Efficacy of Conventional Cytogenetics and FISH for EGR1 To Detect Deletion 5q in Hematological Disorders and To Assess Response to Treatment with Lenalidomide.
Authors: Zou Ying , Fink Stephanie , Stockero Kimberly , Paternoster Sarah , Smoley Stephanie , Tun Han , Reeder Craig , Tefferi Ayalew , Dewald Gordon 
Published: October 2019

Abstract
Background: In 2006 Lenalidomide received FDA approval for myelodysplasia (MDS) with interstitial deletion 5q [del(5q)] based on conventional cytogenetic (CC) results before and after treatment. In clinical practice, FISH studies of interphase nuclei with probes for EGR1 are widely used to detect del(5q), but it is not known whether this method has similar efficacy as CC. Thus, we compared CC and FISH results for various forms of del(5q).
Methods: We selected 145 patients (pts) in our cytogenetic database with del(5q). These pts had various forms of del(5q) and were representative of our clinical practice. This series included 9 pts with MDS that were studied before and after treatment with Lenalidomide. CC studies were done using standard procedures to analyze 20 metaphases from bone marrow. FISH studies were done on the same specimens using stored left-over cells and standard procedures for EGR1 (5q31.2) and D5S23/D5S721 (5p15.2). The cutoff for del(5q) for FISH was <6.0% based on 200 nuclei.
Results: Among 145 pts, 104 were referred for MDS, 9 acute myeloid leukemia, 9 lymphoproliferative disorders, 7 myeloproliferative disorders and 16 without clinical information. A total of 116 pts had breakpoints at del(5)(q13q33), 17 del(5)(q15q33), 8 del(5)(q11.2~q31q31~q35), 3 del(5)(q22q33) and 1 del(5)(q13q22). Del(5q) was detected in 144 pts by both CC and FISH. One pt had del(5)(q13q22) in 20/20 metaphases but was normal by FISH. Percent abnormal cells by FISH was lower in 135/145 pts compared to CC (mean difference 22.5 ± 19.6, range −42 to 98). For 9 pts with MDS, 29 specimens were collected before and after treatment with Lenalidomide: 7 achieved complete cytogenetic remission (four relapsed) and 2 showed a decrease in percent abnormal metaphases. Results of CC and FISH for these 9 pts were concordant for detection of del(5q) and trend of tumor burden due to treatment for 28/29 specimens. The discordant specimen was collected 222 days after treatment; results of CC were normal but FISH was abnormal in 19% of nuclei. Among the 29 specimens, percent abnormal cells by FISH was lower than CC in 27 (mean difference 13.9% ± 22.5, range −19.0 to 73.5). Each of the 9 treated pts had only del(5q) prior to treatment, and was detected by both FISH and CC. After treatment, FISH did not detect a separate cytogenetic clone involving deletion 20q without del(5q) in 2 pts nor did it identify development of other anomalies in 3 pts.
Conclusions: Results of CC and FISH were mostly concordant, but differed in 4 respects. First, 1/145 pts was normal by FISH but had del(5q) by CC. This pt had unusual breakpoints that did not result in loss of EGR1. Second, percentage of cells with del(5q) was usually lower by FISH than CC. This observation is likely related to a different mitotic rate of cells with del(5q) versus normal cells. Third, 1 specimen was abnormal by FISH but normal by CC after treatment, but 2 subsequent specimens were concordant. This discrepancy was likely due to interference of mitosis of del(5q) cells and residual non-proliferating disease. Fourth, 2 treated pts developed a separate cytogenetic clone without del(5q) and 3 developed other anomalies that could not be detected by FISH. We believe FISH for EGR1 is useful in clinical practice, but not a substitute for CC.