The Roles of the Fluorescent In Situ Hybridization (FISH) and Comparative Genomic Hybridization (CGH) Techniques in the Detection of the Breast Cancer

Harem Othman Smail


This paper aimed to understand and compare the two popular cytogenetic techniques of fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH) in detecting breast cancer chromosomal abnormality. Several chromosomal anomalies play a role in the development of breast cancer, and the two above approaches play an important role in confirming fluorescence in situ hybridization in particular (FISH). However, comparative genomic hybridization has developed DNA copy number profiles for most of the publicly available breast cancer cell lines for the FISH methods rely on the fluorescent probes. Chromosomal profiles can be generated for the suspected chromosomal abnormality, copy number changes between the tumour and the DNA control can be compared, and the results can be registered. Today, modern cytogenetic tools such as fluorescence in situ hybridization (FISH) are more commonly used to detect any microdeletion that cannot be detected by conventional cytogenetic karyotypes that involve a high rate of cell division and good chromosomal morphology, which pose challenges for cytogeneticists, and a long period of testing and research. Usually, this is a problem for physicians, and there are still many drawbacks and disadvantages concerning the high benefits, such as false findings. Normal chromosome in situ hybridization requires the hybridization of a labelled DNA probe into denatured chromosomal DNA present in metaphase chromosomes in an air-dried microscope slide preparation. Metaphase spreads are used for traditional chromosome FISH (metaphase FISH). Positive and positive signs of hybridization also appear as a double spot, corresponding to the hybridized probe for both sister chromatids. A further extension of chromosome painting is comparative genomic hybridization (CCI-I). CCH involves simultaneous chromosome painting in two different colours using complete DNA from two similar sources as probes, which reveal variations concerning the benefit or loss of sub-chromosomal regions or even entire chromosomes.


FISH; CGH; probe; classical cytogenetic; Chromosomal regions and hybridization

Full Text:



Alayed, K., Medeiros, L. J., Schultz, R. A., Cortes, J., Lu, G., Bueso-Ramos, C. E., & Konoplev, S. (2013). Value of oligonucleotide-based array comparative genomic hybridization for diagnosis of acute promyelocytic leukemia in a patient negative for t (15; 17) (q24. 1; q21. 2)/promyelocytic leukemia-retinoic acid receptor, alpha by conventional cytogenetics and Fluorescence in situ hybridization. Clinical Lymphoma, Myeloma and Leukemia, 13(4), 507-510.

Albertson, D. G. (2003). Profiling breast cancer by array CGH. Breast cancer research and treatment, 78(3), 289-298.

Bar‐Am, I., Mor, O., Shiloh, Y., Avivi, L., & Yeger, H. (1992). Detection of amplified DNA sequences in human tumor cell lines by Fluorescence in situ hybridization. Genes, Chromosomes and Cancer, 4(4), 314-320.

Bartlett, J. M. (2004). Fluorescence in situ hybridization, in Molecular Diagnosis of Cancer.

Bièche, I., & Lidereau, R. (1995). Genetic alterations in breast cancer. Genes, Chromosomes and Cancer, 14(4), 227-251.

Bièche, I., Champème, M. H., & Lidereau, R. (1995). Loss and gain of distinct regions of chromosome 1q in primary breast cancer. Clinical cancer research, 1(1), 123-127.

Bishop, R. (2010). Applications of Fluorescence in situ hybridization (FISH) in detecting genetic aberrations of medical significance. Bioscience Horizons, 3(1), 85-95.

Bolland, D. J., King, M. R., Reik, W., Corcoran, A. E., & Krueger, C. (2013). Robust 3D DNA FISH using directly labeled probes. JoVE (Journal of Visualized Experiments), (78), e50587.

Bridge, J. A. (2008). Advantages and limitations of cytogenetic, molecular cytogenetic, and molecular diagnostic testing in mesenchymal neoplasms. Journal of Orthopaedic Science, 13(3), 273.

