Immunoglobulin/T-Cell Receptor Gene Rearrangement Analysis Using RNA-Seq.

Area of Science:

• Hematology
• Molecular Biology
• Oncology

Background:

• Accurate monitoring of minimal residual disease (MRD) is essential for acute lymphoblastic leukemia (ALL) patient management.
• Immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements serve as crucial leukemia-specific markers.
• Effective MRD detection aids in risk-group stratification and treatment adjustments.

Purpose of the Study:

• To detail the methodology for generating and analyzing RNA-Seq data to identify IG and TR gene rearrangements.
• To establish a pipeline for detecting minimal residual disease (MRD) markers in acute lymphoblastic leukemia (ALL).
• To discuss potential challenges and pitfalls in the RNA-Seq analysis for MRD detection.

Main Methods:

• RNA-Sequencing (RNA-Seq) data generation from patient samples.
• Bioinformatic analysis of RNA-Seq data using the ARResT/Interrogate tool.
• Identification of unique IG and TR gene rearrangement sequences for MRD monitoring.

Main Results:

• Demonstration of a robust workflow for identifying IG and TR gene rearrangements via RNA-Seq.
• Establishment of potential molecular markers for MRD detection in ALL.
• Discussion of practical considerations and limitations of the described method.

Conclusions:

• RNA-Seq analysis coupled with ARResT/Interrogate provides a powerful approach for identifying IG and TR gene rearrangements.
• This strategy is effective for establishing patient-specific MRD markers in ALL.
• The methodology is adaptable for monitoring other lymphoid malignancies like lymphoma and myeloma.