Potential and pitfalls of whole transcriptome-based immunogenetic marker identification in acute lymphoblastic leukemia; a EuroMRD and EuroClonality-NGS Working Group study
Abstract
Identification of immunoglobulin (IG) and T-cell receptor (TR) gene rearrangements in acute lymphoblastic leukemia (ALL) patients at initial presentation is crucial for monitoring of minimal residual disease (MRD) during subsequent follow-up and thereby for appropriate risk-group stratification. In a diagnostic setting, IG/TR gene rearrangements are generally identified using DNA-based PCR analysis, followed by classical Sanger sequencing or next generation sequencing (NGS).Nowadays, whole transcriptome RNA sequencing (RNAseq) is frequently used to identify fusion genes and to assign patients into distinct molecular subgroups according to WHO 2016 classification, or for protocol-based clinical decisions.
Hence, it would be beneficial if RNAseq data could also be used for the identification of IG/TR gene rearrangements pertaining to the leukemic clone.