title: Detection of ALK gene rearrangements in formalin-fixed, paraffin-embedded tissue using a fluorescence in situ hybridization (FISH) probe: a search for optimum conditions of tissue archiving and preparation for FISH.
abstract: BACKGROUND
  It is widely known that the efficiency of fluorescence in situ hybridization (FISH) probes applied to formalin-fixed, paraffin-embedded tissues is affected by the conditions under which the tissues are fixed and embedded. However, relatively few studies address exactly how tissue archiving conditions affect the performance of FISH probes. We report our experience based on use of an ALK FISH probe, during the validation of its diagnostic utility.
  
  
  METHODS
  We applied the probe to 77 formalin-fixed, paraffin-embedded tissue blocks archived from 1991 through to 2000, and studied the interrelationship between the archival age (which ranged up to 10 years), type and condition of tissue, duration required for optimum hydrolysis, and obtainability of hybridization signals.
  
  
  RESULTS
  We found that as archival age and tissue collagen content increased, not only did hydrolysis times have to be prolonged in order to yield interpretable hybridization signals, but also the likelihood of blocks becoming non-signaling increased. The most striking positive correlations were seen between the archival age of signaling lymphoid blocks and their requisite hydrolysis times.
  
  
  CONCLUSIONS
  The difficulty in applying FISH on archival tissue increases with its archival age and collagen content, and may necessitate changes in laboratory protocol accordingly.
authors.affiliation: Department of Pathology, National University of Singapore, Singapore. pattanl@nus.edu.sg
authors.forename: Leonard Hwan Cheong
authors.initials: LH
authors.lastname: Tan
authors.forename: Elaine
authors.initials: E
authors.lastname: Do
authors.forename: Siew Meng
authors.initials: SM
authors.lastname: Chong
authors.forename: Evelyn Siew Chuan
authors.initials: ES
authors.lastname: Koay
mesh_terms: D000077548:Anaplastic Lymphoma Kinase; D003094:Collagen / Q000032:analysis; D005404:Fixatives; D005557:Formaldehyde; D015321:Gene Rearrangement; D006801:Humans; D006868:Hydrolysis; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008221:Lymphoid Tissue / Q000473:pathology; D009369:Neoplasms / Q000737:chemistry / Q000473:pathology; D016612:Paraffin Embedding; D011505:Protein-Tyrosine Kinases / Q000235:genetics*; D020794:Receptor Protein-Tyrosine Kinases; D013048:Specimen Handling; D013997:Time Factors
chemical_list: D005404:Fixatives; D005557:Formaldehyde; D003094:Collagen; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D011505:Protein-Tyrosine Kinases; D020794:Receptor Protein-Tyrosine Kinases