Brown, L. A., & Huntsman, D. (2007). Fluorescent in situ hybridization on tissue microarrays: challenges and solutions. Journal of molecular histology, 38(2), 151-157.

Chrzanowska, N. M., Kowalewski, J., & Lewandowska, M. A. (2020). Use of Fluorescence In Situ Hybridization (FISH) in Diagnosis and Tailored Therapies in Solid Tumors. Molecules, 25(8), 1864.

Chung, W., Eum, H. H., Lee, H. O., Lee, K. M., Lee, H. B., Kim, K. T., ... & Kan, Z. (2017). Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer. Nature communications, 8(1), 1-12.

Climent, J., Garcia, J. L., Mao, J. H., Arsuaga, J., & Perez-Losada, J. (2007). Characterization of breast cancer by array comparative genomic hybridization. Biochemistry and Cell Biology, 85(4), 497-508.

Cremer, M., Grasser, F., Lanctôt, C., Müller, S., Neusser, M., Zinner, R., ... & Cremer, T. (2012). Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes. In The nucleus (pp. 205-239). Humana Press, Totowa, NJ.

Cui, C., Shu, W., & Li, P. (2016). Fluorescence in situ hybridization: cell-based genetic diagnostic and research applications. Frontiers in cell and developmental biology, 4, 89.

Da Silva, L., & Lakhani, S. R. (2010). Pathology of hereditary breast cancer. Modern Pathology, 23(2), S46-S51.

Daniels, M. J., Wang, Y., Lee, M., & Venkitaraman, A. R. (2004). Abnormal cytokinesis in cells deficient in the breast cancer susceptibility protein BRCA2. Science, 306(5697), 876-879.

Das, K., & Tan, P. (2013). Molecular cytogenetics: recent developments and applications in cancer. Clinical genetics, 84(4), 315-325.

de Ruijter, T. C., Veeck, J., de Hoon, J. P., van Engeland, M., & Tjan-Heijnen, V. C. (2011). Characteristics of triple-negative breast cancer. Journal of cancer research and clinical oncology, 137(2), 183-192.

Fiegl, M., Tueni, C., Schenk, T., Jakesz, R., Gnant, M., Reiner, A., ... & Drach, J. (1995). Interphase cytogenetics reveals a high incidence of aneuploidy and intra-tumour heterogeneity in breast cancer. British journal of cancer, 72(1), 51-55.

Forozan, F., Karhu, R., Kononen, J., Kallioniemi, A., & Kallioniemi, O. P. (1997). Genome screening by comparative genomic hybridization. Trends in Genetics, 13(10), 405-409.

Forozan, F., Mahlamäki, E. H., Monni, O., Chen, Y., Veldman, R., Jiang, Y., ... & Kallioniemi, O. P. (2000). Comparative genomic hybridization analysis of 38 breast cancer cell lines: a basis for interpreting complementary DNA microarray data. Cancer research, 60(16), 4519-4525.

Giollant, M., Bertrand, S., Verrelle, P., Tchirkov, A., du Manoir, S., Ried, T., ... & Tchirkov, A. (1996). Characterization of double minute chromosomes' DNA content in a human high grade astrocytoma cell line by using comparative genomic hybridization and Fluorescence in situ hybridization. Human genetics, 98(3), 265-270.

Gozzetti, A., & Le Beau, M. M. (2000, October). Fluorescence in situ hybridization: uses and limitations. In Seminars in hematology (Vol. 37, No. 4, pp. 320-333). WB Saunders.

Gozzetti, A., & Le Beau, M. M. (2000, October). Fluorescence in situ hybridization: uses and limitations. In Seminars in hematology (Vol. 37, No. 4, pp. 320-333). WB Saunders.

Hovhannisyan, G. G. (2010). Fluorescence in situ hybridization in combination with the comet assay and micronucleus test in genetic toxicology. Molecular Cytogenetics, 3(1), 17.

