Skip to main content

Advertisement

Log in

From array to array: Confirmation of genomic gains and losses discovered by array-based comparative genomic hybridization utilizing fluorescence in situ hybridization on tissue microarrays

  • Original Paper
  • Published:
Journal of Molecular Histology Aims and scope Submit manuscript

Abstract

The combination of array-based comparative genomic hybridization (CGH) with fluorescence in situ hybridization utilizing custom-designed bacterial artificial chromosome (BAC) probes applied to tissue microarrays represents a powerful compendium of techniques–greatly enhancing the throughput of genomic analysis and subsequent target validation. Such approach can be automated at various levels and allows managing large volume of targets and samples in a few experiments. As such, this approach facilitates discovery, validation and implementation of findings in the process of identification of new diagnostic, prognostic and potentially therapeutic molecular markers.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Barrett MT, Scheffer A, Ben-Dor A, Sampas N, Lipson D, Kincaid R, Tsang P, Curry B, Baird K, Meltzer PS, Yakhini Z, Bruhn L, Laderman S (2004) Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A 101:17765–17770

    Article  PubMed  CAS  Google Scholar 

  • Battifora H. The multitumor (sausage) tissue block: novel method for immunohistochemical antibody testing (1986). Lab Invest 55:244–248

  • 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 14:287–295

    Article  PubMed  CAS  Google Scholar 

  • Cowell JK (2004) High throughput determination of gains and losses of genetic material using high resolution BAC arrays and comparative genomic hybridization. Comb Chem High Throughput Screen 7:587–596

    PubMed  CAS  Google Scholar 

  • 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 63:151–158

    CAS  Google Scholar 

  • 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 151:36–51

    Article  CAS  Google Scholar 

  • 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 90:860–865

    Article  CAS  Google Scholar 

  • de Leeuw RJ, Davies JJ, Rosenwald A, Bebb G, Gascoyne RD, Dyer MJ, Staudt LM, Martinez-Climent JA, Lam WL (2004) Comprehensive whole genome array CGH profiling of mantle cell lymphoma model genomes. Hum Mol Genet 13:1827–1837

    Article  PubMed  Google Scholar 

  • Deeb G, Baer MR, Gaile DP, Sait SN, Barcos M, Wetzler M, Conroy JM, Nowak NJ, Cowell JK, Cheney RT (2005) Genomic profiling of myeloid sarcoma by array comparative genomic hybridization. Genes Chromosomes Cancer 44:373–383

    Article  PubMed  CAS  Google Scholar 

  • Edwards J, Krishna NS, Witton CJ, Bartlett JM (2003) Gene amplifications associated with the development of hormone-resistant prostate cancer. Clin Cancer Res 9:5271–5281

    PubMed  CAS  Google Scholar 

  • Garnis C, Coe BP, Lam SL, MacAulay C, Lam WL (2005a) High-resolution array CGH increases heterogeneity tolerance in the analysis of clinical samples. Genomics 85:790–793

    Article  CAS  Google Scholar 

  • Garnis C, Lockwood WW, Vucic E, Ge Y, Girard L, Minna JD, Gazdar AF, Lam S, Macaulay C, Lam WL (2005b) High resolution analysis of non-small cell lung cancer cell lines by whole genome tiling path array CGH. Int J Cancer 118(6):1556–1564

    Google Scholar 

  • Hidalgo A, Baudis M, Petersen I, Arreola H, Pina P, Vazquez-Ortiz G, Hernandez D, Gonzalez J, Lazos M, Lopez R, Perez C, Garcia J, Vazquez K, Alatorre B, Salcedo M (2005) Microarray comparative genomic hybridization detection of chromosomal imbalances in uterine cervix carcinoma. BMC Cancer 5:77

    Article  PubMed  Google Scholar 

  • Huang J, Wei W, Zhang J, Liu G, Bignell GR, Stratton MR, Futreal PA, Wooster R, Jones KW, Shapero MH (2004) Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics 1:287–299

    PubMed  CAS  Google Scholar 

  • 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 36:299–303

    Article  PubMed  CAS  Google Scholar 

  • Kallioniemi OKA, Sudar D, et al (1992) Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 258:818–821

    Article  PubMed  CAS  Google Scholar 

  • Kononen J, Bubendorf L, Kallioniemi A, et al (1998) Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med 4:844–847

    Article  PubMed  CAS  Google Scholar 

  • Lapierre JM, Sanlaville D, Kang J, Ozilou C, Le Lorc’h M, Waill MC, Prieur M, Colleaux L, Munnich A, Turleau C, Benkhalifa M, Mohammed M, Vekemans M, Romana S (2004) A preliminary study to assess the value of the DNA chips SpectralChip to detect subtle constitutional chromosome imbalances. Ann Biol Clin (Paris) 62:203–212

