SCIENTIFIC PROGRAMME
SESSION I
BIOLOGY OF B-CELL
PRECURSOR ALL
SESSION II
BIOLOGY OF T-CELL ALL
SESSION III
MINIMAL RESIDUAL
DISEASE MONITORING
SESSION IV
INDIVIDUALIZED
MANAGEMENT OF ALL
SESSION V
NEW ADVANCES IN ALL
SESSION VI
CAR T-CELLS &
ALLOGENEIC HSCT
SESSION VII
FRONTLINE
INCORPORATION OF
BITES AND ADCS
SESSION VIII
T-CELL ALL AND
LYMPHOBLASTIC
LYMPHOMA
SESSION IX
PH AND PH-LIKE ALL
SELECTED ABSTRACTS
FOR AN ORAL
PRESENTATION
SELECTED ABSTRACTS
AS E-POSTERS
DISCLOSURES
BCR-ABL P190 QUANTITATION EVALUATED BY COMMERCIALLY AVAILABLE ASSAYS
AND THE CEPHEID XPERT® BCR-ABL ULTRA P190 PROTOTYPE‡ASSAY
Adam Aslam, Tran Tran, Vineela Kadiyala, Phat Nguyen, Jessica Dosanjh, Yuanyuan Liu and Lin Yuan
Oncology R&D, Cepheid, Sunnyvale
Aims
The objective of this study was to compare the performance of the novel Cepheid Xpert BCR-ABL
Ultra p190 Prototype Assay to the Asuragen QuantideX® qPCR BCR-ABL minor Kit, the
Qiagen ipsogen® BCR-ABL1 mbcr Kit, and an in-house developed reverse transcriptase digital
droplet PCR (RT-ddPCR) assay using samples contrived using Philadelphia chromosome-positive
(Ph+) ALL patient peripheral blood. Our goal was to create a fast and easy to use
quantitative assay with higher sensitivity than currently available assays for use in the
monitoring of treatment efficacy and minimal residual disease (MRD) in Ph+ ALL patients.
Background
BCR-ABL is a constitutively active tyrosine kinase formed by the t(9;22) reciprocal
translocation, with the p190 transcript being the most frequent variant in Ph+ ALL¹. Tyrosine
kinase inhibitor (TKI) resistance develops in a significant number of Ph+ ALL patients over the
course of treatment²,³,⁴. As 15-20% of children, and about half of adults treated for Ph+ ALL
ultimately relapse, there is need for a more sensitive and easier to use molecular test with a
shorter time-to-result (TTR) for the monitoring of MRD and treatment response in p190-
positive patients³,⁵,⁶.
Methods
Three p190-positive ALL total RNA samples were spiked into p190-negative EDTA whole blood
lysate matrix diluents and serially diluted to target %BCR-ABL p190/ABL outputs from
approximately 25% (LR log reduction 0.60) to near the assays expected limit of detection
(LoD), approximately 0.005% (LR 4.30). A subset of each level underwent sample preparation,
total RNA extraction, and RT-qPCR all in the Cepheid GeneXpert automated cartridge system,
and another subset had total RNA extracted using the Zymo Direct-zol™ RNA Miniprep Plus
Kit. RNA was qualified and quantified using the Thermo Scientific NanoDrop™ 2000
Spectrophotometer before being tested per the comparator assay vendors’
recommendations. The Cepheid Prototype assay utilized 4.5mL of lysate, whereas the
Asuragen assay used 1-2 μg of RNA per test, and the Qiagen and RT-ddPCR assays used 1 μg
of RNA per test.
Results
Deming regressions and associated Bland-Altman plots showed a high degree of correlation
and agreement between comparator assays and the Cepheid Prototype assay. Replicates that
did not detect p190 were not included in this analysis (Figure 1). Dropout rates at low target
%BCR-ABL p190/ABL levels were compared between assays. The Cepheid Prototype assay had
the best performance in terms of hit-rate, followed by the Asuragen, RT-ddPCR, and Qiagen
assays.
Conclusions
The novel Cepheid Prototype assay showed a high level of agreement with the three
comparator assays and gave the lowest LoD overall in this study using samples contrived from
Ph+ ALL patient peripheral blood. TTR was minimized in the Cepheid Prototype assay to 130
minutes, while the comparator assays all had a TTR of approximately five hours or greater.
POSTER 2