Journal of Molecular Histology

, Volume 38, Issue 2, pp 141–150

An approach to the validation of novel molecular markers of breast cancer via TMA-based FISH scanning

  • Raymond R. Tubbs
  • Eric Swain
  • James D. Pettay
  • David G. Hicks
Original Paper

Abstract

Tissue microarrays (TMA) are valuable tools for validating results of array-based comparative genomic hybridization (ACGH) and other translational research applications requiring independent verification of genomic gains and losses by fluorescence in situ hybridization (FISH). However, spatial orientation and accurate manual tracking of the TMA cores is challenging and prone to error. Image analysis combined with core tracking software, implemented via an automated FISH scanning workstation, represents a new approach to FISH and TMA-based validation of novel genomic changes discovered by ACGH in breast and other cancers. Automated large-scale tissue microarray validation FISH studies of genomic gains and losses identified by ACGH for breast cancer are feasible using an automated imaging scanner and tracking/classifying software. Furthermore, by leveraging the bifunctional fluorescent and chromogenic properties of the alkaline phosphatase chromogen fast red K and combining the technology with FISH, correlative and simultaneous phenotype/genotype studies may be enabled.

Keywords

Tissue microarrays Fluorescence in situ hybridization FISH 

References

  1. Albertson DG, Ylstra B, Segraves R, Collins C, Dairkee SH, Kowbel D, Kuo WL, Gray JW, Pinkel D (2000) Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet 25:144–146PubMedCrossRefGoogle Scholar
  2. Beheshti B, Braude I, Marrano P, Thorner P, Zielenska M, Squire JA (2003) Chromosomal localization of DNA amplifications in neuroblastoma tumors using cDNA microarray comparative genomic hybridization. Neoplasia 5:53–62PubMedGoogle Scholar
  3. Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R (2004) High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res 14:287–295PubMedCrossRefGoogle Scholar
  4. Bubendorf L (2001) High-throughput microarray technologies: from genomics to clinics. Eur Urol 40:231–238PubMedCrossRefGoogle Scholar
  5. Carvalho B, Ouwerkerk E, Meijer GA, Ylstra B (2004) High resolution microarray comparative genomic hybridisation analysis using spotted oligonucleotides. J Clin Pathol 57:644–646PubMedCrossRefGoogle Scholar
  6. Cowell JK, Barnett GH, Nowak NJ (2004a) Characterization of the 1p/19q chromosomal loss in oligodendrogliomas using comparative genomic hybridization arrays (CGHa). J Neuropathol Exp Neurol 63:151–158Google Scholar
  7. Cowell JK, Matsui S, Wang YD, Laduca J, Conroy J, Mcquaid D, Nowak NJ (2004b) Application of bacterial artificial chromosome array-based comparative genomic hybridization and spectral karyotyping to the analysis of glioblastoma multiforme. Cancer Genet Cytogenet 151:36–51CrossRefGoogle Scholar
  8. Cowell JK, Wang YD, Head K, Conroy J, Mcquaid D, Nowak NJ (2004c) Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes. Br J Cancer 90:860–865CrossRefGoogle Scholar
  9. du Manoir S, Speicher MR, Joos S, Schrock E, Popp S, Dohner H, Kovacs G, Robert-Nicoud M, Lichter P, Cremer T (1993) Detection of complete and partial chromosome gains and losses by comparative genomic in situ hybridization. Hum Genet 90:590–610Google Scholar
  10. Forozan F, Mahlamaki EH, Monni O, Chen Y, Veldman R, Jiang Y, Gooden GC, Ethier SP, Kallioniemi A, Kallioniemi OP (2000) Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data. Cancer Res 60:4519–4525PubMedGoogle Scholar
  11. Garnis C, Baldwin C, Zhang L, Rosin MP, Lam WL (2003) Use of complete coverage array comparative genomic hybridization to define copy number alterations on chromosome 3p in oral squamous cell carcinomas. Cancer Res 63:8582–8585PubMedGoogle Scholar
  12. Garnis C, Campbell J, Zhang L, Rosin MP, Lam WL (2004) OCGR array: an oral cancer genomic regional array for comparative genomic hybridization analysis. Oral Oncol 40:511–519PubMedCrossRefGoogle Scholar
  13. Gong G, Devries S, Chew KL, Cha I, Ljung B-M, Waldman FM (2001) Genetic changes in paired atypical and usual ductal hyperplasia of the breast by comparative genomic hybridization. Clin Cancer Res 7:2410–2414PubMedGoogle Scholar