Howlader, N., Altekruse, S. F., Li, C. I., Chen, V. W., Clarke, C. A., Ries, L. A., & Cronin, K. A. (2014). US incidence of breast cancer subtypes defined by joint hormone receptor and HER2 status. JNCI: Journal of the National Cancer Institute, 106(5).

Hu, Q., Maurais, E. G., & Ly, P. (2020). Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Research, 1-12.

Huber, D., von Voithenberg, L. V., & Kaigala, G. V. (2018). Fluorescence in situ hybridization (FISH): history, limitations and what to expect from micro-scale FISH?. Micro and Nano Engineering, 1, 15-24.

Hyytinen, E., Visakorpi, T., Kallioniemi, A., Kallioniemi, O. P., & Isola, J. J. (1994). Improved technique for analysis of formalin‐fixed, paraffin‐embedded tumors by Fluorescence in situ hybridization. Cytometry: The Journal of the International Society for Analytical Cytology, 16(2), 93-99.

Jacobsen, A., Arnold, N., Weimer, J., & Kiechle, M. (2000). Comparison of comparative genomic hybridization and interphase fluorescence in situ hybridization in ovarian carcinomas: possibilities and limitations of both techniques. Cancer genetics and cytogenetics, 122(1), 7-12.

Karimi-Nejhad, R., & Ghanadan, A. (2020). Fluorescent In Situ Hybridization: Methods and Application in Cancer Diagnosis. In Cancer Immunology (pp. 711-728). Springer, Cham.

Key, T. J., Verkasalo, P. K., & Banks, E. (2001). Epidemiology of breast cancer. The lancet oncology, 2(3), 133-140.

Kim, H., Yoo, S. B., Choe, J. Y., Paik, J. H., Xu, X., Nitta, H., ... & Chung, J. H. (2011). Detection of ALK gene rearrangement in non-small cell lung cancer: a comparison of Fluorescence in situ hybridization and chromogenic in situ hybridization with correlation of ALK protein expression. Journal of Thoracic Oncology, 6(8), 1359-1366.

Lee, C. N., Lin, S. Y., Lin, C. H., Shih, J. C., Lin, T. H., & Su, Y. N. (2012). Clinical utility of array comparative genomic hybridization for prenatal diagnosis: a cohort study of 3171 pregnancies. BJOG: An International Journal of Obstetrics & Gynaecology, 119(5), 614-625.

Les, T., Markiewicz, T., Osowski, S., Cichowicz, M., & Kozlowski, W. (2014, June). Automatic evaluation system of FISH images in breast cancer. In International Conference on Image and Signal Processing (pp. 332-339). Springer, Cham.

Li, D., Wang, X., Lu, S., Wang, P., Wang, X., Yin, W., ... & Li, S. (2020). Integrated analysis revealing genome wide chromosomal copy number variation in supraglottic laryngeal squamous cell carcinoma. Oncology Letters, 20(2), 1201-1212.

Lianidou, E. S., & Markou, A. (2011). Circulating tumor cells in breast cancer: detection systems, molecular characterization, and future challenges. Clinical chemistry, 57(9), 1242-1255.

Liehr, T., Othman, M. A., Rittscher, K., & Alhourani, E. (2015). The current state of molecular cytogenetics in cancer diagnosis. Expert review of molecular diagnostics, 15(4), 517-526.

Lima, J. F., Maia, P., T. Magalhães, B., Cerqueira, L., & Azevedo, N. F. (2020). A comprehensive model for the diffusion and hybridization processes of nucleic acid probes in Fluorescence in situ hybridization. Biotechnology and Bioengineering, 117(10), 3212-3223.

McNeil, N., & Ried, T. (2000). Novel molecular cytogenetic techniques for identifying complex chromosomal rearrangements: technology and applications in molecular medicine. Expert reviews in molecular medicine, 2000, 1–14.

