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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Comprehensive Protocol to Sample and Process Bone Marrow for Measuring Measurable Residual Disease and Leukemic Stem Cells in Acute Myeloid Leukemia

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Using RNA-seq for detecting MRD in multiple myeloma: high sensitivity and prognostic value.

Yuyue Ren¹, Ming Liu², Jiancheng Fang²

¹Department of Hematopathology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China.

Cancer Gene Therapy

|October 24, 2025

Summary

RNA sequencing (RNA-seq) offers a more sensitive method for monitoring minimal residual disease (MRD) in multiple myeloma (MM) patients compared to targeted DNA sequencing. This approach aids in predicting patient prognosis by detecting clonal immunoglobulin gene expression.

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Area of Science:

Hematological Malignancies
Genomics
Cancer Biomarkers

Background:

Multiple myeloma (MM) is a plasma cell malignancy where minimal residual disease (MRD) assessment is crucial for prognosis.
Current targeted DNA next-generation sequencing (NGS) methods for MRD monitoring are limited by somatic hypermutation (SHM) in MM.
Sensitive and convenient MRD monitoring techniques are needed for effective patient management.

Purpose of the Study:

To compare the sensitivity and convenience of RNA-seq versus targeted IGH-CDR3-DNA-NGS for MRD monitoring in multiple myeloma.
To evaluate the utility of RNA-seq in detecting clonal immunoglobulin (IG) sequences and assessing SHM rates.
To determine the prognostic significance of MRD detection using RNA-seq in peripheral blood (PB) samples.

Main Methods:

Analysis of 125 samples from 35 MM patients and 42 B-ALL patients.
Utilized MiXCR software for processing RNA-seq and targeted-NGS data.
Compared the detection sensitivity and SHM rates between RNA-seq and targeted-NGS methods.

Main Results:

RNA-seq detected clonal IG sequences in all initial bone marrow (BM) and PB samples with a sensitivity of 10^-6, outperforming targeted-NGS.
Higher SHM rates were observed in targeted-NGS-negative samples (9.98%) compared to positive samples (7.27%).
MRD-negative PB samples identified by RNA-seq correlated with improved patient survival, indicating prognostic value.

Conclusions:

RNA-seq is a more sensitive and comprehensive method for MRD monitoring in MM patients than targeted-NGS.
RNA-seq provides valuable genetic information and aids in identifying IG gene expression patterns for MM.
MRD detection in PB samples using RNA-seq effectively predicts prognosis in multiple myeloma.