  14. Hacia JG (1999) Resequencing and mutational analysis using oligonucleotide microarrays. Nat Genet 21:42–47PubMedCrossRefGoogle Scholar
  15. Hoque MO, Lee CC, Cairns P, Schoenberg M, Sidransky D (2003) Genome-wide genetic characterization of bladder cancer: a comparison of high-density single-nucleotide polymorphism arrays and PCR-based microsatellite analysis. Cancer Res 63:2216–2222PubMedGoogle Scholar
  16. Hui AB, Lo KW, Teo PM, To KF, Huang DP (2002) Genome wide detection of oncogene amplifications in nasopharyngeal carcinoma by array based comparative genomic hybridization. Int J Oncol 20:467–473PubMedGoogle Scholar
  17. Hui AB, Lo KW, Yin XL, Poon WS, Ng HK (2001) Detection of multiple gene amplifications in glioblastoma multiforme using array-based comparative genomic hybridization. Lab Invest 81:717–723PubMedCrossRefGoogle Scholar
  18. Ishkanian AS, Malloff CA, Watson SK, Deleeuw RJ, Chi B, Coe BP, Snijders A, Albertson DG, Pinkel D, Marra MA, Ling V, Macaulay C, Lam WL (2004) A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 36:299–303PubMedCrossRefGoogle Scholar
  19. Isola J, Devries S, Chu L, Ghazvini S, Waldman F (1994) Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples. Am J Pathol 145:1301–1308PubMedGoogle Scholar
  20. 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 (2003) Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH. Genome Res 13:294–307PubMedCrossRefGoogle Scholar
  21. Lichter P, Joos S, Bentz M, Lampel S (2000) Comparative genomic hybridization: uses and limitations. Semin Hematol 37:348–357PubMedCrossRefGoogle Scholar
  22. Pandita A, Zielenska M, Thorner P, Bayani J, Godbout R, Greenberg M, Squire JA (1999) Application of comparative genomic hybridization, spectral karyotyping, and microarray analysis in the identification of subtype-specific patterns of genomic changes in rhabdomyosarcoma. Neoplasia 1:262–275PubMedCrossRefGoogle Scholar
  23. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schroder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, van Dekken H (2003) High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol 162:763–770PubMedGoogle Scholar
  24. 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 (2004) Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet 13:1303–1313PubMedCrossRefGoogle Scholar
  25. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D, Collins C, Kuo WL, Chen C, Zhai Y, Dairkee SH, Ljung BM, Gray JW, Albertson DG (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207–211PubMedCrossRefGoogle Scholar
  26. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO (1999) Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet 23:41–46PubMedCrossRefGoogle Scholar
  27. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO (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 99:12963–12968PubMedCrossRefGoogle Scholar
  28. Ross JS, Ginsburg GS (2003) The integration of molecular diagnostics with therapeutics. Implications for drug development and pathology practice. Am J Clin Pathol 119:26–36PubMedCrossRefGoogle Scholar
  29. Roylance R, Gorman P, Harris W, Liebmann R, Barnes D, Hanby A, Sheer D (1999) Comparative genomic hybridization of breast tumors stratified by histological grade reveals new insights into the biological progression of breast cancer. Cancer Res 59:1433–1436PubMedGoogle Scholar
  30. Schraml P, Schwerdtfeger G, Burkhalter F, Raggi A, Schmidt D, Ruffalo T, King W, Wilber K, Mihatsch MJ, Moch H (2003) Combined array comparative genomic hybridization and tissue microarray analysis suggest PAK1 at 11q13.5-q14 as a critical oncogene target in ovarian carcinoma. Am J Pathol 163:985–992PubMedGoogle Scholar
  31. Seo MY, Rha SY, Yang SH, Kim SC, Lee GY, Park CH, Yang WI, Ahn JB, Park BW, Chung HC (2004) The pattern of gene copy number changes in bilateral breast cancer surveyed by cDNA microarray-based comparative genomic hybridization. Int J Mol Med 13:17–24PubMedGoogle Scholar
  32. Shah S, Gregg J, Mohammed M, Yu W, Damani S, Locker R (2002) BAC Microarrays. In: Shah S, Kamberova G (eds) Microarray image analysis-nuts & bolts. DNA Press, LLCGoogle Scholar
  33. Snijders AM, Nowak N, Segraves R, Blackwood S, Brown N, Conroy J, Hamilton G, Hindle AK, Huey B, Kimura K, Law S, Myambo K, Palmer J, Ylstra B, Yue JP, Gray JW, Jain AN, Pinkel D, Albertson DG (2001) Assembly of microarrays for genome-wide measurement of DNA copy number. Nat Genet 29:263–264PubMedCrossRefGoogle Scholar
