Qiagen, 9002036, Rotor-Gene Q MDx System (US)

The therascreen PDGFRA RGQ PCR Kit is a real-time qualitative in vitro diagnostic assay for the detection of the D842V somatic mutation in the PDGFRA gene using genomic DNA extracted from gastrointestinal stromal tumor (GIST) patient’s formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The therascreen PDGFRA RGQ PCR Kit is intended to aid clinicians in identifying patients with GIST who may be eligible for treatment with AYVAKIT (avapritinib) based on a PDGFRA mutation-detected result. FFPE tumor specimens are processed using the QIAamp DSP DNA FFPE Tissue Kit for manual sample preparation and the Rotor-Gene Q MDx (US) instrument for automated amplification and detection.
Clinical study supporting use of AYVAKIT (avapritinib) The effectiveness of treatment with AYVAKIT (avapritinib) when its use is validated with the therascreen PDGFRA RGQ PCR Kit, is shown in data collected in the BLU-285-1101 study of AYVAKIT (avapritinib), reanalyzed in the bridging study. The Clinical Study BLU-285-1101 was an open-label, multicenter, international, Phase 1, first-in-human (FIH) study to evaluate the safety and efficacy of AYVAKIT (avapritinib) in adult patients with unresectable or metastatic GIST. The study was expanded to include patients with advanced GIST based on encouraging initial efficacy observed in dose escalation. A total of 237 patients, with or without a mutation in the PDGFRA gene, were enrolled across all parts of the study and 204 of those patients were treated with at least 1 dose of either 300 mg or 400 mg once daily (quaque die [QD]) of AYVAKYT (avapritinib) (33 patients were treated with a dose of <300 mg QD). The primary endpoints were to determine maximum tolerated dose (MTD) and recommended Phase 2 dose (RP2D) of AYVAKIT (avapritinib), to determine overall safety and tolerability of AYVAKIT (avapritinib), and to determine the overall response rate (ORR) by modified response evaluation criteria in solid tumors (mRECIST) version 1.1 at the MTD/RP2D of AYVAKIT (avapritinib) in patients with GIST: A D842V mutation in PDGFRA; Progressed following treatment with imatinib and at least one other kinase inhibitor, and who are not known to have a D842V mutation in PDGFRA; or Progressed or experienced intolerance to imatinib, including in the adjuvant setting, and who had not received additional kinase inhibitor therapy and did not have a known D842V mutation in PDGFRA. The analysis of effectiveness of AYVAKIT (avapritinib) was based on the primary efficacy endpoints of overall survival (OS) in 40 evaluable patients at the database cutoff. Among the 31 patients in the 300/400 mg starting dose group who had PDGFRA D842V mutations identified by QIAGEN CTA assay, 29 had confirmed complete response (CR) or partial response (PR) based on central radiology review for an ORR of 94% (95% CI: 78.6%, 99.2%). Best response for these 31 patients was CR in two patients, PR in 27 patients, and stable disease (SD) in two patients, for a clinical benefit rate (CBR) of 100%. Median duration of response (DOR) was not reached in the 300/400 mg dose group; 22 patients (76%) were censored at the time of the data cutoff based on FDA censoring rules with 64% and 51% estimated to be in response at 12 months and 18 months, respectively. The BLU-285-1101 Study met its primary objective, demonstrating treatment with AYVAKIT (avapritinib) provides meaningful clinical benefit to PDGFRA D842V mutant GIST patients, as measured by ORR. Collectively, the efficacy and safety results from the BLU-285-1101 study demonstrate that AYVAKIT (avapritinib) has a favorable benefit-risk profile and is a useful treatment in patients with GIST who have PDGFRA D842V mutation. Concordance between CDx assay and CTA (Bridging study) In the BLU-285-1101 study, the PDGFRA D842V mutation status for screening and enrolment of patients was determined by a clinical trial assay (CTA). Concordance between the therascreen PDGFRA RGQ PCR Kit (CDx) and the CTA was assessed on DNA extracted from GIST samples from 154 patients in study BLU-285-1101. Of the 154 samples, 147 gave a valid therascreen PDGFRA RGQ PCR Kit result (CDx-evaluable patients). The estimated PPA, NPA, and OPA between the therascreen PDGFRA RGQ PCR Kit and the CTA (with CTA as the reference method) for CDx-evaluable patients are detailed in Table 1. The result of 98.64% OPA met the study acceptance criteria of ≥80%. Table 1. Measures of agreement between CDx and CTA* Measure of agreement Frequencies percent agreement Percent agreement Lower two-sided 95% confidence limit † Upper two-sided 95% confidence limit † Overall percent agreement 145/147 98.64% 95.17% 99.83% Positive percent agreement 40/42 95.24% 83.84% 99.42% Negative percent agreement 105/105 100.00% 96.55% 100.00% * CTA as reference method and CDx-evaluable patients. † Clopper-Pearson (Exact) Binomial. The seven subjects with invalid therascreen PDGFRA RGQ PCR Kit results were then included as discordant results in the analysis across all CDx-testable patients. The estimated PPA, NPA and OPA between the therascreen PDGFRA RGQ PCR Kit and the CTA (with CTA as reference method) for all CDx-testable patients are detailed in Table 2. The result of 94.16% OPA met the study acceptance criteria of ≥80%. Table 2. Measures of agreement between CDx and CTA* Measure of agreement Frequencies percent agreement Percent agreement Lower two-sided 95% confidence limit † Upper two-sided 95% confidence limit † Overall percent agreement 145/154 94.16% 89.20% 97.29% Positive percent agreement 40/43 93.02% 80.94% 98.54% Negative percent agreement 105/111 94.59% 88.61% 97.99% * CTA as reference method and CDx-testable patients. † Clopper-Pearson (Exact) Binomial. The therascreen PDGFRA RGQ PCR Kit demonstrated overall agreement of 98.64% (95% CI: 95.17, 99.83) for CDx-evaluable patients. Treatment with AYVAKIT (avapritinib) provides meaningful clinical benefit to patients with PDGFRA D842V mutant GIST, as measured by ORR. The ORR for PDGFRA D842V mutation positive patients when using the therascreen PDGFRA RGQ PCR Kit was 0.94 (95% CI: 0.79,0.99), corresponding to 94%.
The therascreen PDGFRA RGQ PCR Kit comprises of one multiplex PCR amplification reaction to detect the point mutation of interest and a control region downstream of this in the same PDGFRA gene. The assay contains the reagents necessary for the amplification and detection of the target DNA sequence using real-time qualitative PCR. It is designed to be used with the Rotor-Gene Q MDx (US) instrument in conjunction with Rotor-Gene AssayManager software. The assay includes a number of controls to be used as part of each assay run. A no template control (NTC) will be used to detect any contamination. A positive control plasmid containing the sequences of interest will be used to ensure the PCR run has performed within expected parameters. The Rotor-Gene AssayManager software generates a Ct value for the D842V and control sequence present in a sample. The Ct value difference (ΔCt) between the D842V Ct value and the control Ct value is used by the software to generate a mutation call (‘D842V Mutation Detected’ or ‘No Mutation Detected’ if the D842V mutation is present or absent).
The simple and straightforward testing workflow begins with DNA extraction from FFPE gastrointestinal stromal tumor tissue using the QIAamp DSP DNA FFPE Tissue Kit. This is followed by sensitive real-time PCR on the Rotor-Gene Q MDx (US) instrument. Finally, Rotor-Gene AssayManager software rapidly and accurately processes and reports results, informing the system operator if D842V mutation is present or absent.