Mego, M., Mani, S. A., & Cristofanilli, M. (2010). Molecular mechanisms of metastasis in breast cancer—clinical applications. Nature reviews Clinical oncology, 7(12), 693-701.

Moter, A., & Göbel, U. B. (2000). Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms.

Munné, S. (2012). Preimplantation genetic diagnosis for aneuploidy and translocations using array comparative genomic hybridization. Current genomics, 13(6), 463-470.

Nguyen, H. T., Dupont, L. N., Cuttaz, E. A., Jean, A. M., Trouillon, R., & Gijs, M. A. (2018). Breast cancer HER2 analysis by extra-short incubation microfluidics-assisted Fluorescence in situ hybridization (ESIMA FISH). Microelectronic Engineering, 189, 33-38.

Ormandy, C. J., Musgrove, E. A., Hui, R., Daly, R. J., & Sutherland, R. L. (2003). Cyclin D1, EMS1 and 11q13 amplification in breast cancer. Breast cancer research and treatment, 78(3), 323-335.

Pandis, N., Heim, S., Bardi, G., Idvall, I., Mandahl, N., & Mitelman, F. (1992). Whole‐arm t (1; 16) and i (1q) as sole anomalies identify gain of 1 q as a primary chromosomal abnormality in breast cancer. Genes, Chromosomes and Cancer, 5(3), 235-238.

Pinkel, D., Gray, J. W., Kallioniemi, A., Kallioniemi, O. P., Waldman, F., & Sakamoto, M. (2011). U.S. Patent No. 8,021,837. Washington, DC: U.S. Patent and Trademark Office.

Prat, A., & Perou, C. M. (2011). Deconstructing the molecular portraits of breast cancer. Molecular oncology, 5(1), 5-23.

Prat, A., Adamo, B., Cheang, M. C., Anders, C. K., Carey, L. A., & Perou, C. M. (2013). Molecular characterization of basal-like and non-basal-like triple-negative breast cancer. The oncologist, 18(2), 123.

Prat, A., Parker, J. S., Karginova, O., Fan, C., Livasy, C., Herschkowitz, J. I., ... & Perou, C. M. (2010). Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast cancer research, 12(5), R68.

Price, C. M. (1993). Fluorescence in situ hybridization. Blood reviews, 7(2), 127-134.

Przybytkowski, E., Lenkiewicz, E., Barrett, M. T., Klein, K., Nabavi, S., Greenwood, C. M., & Basik, M. (2014). Chromosome-breakage genomic instability and chromothripsis in breast cancer. BMC genomics, 15(1), 579.

Qaisar, U., Tayyeb, A., & Bhat, T. A. (2017). Techniques of Chromosomal Studies. In Chromosome Structure and Aberrations (pp. 307-330). Springer, New Delhi.

Reinholz, M. M., Bruzek, A. K., Visscher, D. W., Lingle, W. L., Schroeder, M. J., Perez, E. A., & Jenkins, R. B. (2009). Breast cancer and aneusomy 17: implications for carcinogenesis and therapeutic response. The lancet oncology, 10(3), 267-277.

Reis-Filho, J. S., Simpson, P. T., Gale, T., & Lakhani, S. R. (2005). The molecular genetics of breast cancer: the contribution of comparative genomic hybridization. Pathology-Research and Practice, 201(11), 713-725.

Ribeiro, I. P., Melo, J. B., & Carreira, I. M. (2019). Cytogenetics and Cytogenomics Evaluation in Cancer. International journal of molecular sciences, 20(19), 4711.

Richardson, A. L., Wang, Z. C., De Nicolo, A., Lu, X., Brown, M., Miron, A., ... & Ganesan, S. (2006). X chromosomal abnormalities in basal-like human breast cancer. Cancer cell, 9(2), 121-132.

