Detection and molecular monitoring of FIP1L1-PDGFRA-positive diseases by analysis of patient-specific genomic DNA fusion junctions

Score, J., Walz, C., Jovanovic, J.V., Jones, A.V., Waghorn, K., Hidalgo-Curtis, C., Lin, F., Grimwade, D., Grand, F., Reiter, A. and Cross, N.C.P. (2009) Detection and molecular monitoring of FIP1L1-PDGFRA-positive diseases by analysis of patient-specific genomic DNA fusion junctions. Leukemia, 23 (2), 332-339. (doi:10.1038/leu.2008.309).

Abstract

To evaluate current detection methods for FIP1L1-PDGFRA in hypereosinophilic syndrome (HES), we developed a means to rapidly amplify genomic break points. We screened 202 cases and detected genomic junctions in all samples previously identified as RT-PCR positive (n=43). Genomic fusions were amplified by single step PCR in all cases whereas only 22 (51%) were single step RT-PCR positive. Importantly, FIP1L1-PDGFRA was detected in two cases that initially tested negative by RTPCR or fluorescence in situ hybridization. Absolute quantitation of the fusion by real-time PCR from genomic DNA (gDNA) using patient-specific primer/probe combinations at presentation (n=13) revealed a 40-fold variation between patients (range, 0.027-1.1 FIP1L1-PDGFRA copies/haploid genome). In follow up samples, quantitative analysis of gDNA gave 1-2 log greater sensitivity than RQ-PCR of cDNA. Minimal residual disease assessment using gDNA showed that 11 of 13 patients achieved complete molecular response to imatinib within a median of 9 months (range, 3-17) of starting treatment, with a sensitivity of detection of up to 1 in 10 5. One case relapsed with an acquired D842V mutation. We conclude that detection of FIP1L1-PDGFRA from gDNA is a useful adjunct to standard diagnostic procedures and enables more sensitive follow up of positive cases after treatment. Leukemia (2009) 23, 332-339; doi:10.1038/leu.2008.309; published online 6 November 2008 Copyright (C) 2009 Nature Publishing Group

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Contributors

Author: N.C.P. Cross

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