  34. Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P (1997) Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20:399–407PubMedCrossRefGoogle Scholar
  35. Squire JA, Pei J, Marrano P, Beheshti B, Bayani J, Lim G, Moldovan L, Zielenska M (2003) High-resolution mapping of amplifications and deletions in pediatric osteosarcoma by use of CGH analysis of cDNA microarrays. Genes Chromosomes Cancer 38:215–225PubMedCrossRefGoogle Scholar
  36. Stange DE, Radlwimmer B, Schubert F, Traub F, Pich A, Toedt G, Mendrzyk F, Lehmann U, Eils R, Kreipe H, Lichter P (2006) High resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer. Clin Cancer Res 12:345–352PubMedCrossRefGoogle Scholar
  37. Tabar L, Shen H, Duffy S, Yen M, Chiang C, Dean P, Smith R (2000) A novel method for prediction of long-term outcome of women with T1a, T1b, and 10–14 mm invasive breast cancers: a prospective study. Lancet 355:429–433PubMedGoogle Scholar
  38. Tubbs R, Pettay J, Roche P, Stoler M, Julius R, Myles J, Grogan T (2000) Concomitant oncoprotein detection with fluorescence in situ hybridization (CODFISH). A fluorescence based assay enabeling simultaneous visualization of gene amplification and encoded protein expression. J Mol Diagn 2:78–83PubMedGoogle Scholar
  39. Ulger C, Toruner GA, Alkan M, Mohammed M, Damani S, Kang J, Galante A, Aviv H, Soteropoulos P, Tolias PP, Schwalb MN, Dermody JJ (2003) Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line. Cancer Genet Cytogenet 147:28–35PubMedCrossRefGoogle Scholar
  40. van‘t Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530–536Google Scholar
  41. 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 (2002) A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347:1999–2009Google Scholar
  42. Veltman IM, Veltman JA, Arkesteijn G, Janssen IM, Vissers LE, de Jong PJ, van Kessel AG, Schoenmakers EF (2003a) Chromosomal breakpoint mapping by array CGH using flow-sorted chromosomes. Biotechniques 35:1066–1070Google Scholar
  43. Veltman JA, Fridlyand J, Pejavar S, Olshen AB, Korkola JE, Devries S, Carroll P, Kuo WL, Pinkel D, Albertson D, Cordon-Cardo C, Jain AN, Waldman FM (2003b) Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. Cancer Res 63:2872–2880Google Scholar
  44. Vissers LE, de Vries BB, Osoegawa K, Janssen IM, Feuth T, Choy CO, Straatman H, van der Vliet W, Huys EH, van Rijk A, Smeets D, van Ravenswaaij-Arts CM, Knoers NV, van der Burgt I, de Jong PJ, Brunner HG, van Kessel AG, Schoenmakers EF, Veltman JA (2003) Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 73:1261–1270Google Scholar
  45. Weiss MM, Kuipers EJ, Postma C, Snijders AM, Stolte M, Vieth M, Pinkel D, Meuwissen SG, Albertson D, Meijer GA (2003) Genome wide array comparative genomic hybridisation analysis of premalignant lesions of the stomach. Mol Pathol 56:293–298PubMedCrossRefGoogle Scholar
  46. 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 62:7110–7117Google Scholar
  47. Wessendorf S, Fritz B, Wrobel G, Nessling M, Lampel S, Goettel D, Kuepper M, Joos S, Hopman T, Kokocinski F, Dohner H, Bentz M, Schwaenen C, Lichter P (2002) Automated screening for genomic imbalances using matrix-based comparative genomic hybridization. Lab Invest 82:47–60PubMedGoogle Scholar
  48. Wolf M, Mousses S, Hautaniemi S, Karhu R, Huusko P, Allinen M, Elkahloun A, Monni O, Chen Y, Kallioniemi A, Kallioniemi OP (2004) High-resolution analysis of gene copy number alterations in human prostate cancer using CGH on cDNA microarrays: impact of copy number on gene expression. Neoplasia 6:240–247PubMedCrossRefGoogle Scholar
  49. Zhao J, Roth J, Bode-Lesniewska B, Pfaltz M, Heitz PU, Komminoth P (2002) Combined comparative genomic hybridization and genomic microarray for detection of gene amplifications in pulmonary artery intimal sarcomas and adrenocortical tumors. Genes Chromosomes Cancer 34:48–57PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Raymond R. Tubbs
    • 1
  • Eric Swain
    • 1
  • James D. Pettay
    • 1
  • David G. Hicks
    • 1
  1. 1.Departments of Anatomical and Clinical PathologyThe Cleveland Clinic Foundation, The Lerner College of MedicineClevelandUSA

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