA. Genes Chromosomes Cancer 2003;38:168-176.
43. Fiegler H, Geigl JB, Langer S, Rigler D, Porter K, Unger K, Carter NP, Speicher MR: High resolution array-CGH analysis of single cells. Nucleic Acids Res 2007;35:e15.
44. Aviel-Ronen S, Qi Zhu C, Coe BP, Liu N, Watson SK, Lam WL, Tsao MS: Large fragment Bst DNA polymerase for whole genome amplification of DNA from formalin-fixed paraffin-embedded tissues. BMC Genomics 2006;7:312.
45. Lovmar L, Syvanen AC: Multiple displacement amplification to create a long-lasting source of DNA for genetic studies. Hum Mutat 2006;27:603-614.
46. Lage JM, Leamon JH, Pejovic T, Hamann S, Lacey M, Dillon D, Segraves R, Vossbrinck B, Gonzalez A, Pinkel D, Albertson DG, Costa J, Lizardi PM: Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 2003;13:294-307.
47. Courjal F, Cuny M, Simony-Lafontaine J, Louason G, Speiser P, Zeillinger R, Rodriguez C, Theillet C: Mapping of DNA amplifications at 15 chromosomal localizations in 1,875 breast tumors: definition of phenotypic groups. Cancer Res 1997;57:4360-4367.
48. Gelsi-Boyer V, Orsetti B, Cervera N, Finetti P, Sircoulomb F, Rouge C, Lasorsa L, Letessier A, Ginestier C, Monville F, Esteyries S, Adelaide J, Esterni B, Henry C, Ethier SP, Bibeau F, Mozziconacci MJ, Charafe-Jauffret E, Jacquemier J, Bertucci F, Birnbaum D, Theillet C, Chaffanet M: Comprehensive profiling of 8p11-12 amplification in breast cancer. Mol Cancer Res 2005;3:655-667.
49. Ginestier C, Cervera N, Finetti P, Esteyries S, Esterni B, Adelaide J, Xerri L, Viens P, Jacquemier J, Charafe-Jauffret E, Chaffanet M, Birnbaum D, Bertucci F: Prognosis and gene expression profiling of 20q13-amplified breast cancers. Clin Cancer Res 2006;12:4533-4544.
50. Natrajan R, Williams RD, Grigoriadis A, Mackay A, Fenwick K, Ashworth A, Dome JS, Grundy PE, Pritchard-Jones K, Jones C: Delineation of a 1Mb breakpoint region at 1p13 in Wilms tumors by fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 2007;46:607-615.
51. Dobbin K, Simon R: Sample size determination in microarray experiments for class comparison and prognostic classification. Biostatistics 2005;6:27-38.
52. Ein-Dor L, Zuk O, Domany E: Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 2006;103:5923-5928.
53. Simon R: Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol 2005;23:7332-7341.
54. Pawitan Y, Murthy KR, Michiels S, Ploner A: Bias in the estimation of false discovery rate in microarray studies. Bioinformatics 2005;21:3865-3872.
55. Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H: Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet 2004;13:1303-1313.
56. Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J: QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007;35:2013-2025.
57. Hupe P, Stransky N, Thiery JP, Radvanyi F, Barillot E: Analysis of array CGH data: from signal ratio to gain and loss of DNA regions. Bioinformatics 2004;20:3413-3422.
58. Shah SP, Xuan X, DeLeeuw RJ, Khojasteh M, Lam WL, Ng R, Murphy KP: Integrating copy number polymorphisms into array CGH analysis using a robust HMM. Bioinformatics 2006;22:e431-e439.
59. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002;30:e15.
60. van Beers EH, Nederlof PM: Array-CGH and breast cancer. Breast Cancer Res 2006;8:210.
61. Ginzinger DG: Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 2002;30:503-512.
62. Di Palma S, Lambros MB, Savage K, Jones C, Mackay A, Dexter T, Iravani M, Fenwick K, Ashworth A, Reis-Filho JS: Oncocytic change in pleomorphic adenoma: molecular evidence in support of an origin in neoplastic cells. J Clin Pathol 2007;60:492-499.
63. Lambros MB, Simpson PT, Jones C, Natrajan R, Westbury C, Steele D, Savage K, Mackay A, Schmitt FC, Ashworth A, Reis-Filho JS: Unlocking pathology archives for molecular genetic studies: a reliable method to generate probes for chromogenic and fluorescent in situ hybridization. Lab Invest 2006;86:398-408.
64. Natrajan R, Reis-Filho JS, Little SE, Messahel B, Brundler MA, Dome JS, Grundy PE, Vujanic GM, Pritchard-Jones K, Jones C: Blastemal expression of type I insulin-like growth factor receptor in Wilms' tumors is driven by increased copy number and correlates with relapse. Cancer Res 2006;66:11148-11155.
