Conventional PCR Versus Next Generation Sequencing for Diagnosis of FLT3, IDH and NPM1 Mutations in Acute Myeloid Leukemia: Results of the PETHEMA PCR-LMA Study

• DOI: 10.3390/cancers17050854
• Publication Date: 2025-03-03T15:15:03Z
• Authors: Blanca Boluda; Rebeca Rodriguez-...; Claudia Sargas; Rosa Ayala; María J. Larráyoz; María Carmen Chillón; Elena Soria-Saldise; Cristina Bilbao; Esther Prados Pra...; Irene Navarro; David Martinez-Cu...; Cristina Gil; Teresa Bernal; Juan Bergua; Lorenzo Algarra; Mar Tormo; Pilar Martínez-Sa...; Estrella Carrillo...; Josefina Serrano; Juan M. Alonso-Do...; Raimundo García; Maria Luz Amigo; Pilar Herrera-Puente; María J. Sayas; Esperanza Lavilla...; María José García...; Julia Morán; Esther Pérez-Sant...; Natalia Alonso-Vence; Ana Oliva; Juan Antonio López; Manuel Barrios; María García-Fortes; María Teresa Olave; Jorge Labrador; Joaquín Martínez-...; María J. Calasanz; Ramón García-Sanz; José A. Pérez-Simón; María T. Gómez-Ca...; Joaquín Sánchez-G...; Yolanda Mendizabal; Eva Barragán; Pau Montesinos

Background/Objectives: This PETHEMA PCR-LMA study aimed to evaluate whether mutations detected by NGS (VAF cut-off of ≥5%) correlate with NPM1, FLT3-ITD, FLT3-TKD, IDH1, and IDH2 mutations detected using conventional PCR (analytical sensitivity 3%) in a nationwide network of seven reference laboratories. Methods: Between 2019 and 2021, 1685 adult AML patients with at least one centralized sample (NGS or PCR) at primary diagnosis or relapse/refractory episode were included. Results: During this period, 1288 paired NGS/PCR samples (1094 at diagnosis, 103 at relapse and 88 at refractoriness) were analyzed. Considering PCR the gold-standard, for NPM1 NGS sensitivity was 98.5% and specificity 98.9%, for FLT3-ITD 73.8% and 99.6%, for FLT3-TKD 84.5% and 99.3%, for IDH1 98.7% and 98.7%, and for IDH2 99.1% and 97.7%, respectively. Overall concordance rate of positive results between NGS (and PCR was 95% (262/276) for NPM1, 72% (149/206) for FLT3-ITD, 74% (49/66) for FLT3-TKD, 87% (77/89) for IDH1 and 84% (107/127) for IDH2. Overall, median days from sample reception until report were 7 for PCR and 28 for NGS. Conclusions: This study shows high concordance between NPM1 and IDH results using PCR and NGS. However, sensible important discrepancies are observed for FLT3 mutations. In our context, rapid screening for these druggable mutations should be performed by conventional PCR.