Rondón-Lagos, M., Di Cantogno, L. V., Marchiò, C., Rangel, N., Payan-Gomez, C., Gugliotta, P., ... & Sapino, A. (2014). Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis. Molecular cytogenetics, 7(1), 8.

Schnitt, S. J. (2010). Classification and prognosis of invasive breast cancer: from morphology to molecular taxonomy. Modern Pathology, 23(2), S60-S64.

Selig, S., Okumura, K., Ward, D. C., & Cedar, H. (1992). Delineation of DNA replication time zones by Fluorescence in situ hybridization. The EMBO journal, 11(3), 1217-1225.

Shakoori, A. R. (2017). Fluorescence In Situ Hybridization (FISH) and Its Applications. In Chromosome Structure and Aberrations (pp. 343-367). Springer, New Delhi.

Simpson, P. T., Reis‐Filho, J. S., Gale, T., & Lakhani, S. R. (2005). Molecular evolution of breast cancer. The Journal of Pathology: A Journal of the Pathological Society of Great Britain and Ireland, 205(2), 248-254.

Smail, H. O. (2020). Dermatoglyphics in common: genetic disorders and cancers. MicroMedicine, 8(2), 55-62.

Smail, H.O., 2016. Qualitative and Quantitative Identification of DNA Methylation Changes in Blood of the Breast Cancer patients (MSC thesis, University of Sulaimani).

Speicher, M. R., & Carter, N. P. (2005). The new cytogenetics: blurring the boundaries with molecular biology. Nature reviews genetics, 6(10), 782-792.

Thompson, C. T., & Gray, J. W. (1993). Cytogenetic profiling using Fluorescence in situ hybridization (FISH) and comparative genomic hybridization (CGH). Journal of Cellular Biochemistry, 53(S17G), 139-143.

Turner, T. H., Alzubi, M. A., Sohal, S. S., Olex, A. L., Dozmorov, M. G., & Harrell, J. C. (2018). Characterizing the efficacy of cancer therapeutics in patient-derived xenograft models of metastatic breast cancer. Breast Cancer Research and Treatment, 170(2), 221-234.

Ueno, T., Emi, M., Sato, H., Ito, N., Muta, M., Kuroi, K., & Toi, M. (2012). Genome-wide copy number analysis in primary breast cancer. Expert opinion on therapeutic targets, 16(sup1), S31-S35.

Varella‐Garcia, M. (2003). Molecular cytogenetics in solid tumors: laboratorial tool for diagnosis, prognosis, and therapy. The Oncologist, 8(1), 45-58.

Waminal, N. E., Pellerin, R. J., Kim, N. S., Jayakodi, M., Park, J. Y., Yang, T. J., & Kim, H. H. (2018). Rapid and efficient FISH using pre-labeled oligomer probes. Scientific reports, 8(1), 1-10.

Watters, A. D., Going, J. J., Cooke, T. G., & Bartlett, J. M. S. (2003). Chromosome 17 aneusomy is associated with poor prognostic factors in invasive breast carcinoma. Breast cancer research and treatment, 77(2), 109-114.

Weigelt, B., Mackay, A., A'hern, R., Natrajan, R., Tan, D. S., Dowsett, M., ... & Reis-Filho, J. S. (2010). Breast cancer molecular profiling with single sample predictors: a retrospective analysis. The lancet oncology, 11(4), 339-349.

Zhang, J., Zhang, H., Xu, X., Wang, M., & Yu, Z. (2015). Comparative genomic hybridization analysis of invasive ductal breast carcinomas in the Chinese population. Oncology letters, 10(4), 2100-2106.



  • There are currently no refbacks.

Copyright (c) 2022 Harem Othman Smail

Biology, Medicine, & Natural Product Chemistry
ISSN 2089-6514 (paper) - ISSN 2540-9328 (online)
Published by Sunan Kalijaga State Islamic University & Society for Indonesian Biodiversity.

Creative Commons License
This work is licensed under a CC BY-NC