65. Natrajan R, Little SE, Reis-Filho JS, Hing L, Messahel B, Grundy PE, Dome JS, Schneider T, Vujanic GM, Pritchard-Jones K, Jones C: Amplification and overexpression of CACNA1E correlates with relapse in favorable histology Wilms' tumors. Clin Cancer Res 2006;12:7284-7293.
66. Vincent-Salomon A, Gruel N, Lucchesi C, Mac Grogan G, Dendale R, Sigal-Zafrani B, Longy M, Raynal V, Pierron G, de Mascarel I, Taris C, Stoppa-Lyonnet D, Pierga JY, Salmon R, Sastre-Garau X, Fourquet A, Delattre O, de Cremoux P, Aurias A: Identification of typical medullary breast carcinoma as a genomic sub-group of basal-like carcinomas, a heterogeneous new molecular entity. Breast Cancer Res 2007;9:R24.
67. Carter NP: Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 2007;39:S16-S21.
68. Loo LW, Grove DI, Williams EM, Neal CL, Cousens LA, Schubert EL, Holcomb IN, Massa HF, Glogovac J, Li CI, Malone KE, Daling JR, Delrow JJ, Trask BJ, Hsu L, Porter PL: Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 2004;64:8541-8549.
69. Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D: Molecular portraits of human breast tumours. Nature 2000;406:747-752.
70. Pierga JY, Reis-Filho JS, Cleator SJ, Dexter T, Mackay A, Simpson P, Fenwick K, Iravani M, Salter J, Hills M, Jones C, Ashworth A, Smith IE, Powles T, Dowsett M: Microarray-based comparative genomic hybridisation of breast cancer patients receiving neoadjuvant chemotherapy. Br J Cancer 2007;96:341-351.
71. Stange DE, Radlwimmer B, Schubert F, Traub F, Pich A, Toedt G, Mendrzyk F, Lehmann U, Eils R, Kreipe H, Lichter P: Highresolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer. Clin Cancer Res 2006;12:345-352.
72. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R: A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 2002;347:1999-2009.
73. Garcia MJ, Pole JC, Chin SF, Teschendorff A, Naderi A, Ozdag H, Vias M, Kranjac T, Subkhankulova T, Paish C, Ellis I, Brenton JD, Edwards PA, Caldas C: A 1 Mb minimal amplicon at 8p11-12 in breast cancer identifies new candidate oncogenes. Oncogene 2005;24:5235-5245.
74. Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell 2006;10:515-527.
75. Jonsson G, Staaf J, Olsson E, Heidenblad M, Vallon-Christersson J, Osoegawa K, de Jong P, Oredsson S, Ringner M, Hoglund M, Borg A: High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization. Genes Chromosomes Cancer 2007;46:543-558.
76. Greshock J, Nathanson K, Martin AM, Zhang L, Coukos G, Weber BL, Zaks TZ: Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization. Cancer Res 2007;67:3594-3600.
77. Elbauomy Elsheikh S, Green AR, Lambros MB, Turner NC, Grainge MJ, Powe D, Ellis IO, Reis-Filho JS: FGFR1 amplification in breast carcinomas: a chromogenic in situ hybridisation analysis. Breast Cancer Res 2007;9:R23.
78. Feber A, Clark J, Goodwin G, Dodson AR, Smith PH, Fletcher A, Edwards S, Flohr P, Falconer A, Roe T, Kovacs G, Dennis N, Fisher C, Wooster R, Huddart R, Foster CS, Cooper CS: Amplification and overexpression of E2F3 in human bladder cancer. Oncogene 2004;23:1627-1630.
79. Kao J, Pollack JR: RNA interference-based functional dissection of the 17q12 amplicon in breast cancer reveals contribution of coamplified genes. Genes Chromosomes Cancer 2006;45:761-769.
80. Bosl WJ: Systems biology by the rules: hybrid intelligent systems for pathway modeling and discovery. BMC Syst Biol 2007;1:13.
81. Hornberg JJ, Bruggeman FJ, Westerhoff HV, Lankelma J: Cancer: a systems biology disease. Biosystems 2006;83:81-90.
82. Reif DM, White BC, Moore JH: Integrated analysis of genetic, genomic and proteomic data. Expert Rev Proteomics 2004;1:67-75.
83. Greenbaum D, Jansen R, Gerstein M: Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 2002;18:585-596.
84. Rivera MN, Kim WJ, Wells J, Driscoll DR, Brannigan BW, Han M, Kim JC, Feinberg AP, Gerald WL, Vargas SO, Chin L, Iafrate AJ, Bell DW, Haber DA: An X chromosome gene, WTX, is commonly inactivated in Wilms tumor. Science 2007;315:642-645.