Next-generation sequencing RNA fusion panel for the diagnosis of haematological malignancies

Abstract

Haematological malignancies are being increasingly defined by gene rearrangements, which have traditionally been detected by karyotype, fluorescent in situ hybridisation (FISH) or reverse-transcriptase polymerase chain reaction (RT-PCR). However, these traditional methods may miss cryptic gene rearrangements and are limited by the number of gene rearrangements screened at any one time. A next-generation sequencing (NGS) RNA fusion panel is an evolving technology that can identify multiple fusion transcripts in a single molecular assay, even without prior knowledge of breakpoints or fusion partners. We explored the utility of the Illumina TruSight RNA Fusion Panel for use in haematological malignancies by sequencing 30 peripheral blood or bone marrow aspirate samples. Secondary and tertiary analyses were performed using the Illumina DRAGEN RNA pipeline and PierianDx Clinical Genomics Workspace platform. Our RNA fusion panel was able to reliably detect known fusion transcripts, such as BCR::ABL1, ETV6::RUNX1 and KMT2A::AFF1, in acute lymphoblastic leukaemia (ALL), KMT2A::MLLT3, KMT2A::MLLT6, PML::RARA and CBFB::MYH11 in acute myeloid leukaemia (AML), and FIP1L1::PDGFRA in myeloid/lymphoid neoplasm with eosinophilia (MLN-Eo). In addition, it was able to detect rare KAT6A::CREBBP and CHIC2::ETV6 fusions, which could not be confirmed by traditional methods. The assay had a transcript limit of detection of approximately 5-10% of positive controls. These findings confirm the unique utility of the NGS-based RNA fusion panel as a diagnostic tool to identify gene rearrangements that drive haematological malignancies. It can identify novel and rare gene rearrangements to assist with diagnosis, prognostication and treatment decisions.

Keywords: ALL; AML; CML; RNA; fusion; haematological.