Introduction
Monitoring BCR-ABL transcript levels in peripheral blood of patients using real-time quantitative PCR is standard of care in the management of Chronic Myeloid Leukemia. Xpert BCR-ABL Ultra is an automated cartridge-based assay developed by Cepheid for sensitive assessment of BCR-ABL transcript levels. However, in clinical situations the total RNA isolated from white blood cell (WBC) in the patient's blood is insufficient to ensure assay LoD of 0.003% (IS)/MR4.52, or high WBCC in specimen can overload the Ultra cartridge, resulting in inaccurate test results. Therefore, it is necessary to determine proper WBCC input, to ensure accurate assay quantification results.
Objectives
The objective of this study was to determine the correlation between ABL copy number input and Ct value, determine lower and upper WBCC input limits for the Xpert BCR-ABL Ultra assay and establish the ABL Ct cut-offs.
Methods
To establish an upper ABL Ct limit that corresponds to a minimal ABL CN input of 32,000 for supporting LoD, a BCR-ABL plasmid DNA (pDNA, ERM-AD623) was serially diluted and tested in an EDTA whole blood background to make a calibration panel. A standard curve was generated against which the ABL Ct could be estimated as a function of ABL copy number.
To estimate the lower WBCC limit, CML negative EDTA lysate with normal WBCC was serially diluted with WBC depleted EDTA lysate.
To estimate the upper WBCC limit, EDTA lysate from a specimen with high WBCC (69.9×106cells/mL) was diluted with CML negative lysate with normal WBCC (3.5×106 cells/mL).
To validate the WBCC limit, CML positive lysate with high WBCC (40×106cells/mL) was diluted with high WBCC (40×106cells/mL) CML negative lysate to produce five BCR-ABL levels within 0.03% (IS)/MR3.52 to 65% (IS)/MR0.19. Each level was further diluted with PBS lysate to achieve 8 levels of WBCC from 40×106 to 0.04×106 cells/mL.
Results
ABL Ct value of ~19 corresponding to a minimum ABL copy number input of 32,000 was established to support assay LoD of 0.003% (IS)/MR4.52 (Figure.1). To allow for a one Ct buffer, the upper ABL Ct cut-off was set at 18.
The lower WBCC input limit, corresponding to the upper ABL Ct limit of ~18 with estimated ABL copy number greater than 64,000, was established to be 0.15×106 cells/mL (Figure.2)
The upper WBCC input limit was established to be 30×106 cells/mL. This corresponds approximately to a Ct value of 10 (Figure.3). The Xpert BCR-ABL Ultra test monitors RNA expression levels of the BCR-ABL fusion transcript and the ABL transcript. Unlike a gene DNA marker, RNA expression levels are variable and can fluctuate. To accommodate for the variability in RNA expression levels and based on results from this study, the upper ABL Ct cut-off was lowered to 8.
The lower and upper WBCC input limit, together with ABL Ct cut-off, were validated with CML patient specimens with WBCC input ranging from 0.04 to 40 × 106 /ml within IS% range of 0.03% to 65% (Table.1). The normal WBCC of 4 to 10 × 106/mL across all tested concentrations yielded ABL Ct range from 13.2 to 11.7 with estimated ABL copy number of 2.5×106 to 7.8×106.
Conclusions
A correlation between ABL copy number input and ABL Ct value was established with the standard curve generated from a pDNA calibration panel.
The lower WBCC limit was set at 1.5×105 cells/mL and upper WBCC limit was set at 3.0×107 cells/mL, together with ABL Ct cut-offs of 18 and 8 and ABL copy number of 6.4×104 to 1.4×108, to support Xpert BCR-ABL Ultra assay performance.
The normal WBCC of 4 to10×106/mL across all tested concentrations yielded an ABL Ct range from 13.2 to 11.7 with estimated ABL copy number of 2.5×106 to 7.8×106, indicating Xpert BCR-ABL Ultra assay normally provided more than 10 times the required minimum ABL Copy number to support the assay LoD claim at 0.003% (IS).
*Product in development. Not for use in diagnostic procedures. Not reviewed by any regulatory body.
No relevant conflicts of interest to declare.
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