Efficient Duplex Real-Time Quantitative RT-PCR of BCR-ABL and ABL Gene Transcripts for Monitoring of Minimal Residual Disease
Authors: Jiang Qianli , Jiang Shan , Meng Fanyi , Feng Ru , Xu Bing , Song Lanlin , Yang Liu , Li Bing , Lin Rong , Xu Xiaolan , Zhou Shuyun 
Published: April 2020

Abstract
BCL-ABL fusion gene can be found in 100% chronic myelogenous leukemia (CML) and about 25% adult acute lympholid leukemia where its expression level is a crucial parameter for monitoring of minimal residual disease (MRD). Depending on the breakpoint in BCR, exon 2 of ABL (a2) joins with exons 1 (e1), 13 (b2), or 14 (b3), or rarely to exon 19 (e19) of BCR resulting in chimeric proteins of p190, p210 and p230, respectively. The c-ABL gene is one of the best controls for MRD detection by real-time quantitative RT-PCR (RQ-RT-PCR). In most studies published before, PCR probes were labeled by single fluorescence such as FAM, and BCR-ABL and ABL transcripts were detected in separate PCR reactions.
Purpose: To design and evaluate a duplex, real-time quantitative RT-PCR (RQ-RT-PCR) system labeled with double fluorescence Taqman probes to simultaneously measure both BCR-ABL and ABL transcripts.
Methods:
Positive controls are plasmids containing full-length target sequence of BCR-ABLP210 and ABL. 70 cases of CML bone marrow samples collected in Nanfang Hospital from Jane 2005 to July 2008 were examined. Patients were untreated ones and those treated with STI571 or allo-hematological stem cell transplantation. RQ-RT-PCR value=copies of BCR-ABL/copies of ABL. The results are compared with fluorescence chromosomal in situ hybridization (FISH) for BCR-ABL. Probes and primers recommended by Europe Anti-Cancer group in 2003 were used as gold standard control; probe and primers for bcr-ablP210 gene are ENF541, ENP501 and ENR561, respectively; probe and primers for abl gene are ENPr1043, ENF1003 and ENR1063, respectively. Both Taqman probes are FAM labed. For duplex RQ-RT-PCR, HEX labeled probe is used for the ABL gene, along with corresponding primers, ENP541 labeled with FAM fluorescence and ENF501 and ENR561 were also used for BCR-ABLP210.
The experiments were carried out in the same tube on a Biorad Opticon2 RQ-PCR unit. The end concentration is 0.3μmoL/L for primers and 0. 2 μmoL/L for probe. The PCR reaction was carried out in 25μL. PCR condition is at 50°C×2min+95°C×10min, then followed 95°C×15s+60°C×1min for 50cycle.
Result: Testing using serial dilutions of plasmid positive control suggested that HEX-FAM duplex is readily amplified with the FAM Taqman probes of BCR-ABLP210, and the HEX-ABL results is same with those with FAM-ABL (recommeded by Europe Anti-Cancer group). Coefficiency of variation among different experiments is less than 5%. The 70 CML cases can be divide into 3 groups based on FISH value: ≥10% (n=32), 0.5% 10% (n=27) and negative (n=11). The corresponding RQ-PCR ratio of BCR-ABL/ABL are 0.590±0.264, 0.044±0.041 and (9.46±6.99)×10|4, respectively, P&lt;0.01 between each group.
Conclusion: We have established an efficient duplex RQ-RT-PCR method with FAM and HEX Taqman probes. This approach enables acquisition of more information from each test and hence reduces the amount of sample needed for each test. We believe this method will be useful to MRD monitoring in CML and BCL-ABL + B-ALL.