The detection of del(5q) in myelodysplastic syndrome (MDS) provides useful information to guide the choice of therapy, given the efficacy of lenalidomide in cases containing this abnormality. Fluorescence in situ hybridization (FISH) analysis offers the opportunity to specifically detect chromosomal abnormalities much more rapidly than metaphase cytogenetics, which may have a turnaround time of several weeks. However, it is currently unclear which chromosomal loci are the most appropriate to examine for detection of del(5q) in routine practice. The breakpoints on chromosome 5q are heterogeneous and two commonly deleted regions (CDR) have been described. The first CDR occurs in acute myeloid leukemia (AML) and high grade MDS and encompasses a region at 5q31 including the EGR1 locus. A second CDR, occurring in at least some cases reported as 5q- syndrome, centers around 5q33 and includes the CSF1R locus. We therefore examined whether FISH studies for EGR1, CSF1R, or a combination of both probes would provide the greatest clinical utility for detection of del(5q). 51 cases of myeloid neoplasms with del(5q) by metaphase cytogenetics were analyzed, including 5q- syndrome (n=8), refractory anemia with excess blasts (RAEB, n=8), refractory cytopenia with multilineage dysplasia (RCMD, n=6), MDS unclassifiable (n=1), therapy related MDS (n=1), myelodysplastic/myeloproliferative overlap syndromes (MDS/MPD, n=6), and AML (n=21). FISH studies using EGR1/D5S23, D5S721 and CSF1R/D5S23, D5S721 probes (Abbot Molecular, Abbot Park, IL) were performed on archival bone marrows (45 coverslip aspirate smears, 4 cytogenetic culture cell pellets, and 2 formalin fixed paraffin embedded clot sections). Normal ranges were established for each probe by analysis of appropriate negative control samples. Deletion of the EGR1 locus was detected in 49/51 (96%) cases, including each case of 5q- syndrome. The CSF1R locus, which could be analyzed in 48 cases, was deleted in 44 cases (92%). In cases with concordant results, a similar percentage of abnormal nuclei was identified with each probe. Two cases (1 MDS/MPD and 1 AML) displayed deletion of the EGR1 locus but a normal pattern for CSF1R. Two cases (1 AML and 1 MDS/MPD) showed no evidence of EGR1 or CSF1R deletion despite a del(5q) identified by metaphase cytogenetics. In conclusion, FISH for EGR1 is sufficient to successfully detect del(5q) in the vast majority of cases of MDS and AML containing this abnormality, including at least most cases of 5q- syndrome. Additional FISH studies for the CSF1R locus did not increase the diagnostic yield. Further studies will be required to determine if deletions of 5q involving EGR1 but not CSF1R influence the response to lenalidomide. A small number of cases of del(5q) are detected only by metaphase cytogenetics, possibly due to a small number of abnormal cells present prior to in vitro culture.

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