A RUNX1: RUNX1T1 AML with a simultaneous false positive KMT2A rearrangement: FISH interpretation pitfalls

• Published in: Hematology (Luxembourg) 2024-12, Vol.29 (1), p.2420306
• Main Authors: Zhang, Chi, Lang, Xingping, Liu, Lingfeng, Chen, Nan, Chen, Huafei, Chen, Xiaojun, Chen, Yongyan, Jin, Liqin, Liu, Chengyin, Wang, Huan, Fu, Ailin, Xiao, Sheng
• Format: Article
• Language: English
• Subjects: Core Binding Factor Alpha 2 Subunit - genetics; False Positive Reactions; Female; FISH; Gene Rearrangement; Histone-Lysine N-Methyltransferase - genetics; Humans; In Situ Hybridization, Fluorescence; KMT2A; Leukemia, Myeloid, Acute - diagnosis; Leukemia, Myeloid, Acute - genetics; Male; Middle Aged; Myeloid-Lymphoid Leukemia Protein - genetics; Oncogene Proteins, Fusion - genetics; RUNX1; RUNX1 Translocation Partner 1 Protein - genetics; RUNX1T1
• ISSN: 1607-8454; 1607-8454
• DOI: 10.1080/16078454.2024.2420306

rearrangement ( ) is a common genomic alteration in acute leukemia that can be effectively targeted by menin inhibitors. While FISH is the standard laboratory test for , false positives can occur. We present a case of AML in which both and were identified by karyotype analysis and FISH. Although a targeted RNA next generation sequencing (NGS) assay confirmed the presence of the fusion, it did not detect a fusion transcript. To investigate the discrepancy between the positive FISH result and the negative fusion transcript, we performed whole-genome mate-pair DNA NGS to examine the locus on chromosome 11q23. This analysis revealed a breakpoint located 5.8 kb downstream of , which did not disrupt the gene itself. Given that FISH probes cover approximately 1 Mb around , this subtle shift led to a split-apart signal pattern mimicking a genuine rearrangement, resulting in a false positive FISH interpretation. This case highlights a false positive in primary AML, indicating the need for additional molecular testing for confirmation.