A Novel Next-Generation Sequencing Assay for the Identification of BCR::ABL1 Transcript Type and Accurate and Sensitive Detection of TKI-Resistant Mutations.
J Appl Lab Med
; 2024 Sep 03.
Article
en En
| MEDLINE
| ID: mdl-39225048
ABSTRACT
BACKGROUND:
The clinical management of chronic myeloid leukemia (CML) patients requires the identification of the type of BCRABL1 transcript at diagnosis and the monitoring of its expression and potential tyrosine kinase inhibitor (TKI) resistance mutations during treatment. Detection of resistant mutation requires transcript type-specific amplification of BCRABL1 from RNA.METHODS:
In this study, a custom RNA-based next-generation sequencing (NGS) assay (Dup-Seq BCRABL1) that enables (a) the identification of BCRABL1 transcript type and (b) the detection of resistance mutations from common and atypical BCRABL1 transcript types was developed and validated. The assay design covers BCR exon 1 to ABL1 exon 10 and employs duplicate PCR amplification for error correction. The custom data analysis pipeline enables breakpoint determination and overlapped mutation calling from duplicates, which minimizes the low-level mutation artifacts.RESULTS:
This study demonstrates that this novel assay achieves high accuracy (positive percent agreement (PPA) for fusion 98.5%; PPA and negative percent agreement (NPA) for mutation at 97.8% and 100.0%, respectively) and sensitivity (limit of detection (LOD) for mutation detection at 3% from 10 000 copies of BCRABL1 input).CONCLUSIONS:
The Dup-Seq BCRABL1 assay not only allows for the identification of BCRABL1 typical and atypical transcript types and accurate and sensitive detection of TKI-resistant mutations but also simplifies molecular testing work flow for the clinical management of CML patients.
Texto completo:
1
Colección:
01-internacional
Base de datos:
MEDLINE
Idioma:
En
Revista:
J Appl Lab Med
Año:
2024
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Reino Unido