Numerical aberrations of chromosome 7 detected in 15 microns paraffin-embedded tissue sections of primary cutaneous melanomas by fluorescence in situ hybridization and confocal laser scanning microscopy

Clonal trisomy 4 cells detected in the ossifying renal tumor of infancy: study of 3 cases

The ossifying renal tumor of infancy is a rare neoplasm diagnosed in the first 2 years of life, predominantly in boys. The neoplasm is primarily characterized by the presence of a large ossifying component. Its most common mode of presentation is hematuria, and it has a uniformly benign behavior. The karyotypic makeup of the process has not been reported. Thus, a study was undertaken and it allowed demonstration of clonal trisomy 4, which was confirmed by the fluorescent in-situ hybridization-probing of two additional archival formalin-fixed, paraffin-imbedded similar tumors. On the basis of the findings in these three cases, it seems that clonal trisomy 4 may be considered as a characteristic of the tumor, which makes it distinct from any other infantile renal tumor.

Simultaneous phenotyping and genotyping (FICTION-methodology) on paraffin sections and cytologic specimens: a comparison of 2 different protocols

Combining immunofluorescence labeling with fluorescence in situ hybridization (FISH) is a powerful technique simultaneously studying immunophenotypic markers and genetic abnormalities present in tumor cells [the FICTION method (fluorescence immunophenotyping, and interphase cytogenetics as a tool for the investigation of neoplasms)]. However, few studies have been applied to the technical problems posed by antigen retrieval and accessibility of genetic probes to target-DNA, using formalin-fixed, paraffin-embedded tissue. In this study, we compared 2 immunofluorescence detection systems, the 3-step IF (TIF) method against the Tyramide Signal Amplification techniques (TSA). The FICTION-TSA technique significantly improved the sensitivity for detection of the immunophenotypic markers without influencing specific probe hybridization to target-DNA, compared with the results obtained with the TIF method. The reaction product of the TSA system was robust to the following FISH procedure in contrast to the TIF technique. The TSA technique used also allowed synchronous detection of nuclear antigens and FISH signals using both fusion (IgH/CCND1) and break-apart (CCND1) probes on formalin-fixed paraffin-embedded tissue.

Significance of HER2 low-level copy gain in Barrett's cancer: implications for fluorescence in situ hybridization testing in tissues

PURPOSE

HER2 may be a relevant biomarker in Barrett's cancer. We compared three HER2 laboratory methods, standard fluorescence in situ hybridization (FISH), image-based three-dimensional FISH in thick (16 microm) sections, and immunohistochemistry, to predict patient outcome.

EXPERIMENTAL DESIGN

Tissue microarray sections from 124 Barrett's cancer patients were analyzed by standard FISH on thin (4 microm) sections and by image-based three-dimensional FISH on thick (16 microm) sections for HER2 and chromosome-17, as well for p185(HER2) by immunohistochemistry. Correlations with clinical and follow-up data were examined.

RESULTS

Only three-dimensional FISH on thick (16 microm) sections revealed HER2 gene copy gain to be associated with increased disease-specific mortality (relative risk, 2.1; 95% confidence interval, 1.06-4.26; P = 0.033). In contrast, standard FISH on thin (4 microm) sections and immunohistochemistry failed to predict clinical outcome. Low-level gain of HER2 occurred frequently in Barrett's cancer (>or=2.5-4.0 HER2 copies, 59.7%; HER2-to-chromosome-17 ratio, >or=1.1-2.0; 61.2%) and defined a subpopulation for patient outcome as unfavorable as HER2 gene amplification [disease-free survival, P = 0.017 (HER2 copies)]. This low-level group was neither definable by standard FISH nor immunohistochemistry. No prognostic significance was found for chromosome-17 aneusomy.

CONCLUSIONS

Low-level copy gains of HER2 define a biologically distinct subpopulation of Barrett's cancer patients. Importantly, these subtle copy number changes are not reliably detected by standard FISH in thin (4 microm) tissue sections, highlighting a thus far unrecognized weakness in HER2 FISH testing. These results should be taken into account for accurate evaluation of biomarkers by FISH and for HER2 FISH testing in tissue sections.

FISH analysis for the detection of lymphoma-associated chromosomal abnormalities in routine paraffin-embedded tissue

Over the last decade, fluorescence in situ hybridization (FISH) has become a firmly established technique in the diagnosis and assessment of lymphoid malignancies. However, this technique is not wide-ly used in the routine diagnostic evaluation of paraffin-embedded biopsies, most likely because of a perception that it is technically more demanding. There are also uncertainties regarding diagnostic thresholds and the way in which results should be interpreted. In this Review, we describe practical strategies for using FISH analysis to detect lymphoma-associated chromosomal abnormalities in routine paraffin-embedded lymphoma biopsies. Furthermore, we provide proposals on how FISH results should be interpreted (including how to calculate cutoff levels for FISH probes), recorded, and reported. An online appendix (available at http://jmd.amjpathol.org) details various simple, yet robust procedures for paraffin FISH analysis; it also provides additional information on the production of FISH probes, evaluating and reporting FISH results, sources for reagents and equipment, and troubleshooting. We hope that these suggestions will make FISH technology for the study of lymphoma biopsies more accessible to routine diagnostic and research laboratories.

Detection by the fluorescence in situ hybridization technique of MYC translocations in paraffin-embedded lymphoma biopsy samples

The detection of chromosomal translocations by fluorescence in situ hybridization (FISH) is widely performed, but very few studies have attempted to apply this technique to paraffin-embedded routine biopsy samples. We report the analysis of paraffin sections from 36 B-cell lymphoma biopsies for MYC translocation breakpoints by FISH. The probes consisted of multi-YAC constructs that flanked the breakpoint region and that, therefore, separate upon a chromosomal translocation and generate split (or "segregated") signals (rather than a more ambiguous "co-localization" pattern, obtained when the two partners in a hybrid gene are detected). The results were assessed by a simple approach that avoids the counting of signal numbers per nucleus and so is appropriate for use in routine practice. A total of 19 of the 36 lymphomas were scored as positive for MYC translocation and this included 16 of the 20 patients in whom classic cytogenetics had shown the presence of the (8;14) translocation (or one of its two variants). We conclude that this two-colour "split-signal" technique based on breakpoint flanking probes can readily detect chromosomal translocations in paraffin sections. Furthermore, our results suggest that cases categorized as "atypical Burkitt's/Burkitt-like" lymphoma (at least for adult patients) are heterogeneous with respect to translocations involving the MYC oncogene, as well as immunophenotype and clinical features.