Abstract
Fluorescent in situ hybridization (FISH) techniques can be used to identify a range of chromosome abnormalities that are clinically significant in many cancers. Multicolor FISH can be used to identify multiple targets, which can be simultaneously detected in individual cells using digital imaging microscopy. In an era of precision medicine there is a requirement to make a precise diagnosis and to have a molecular classification of the tumor that can guide therapy. Cancer genomics is now regarded as a sub-specialism in pathology and genomic testing needs to be robustly integrated into the routine diagnostic practice.
The FISH techniques described in this chapter have been developed over many years in a busy hematopathology diagnostic laboratory. We describe robust in-house methods for both liquid samples (blood and bone marrow mainly) and formalin-fixed paraffin-embedded (FFPE) tissue biopsies that allow for large numbers of slides to be set up in batches. The techniques described are for interphase cells in tissues where metaphase chromosome techniques are generally not applicable. Some of the FISH tests need to be carried out as an “out-of-hours” emergency test to make a critical diagnosis while others provide prognostic information and are used to guide downstream patient management.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70
Mitelman F, Johansson B, Mertens F (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233–245
Swerdlow SH, Campo E, Harris NL et al (2016) WHO classification of tumours of haematopoietic and lymphoid tissues, 4th edn. International Agency for Research on Cancer, Lyon
Summersgil B, Clark J, Shipley J (2008) Fluorescence and chromogenic in situ hybridization to detect genetic aberrations in formalin-fixed paraffin embedded material, including tissue microarrays. Nat Protoc 3(2):220–234
ISO15189:2012. Medical laboratories – requirements for quality and competence
Srinivasan M, Sedmak D, Jewell S (2002) Effect of fixatives and tissue processing on the content and integrity of nucleic acids’. Am J Pathol 161(6):1961–1971
Rack K, van den Berg E, Haferlach C et al (2019) European recommendations and quality assurance for cytogenomic analysis of haematological neoplasms. Leukemia 33(8):1851–1867
Claustres M, Claustres M, Kožich V, On behalf of the ESHG Quality Committee et al (2013) Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic). Eur J Hum Genet 22:160–170
Haferlach C, Rieder H, Lillington DM, on behalf of the European Leukemia Net–Workpackage Cytogenetics et al (2007) Proposals for standardized protocols for cytogenetic analyses of acute leukemias, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic myeloproliferative disorders, and myelodysplastic syndromes. Genes Chromosomes Cancer 46(5):494499
Howat WJ, Wilson BA (2014) Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods 70(1):12–19
Groelz D, Sobin L, Branton P et al (2013) Non-formalin fixative versus formalin-fixed tissue: a comparison of histology and RNA quality. Exp Mol Pathol 94(1):188–194
Cory JM, Rapp F, Ohlsson-Wilhelm BM (1990) Effects of cellular fixatives on human immunodeficiency virus production. Cytometry 11(5):647–651
Ross FM, Avet-Loiseau H, Ameye G, European Myeloma Network et al (2012) Report from the European Myeloma Network on interphase FISH in multiple myeloma and related disorders. Haematologica 97(8):1272–1277
McGowan-Jordan J, Simons A, Schmid M (2016) ISCN 2016: an international system for human cytogenomic nomenclature. S. Karger, Basel
Other Useful Resources
HUGO Gene Nomenclature Committee. http://www.genenames.org/
Mitelman F, Johansson B, Mertens F. Mitelman database of chromosome aberrations and gene fusions in cancer. 2018. http://cgap.nci.nih.gov/Chromosomes/Mitelman
National Guidelines
AUSTRALIA Guidelines for cytogenetics laboratories: National Pathology Accreditation Advisory Council - Commonwealth of Australia 2001
BELGIUM Guidelines for Clinical Cytogenetic Diagnostic Laboratories in Belgium – Belgium Society of Human Genetics, 2004. CANADA CCMG Cytogenetic Guidelines – Canadian College of Medical Genetics, 2003
FRANCE Guide de Bonnes Pratiques en Cytogénétique – Association des Cytogénéticiens de Langue Française, 2011
GERMANY S2-Leitlinie Humangenetische Diagnostik. Deutsche Gesellschaft fur Humangenetik e.V. (GfH), Berufsverband Deutscher Humangenetiker e.V. (BVDH), 2011, medgen 23: 281–322. (Acquired cytogenetics on pages 309–313. The pdf can also be found at: http://www.gfhev.de/de/leitlinien/LL_und_Stellung nahmen/2011_06_24_S2_LL_Humangenetik.pdf ITALY Linee guida per la diagnosi citogenetica Consensus 2007
NETHERLANDS Guidelines WHGD: http://www.vkgl.nl/LOC.php UK ACC Professional Guidelines for Clinical Cytogenetics: General Best Practice v1.04, 2007
UK ACC Professional Guidelines for Clinical Cytogenetics. Haemato-Oncology Best Practice Guidelines v1.01. March 2007
ACC Professional Guidelines for Clinical Cytogenetics: Acute lymphoblastic leukaemias. July 2011
ACC Professional Guidelines for Clinical Cytogenetics: CML and other myeloproliferative neoplasms. July 2011
The British Committee for Standards in Haematology (BCSH) Guidelines. (www.bcshguidelines.com/)
United States Standards and Guidelines for Clinical Genetics Laboratories - American College of Medical Genetics, 2006
International/European Standards
ISCN 2013: Shaffer LG, McGowan-Jordan J, Schmid M (2013) ISCN 2013: An International System for Human Cytogenetic Nomenclature. S. Karger, Basel
ICD-10; International Classification of disease. WHO
European General Cytogenetic Guidelines and Quality Assurance (2011). http://e-c-a.eu/files/downloads/ E.C.A._General_Guidelines_Version%202.0.pdf
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
O’Connor, S.J.M., Turner, K.R., Barrans, S.L. (2020). Practical Application of Fluorescent In Situ Hybridization Techniques in Clinical Diagnostic Laboratories. In: Nielsen, B.S., Jones, J. (eds) In Situ Hybridization Protocols . Methods in Molecular Biology, vol 2148. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0623-0_3
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0623-0_3
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0622-3
Online ISBN: 978-1-0716-0623-0
eBook Packages: Springer Protocols