Targeted RNA-sequencing for the quantification of measurable residual disease in acute myeloid leukemia

We report the development of a multi-gene, targeted RNA-sequencing (RNA-seq)-based method for the sensitive detection and quantitation of known AML genetic signatures. This AML RNA-seq panel utilizes a pool of target-specific primers containing 12 nucleotide (nt) unique molecular indices (UMIs) which capture and individually tag RNA molecules of interest during reverse transcription, followed by targeted PCR of the barcoded cDNA, library construction, and sequencing on the Illumina platform. Assay sensitivity and limit of detection were determined using RNA samples collected from cell lines or patient PBMC samples expressing target transcripts serially diluted into healthy donor PBMCs. We showed that the assay can detect the targets down to 1:100,00 cells and can track MRD in serial patient samples up to 3 months prior to clinical relapse.