Successful application of a direct detection slide-based sequential phenotype/genotype assay using archived bone marrow smears and paraffin embedded tissue sections.

Identification of genetic abnormalities in pathological samples is critical for accurate diagnosis, risk stratification, detection of minimal residual disease, and assessment of response to therapy. Interphase fluorescence in situ hybridization analysis is the standard cytogenetic assay used by many laboratories to detect specific clonal karyotypic aberrations in formalin-fixed, paraffin-embedded tissue. However, direct correlation with immunophenotype or morphology in individual cells is rarely performed because the procedural steps are labor intensive and usually require extensive troubleshooting. In this study, we present a sequential fluorescence in situ hybridization-based technique that uses the identical archived bone marrow smears or paraffin-embedded tissue sections previously evaluated by a pathologist for morphological or immunohistochemical characteristics. This approach is relatively straightforward, using uncomplicated pretreatment and hybridization conditions and basic equipment attached to an automated image analyzer with image capture software to record the location of targeted cells for genotypic/phenotype correlation. Furthermore, the method has proved reliable and reproducible on test samples regardless of specimen age, tissue type, or referring institution.