RNA NGS testing provides additional diagnostic and prognostic information over metaphase karyotyping in routine clinical evaluation of acute leukemias and chronic myeloid neoplasms

Pathogenic fusion genes are increasingly relevant to the diagnosis and classification of acute leukemias and chronic myeloid neoplasms per the new 2022 ICC and WHO-HAEM5 classifications. Although DNA based NGS testing is now commonly employed, RNA-based NGS is not yet widely performed in routine practice. Using techniques such as anchored multiplex PCR enrichment, RNA NGS is capable of detecting fusion genes even without knowledge of the fusion partner gene, and can also identify prognostically relevant splicing variants including KMT2A partial tandem duplications (PTD) and IKZF1 deletions. We reviewed the results of our in-house acute leukemia assay (63 DNA genes and 107 RNA genes) in a real world, consecutive series of 350 unique patients. RNA NGS analysis was abnormal in 70/350 patients (20%). Metaphase karyotyping was performed in 68/70 patients (97%) with RNA NGS abnormalities. Of these, 30 (44%) showed concordant RNA NGS and karyotype results, while 38 (56%) RNA abnormalities were not identified by karyotyping alone including 14 KMT2A-PTD, 7 IKZF deletions, and 17 cases carrying various fusions. The RNA NGS results defined a specific ICC or WHO diagnostic category in 51 cases and were prognostically relevant in an additional 21. RNA-based NGS testing identifies fusion genes or pathogenic splicing variants in a subset of acute leukemias and chronic myeloid neoplasms. The abnormalities detected by RNA NGS offer additional diagnostic and prognostic information which is often not available through metaphase karyotyping alone. RNA-based fusion testing is a useful adjunct in hematopoietic neoplasm diagnosis and management which can be readily incorporated into routine clinical practice.