    CAS  Google Scholar 

  • MaguireHC (1989) The neu (c-erbB-2) oncogene. Semin Oncol 16:148–160

    PubMed  CAS  Google Scholar 

  • Nowak NJ, Gaile D, Conroy JM, McQuaid D, Cowell J, Carter R, Goggins MG, Hruban RH, Maitra A (2005) Genome-wide aberrations in pancreatic adenocarcinoma. Cancer Genet Cytogenet 161:36–50

    Article  PubMed  CAS  Google Scholar 

  • Pettus JA, Cowley BC, Maxwell T, Milash B, Stephenson RA, Rohr LR, Hoff C, Brothman AR (2004) Multiple abnormalities detected by dye reversal genomic microarrays in prostate cancer: a much greater sensitivity than conventional cytogenetics. Cancer Genet Cytogenet 154:110–118

    Article  PubMed  CAS  Google Scholar 

  • Pinkel DSR, Sudar D, et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207–211

    Article  PubMed  CAS  Google Scholar 

  • 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 23:41–46

    Article  PubMed  CAS  Google Scholar 

  • 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 99:12963–12968

    Article  PubMed  CAS  Google Scholar 

  • Rossi MR, Gaile D, Laduca J, Matsui S, Conroy J, McQuaid D, Chervinsky D, Eddy R, Chen HS, Barnett GH, Nowak NJ, Cowell JK (2005a) Identification of consistent novel submegabase deletions in low-grade oligodendrogliomas using array-based comparative genomic hybridization. Genes Chromosomes Cancer 44:85–96

    Article  CAS  Google Scholar 

  • Rossi MR, La Duca J, Matsui S, Nowak NJ, Hawthorn L, Cowell JK (2005b) Novel amplicons on the short arm of chromosome 7 identified using high resolution array CGH contain over expressed genes in addition to EGFR in glioblastoma multiforme. Genes Chromosomes Cancer 44:392–404

    Article  CAS  Google Scholar 

  • Sasaki T, Arai H, Beppu T, Ogasawara K (2003) Detection of gene amplification and deletion in high-grade gliomas using a genome DNA microarray (GenoSensor Array 300). Brain Tumor Pathol 20:59–63

    Article  PubMed  CAS  Google Scholar 

  • Schoumans J, Ruivenkamp C, Holmberg E, Kyllerman M, Anderlid BM, Nordenskjold M (2005) Detection of chromosomal imbalances in children with idiopathic mental retardation by array based comparative genomic hybridisation (array-CGH). J Med Genet 42:699–705

    Article  PubMed  CAS  Google Scholar 

  • 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 163:985–992

    PubMed  CAS  Google Scholar 

  • Suzuki T, Maruno M, Wada K, Kagawa N, Fujimoto Y, Hashimoto N, Izumoto S, Yoshimine T (2004) Genetic analysis of human glioblastomas using a genomic microarray system. Brain Tumor Pathol 21:27–34

    Article  PubMed  CAS  Google Scholar 

  • 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 147:28–35

    Article  PubMed  CAS  Google Scholar 

  • Venter JC AM, Myers EW, et al (2001) The sequence of the human genome. Science 291:1304–1351

    Article  PubMed  Google Scholar 

  • Wada K, Maruno M, Suzuki T, Kagawa N, Hashiba T, Fujimoto Y, Hashimoto N, Izumoto S, Yoshimine T (2004) Chromosomal and genetic aberrations differ with meningioma subtype. Brain Tumor Pathol 21:127–133

    Article  PubMed  CAS  Google Scholar 

  • Wada K, Maruno M, Suzuki T, Kagawa N, Hashiba T, Fujimoto Y, Hashimoto N, Izumoto S, Yoshimine T (2005) Chromosomal and genetic abnormalities in benign and malignant meningiomas using DNA microarray. Neurol Res 27:747–754

    Article  PubMed  CAS  Google Scholar 

  • Wan WH, Fortuna MB, Furmanski P (1987) A rapid and efficient method for testing immunohistochemical reactivity of monoclonal antibodies against multiple tissue samples simultaneously. J Immunol Methods 103:121–129

    Article  PubMed  CAS  Google Scholar 

  • Zhou X, Mok SC, Chen Z, Li Y, Wong DT (2004) Concurrent analysis of loss of heterozygosity (LOH) and copy number abnormality (CNA) for oral premalignancy progression using the Affymetrix 10K SNP mapping array. Hum Genet 115:327–330

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Marek Skacel.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Skacel, M., Siva, A., Xu, B. et al. From array to array: Confirmation of genomic gains and losses discovered by array-based comparative genomic hybridization utilizing fluorescence in situ hybridization on tissue microarrays. J Mol Hist 38, 135–140 (2007). https://doi.org/10.1007/s10735-006-9051-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10735-006-9051-8

Keywords

Navigation