Evaluation of the GeneXpert Assay for the Monitoring of BCR-ABL Transcript Levels In Chronic Myeloid Leukemia (CML) Patients: Preliminary Results of a Comparison with the Manual and Traditional Manual TaqMan RQ-PCR Assay
Authors: Suriano Marco , Martinelli Giovanni , Poerio Angela , Amabile Marilina , Rosti Gianantonio , Castagnetti Fausto , Iacobucci Ilaria , Soverini Simona , Lonetti Annalisa , Papayannidis Cristina , Abbenante Mariachiara , Parisi Sarah , Palandri Francesca , Baccarani Michele 
Published: October 2019

Abstract
Abstract 4831
Patient with CML harbor the chromosomal translocation t(9;22) which corresponds to fusion of the BCR and ABL genes at the DNA level. Traditionally, CML disease status has been monitored by detecting the t(9;22) translocation by cytogenetics, fluorescence in situ hybridization or southern blot. To date, reverse transcriptase-polymerase chain reaction (RQ-PCR) is considered the most sensitive method available for detecting low copy numbers of the BCR-ABL gene fusion. Current RQ-PCR Taqman assay used to detect the BCR-ABL transcript are relatively time consuming because they require RNA purification and reaction setup steps. The GeneXpert BCR-ABL Monitor Assay (Cepheid, Sunnyvale, Calif) simplifies the testing procedure by using a single use cartridge, which automates the step involved and therefore significantly reduces the technical time required to run the assay. The closed system used in this assay also reduces the chance of contamination. The aim of this study was to compare the two methods of BCR-ABL quantification: the manual TaqMan RQ-PCR and the GeneXpert based assay.
We analyzed 100 peripheral blood samples from CML patients with both methods. First of all, we performed a comparison in terms of quality of the ABL control gene. We found that:
87/100 (87%) samples evaluated with the TaqMan standard assay had the control gene transcript value more than 1000 copies;
100/100 (100%) samples evaluated with the GeneXpert had the control gene transcript value more than 1000 copies;
Thereafter, we analyzed the concordance of the two methods in the quantification of the target gene BCR-ABL. We considered for this analysis only samples with a good quality of the ABL control gene (> 1000 copies) and we subdivided them in two groups:,: patient who achieved a major molecular response (MMR) and patients who did not achieve a MMR. The MMR wass defined as the achievement of a ratio BCR-ABL/ABLx100<0,1, according to the International Scale. We found that:
78/87 (90%) patients analyzed with the standard TaqMan assay achieved a MMR;
9/87 (10%) patients did not achieve a MMR if analyzed with the standard TaqMan protocol;
69/87 (79%) patients analyzed with the GeneXpert achieved a MMR;
18/87 (21%) patients didn't achieve a MMR if analyzed with the GeneXpert.
In conclusion, our preliminary results showed that GeneXpert assay may be a valid alternative to conventional and traditional TaqMan RQ-PCR methods, allowing a better standardization of the molecular techniques used for the monitoring of minimal residual disease in CML patients.
Supported by European LeukemiaNet, AIL, AIRC, FIRB 2006, PRIN 2008, Ateneo RFO grants, Project of integrated program (PIO), Programma di Ricerca Regione – Università 2007 – 2009.

Disclosures:
Martinelli: Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria; Pfizer: Consultancy. Rosti: Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria. Baccarani: Novartis: Consultancy, Honoraria; BMS: Consultancy, Honoraria.