Detection and molecular monitoring of FIP1L1-PDGFRA-positive disease by analysis of patient-specific genomic DNA fusion junctions.
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 RT-PCR 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.
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Wessex Regional Genetics Laboratory, University of Southampton, Salisbury, UK.
Walz
C
C
Jovanovic
J V
JV
Jones
A V
AV
Waghorn
K
K
Hidalgo-Curtis
C
C
Lin
F
F
Grimwade
D
D
Grand
F
F
Reiter
A
A
Cross
N C P
NC
D017931:DNA Primers; D015321:Gene Rearrangement; D015894:Genome, Human; D006801:Humans; D017681:Hypereosinophilic Syndrome / Q000175:diagnosis*; D018365:Neoplasm, Residual / Q000175:diagnosis*; D015514:Oncogene Proteins, Fusion / Q000032:analysis* / Q000235:genetics; D016133:Polymerase Chain Reaction; D020796:Receptor, Platelet-Derived Growth Factor alpha / Q000032:analysis* / Q000235:genetics; D011995:Recombination, Genetic; D012680:Sensitivity and Specificity; D039221:mRNA Cleavage and Polyadenylation Factors / Q000032:analysis* / Q000235:genetics
D017931:DNA Primers; D015514:Oncogene Proteins, Fusion; D039221:mRNA Cleavage and Polyadenylation Factors; C479819:FIP1L1-PDGFRA fusion protein, human; D020796:Receptor, Platelet-Derived Growth Factor alpha