Abstract 328: A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions
Authors: Huang Jiajie , Gu Haigang , Orton Janet , Sedova Marina , Rozenzhak Sophie , Hyland Fiona , Liu Guang 
Published: March 2024

Introduction: Myeloid malignancies encompass diverse hematopoietic disorders, including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). We developed two assays to address the genetic complexity of myeloid malignancies, OncomineTM Myeloid Assay and OncomineTM Myeloid Assay GX v2, detecting mutations in 45 DNA genes and &gt;30 fusion driver genes, including &gt;700 fusion isoforms. Our panel includes genetic alterations such as FLT3-Internal Tandem Duplications (ITDs), IDH1/2, CEBPA, CALR, and TP53.

Methods: Here we describe the genomic profiles of 8503 clinical research samples (including AML, MPN, MDS, CML, CMML, or JMML). A total of 4723 samples were run on the Ion GeneStudioTM S5 System and analyzed using the OncomineTM Myeloid Research workflow on Ion ReporterTM 5.18. A total of 3780 samples were run on the Ion TorrentTM Genexus Software 6.6 and analyzed using the OncomineTM Myeloid Assay GX v2.

Results: On Genexus, the turnaround time (the time between starting the run and NGS data report) was 23-25 hours and the hands-on time was around 1 hour. The success rate of the samples was 100%.

Frequency of relevant mutations and variant allele frequency by gene: Genes like TET2 (detected in 12.6% of samples), ASXL1 (9.3%), DNMT3A (7.8%), TP53 (7.5%) exhibited high mutation rates. 56.4% of samples had mutations, averaging 2.3 mutations per sample. Common co-occurring mutations included ASXL1-TET2 and SRSF2-TET2. Variant allele frequency varied greatly, e.g., ANKRD26 had a median VAF of 66%, while MYD88 had only 7%.

Mutation spectrum of FLT3ITD variants: FLT3-ITD was observed in 3% of samples, with an average VAF of 0.32, featuring a multi-modal length with the highest peak at around 34 bp and maximum length at 151 bp.

Mutation spectrums of fusions: 710 (8.4%) samples were fusion-positive with read counts ranging 21-113,000. ABL1 was the most common driver and BCR-ABL1 was the most common gene pair. Other common drivers included KMT2A, MYH11, RARA, and RUNX1. 17 distinct driver genes, 49 gene pairs, and 110 gene isoforms were observed, including rare fusions like ZMYM2-FGFR1 and KAT6A-CREBBP that are not detectable by traditional methods like qPCR (quantitative polymerase chain reaction) or FISH (fluorescence in-situ hybridization).

Conclusions: The Oncomine Myeloid Assay is a fast, robust, and reproducible solution for comprehensive genomic profiling of myeloid malignancies. We describe the mutational spectrum of DNA variants and RNA fusions in a range of clinical research samples. (For research use only. Not for use in diagnostic procedures. © 2023 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified.)

Citation Format: Jiajie Huang, Haigang Gu, Janet Orton, Marina Sedova, Sophie Rozenzhak, Fiona Hyland, Guang Liu. A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 328.