Abstract 7172: Comprehensive whole genome sequencing (WGS) assay provides diagnostic insight into clinically relevant genomic alterations across myeloid malignancies
Authors: Robert Huether, Derick Hoskinson, Pavana Anur, Raul Torres, Karl R. Beutner, Kristiyana Kaneva, Yan Yang, Kelly A. Potts, Andrew Frazier, Iris Braunstein, Brett M. Mahon, Michael A. Thompson, Kate Sasser, Halla Nimeiri, Lewis J. Kraft, Francisco M. De La Vega, Guillermo Garcia-Manero
Journal: Cancer Research (2025)

Abstract Identification of NCCN and WHO guideline-indicated genetic variation is crucial for diagnosis, risk assessment, and therapeutic decision-making in patients with myeloid malignancies. Current practice often utilizes small mutation panels, cytogenetics (CG), and/or fluorescence in situ hybridization—independent tests that require a separate specimen and have timeline and performance limitations. Whole-genome sequencing (WGS) is a promising alternative with rapid turnaround times and low sample requirements, but evidence showing concordance with other methods is still limited. Here, we report the performance of a WGS assay on patients with acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), myelodysplastic syndromes (MDS) and other hematological malignancies (HM). We show high concordance with matched findings using Tempus xT-Heme (a 648 gene targeted DNA-seq panel), Tempus xR (a whole transcriptome RNA-seq assay), and available cytogenetic results. All 230 patients in our cohort had targeted DNA panel results, 215 had RNA-seq results, and 10 had cytogenetic data. For the WGS assay, DNA obtained from blood or bone marrow aspirates was used to construct paired-end libraries via tagmentation and WGS to 80X mean coverage with the Illumina NovaSeq-X platform. Data were analyzed using the DRAGEN Platform with custom post-processing filters. We filtered SNV/Indel alterations to 40 genes with VAF ≥10%, 608 recurrent rearrangements, and CNAs greater than 5MB. In our cohort (68% AML, 18% MDS, 12% CML and 2% other HM) the WGS assay identified 504 reportable SNV/indels, 119 SVs, and 14 large CNAs, which were highly concordant with other assays. Specifically, 99.4% of SNVs/indels and 95.1% of SVs were concordant between xT-Heme and WGS. A subset of guideline-recommended SVs (e.g. RUNX1-RUNX1T1, ELN adverse risk fusion) detected by WGS were not identified by xT-Heme (10.7% [13/121]) but were confirmed via RNA-seq. Large CNAs detected by WGS were 100% concordant (14/14) with available clinically reported CG. Notably, our cohort included 26 FLT3 internal tandem duplications (ITDs) ranging from 12 to 97 nucleotides in length, and 24 of these were identified by WGS —the missed ITDs had xT-Heme VAFs of less than 4%. WGS was less sensitive at low VAFs (targeted sequencing depths of ∼600x) that were likely subclonal. We demonstrate high concordance (97%) between our WGS assay and conventional methods in identifying guideline recommended genomic alterations, including large CNAs, in myeloid malignancies. The ability to obtain large CNA results, historically reserved for CG testing, has the potential to save costs and fill an unmet clinical need globally where cytogenetic resources are limited. Additionally, WGS can identify unique SVs that may be missed by conventional methods and may enhance personalized treatment strategies. Citation Format: Robert Huether, Derick Hoskinson, Pavana Anur, Raul Torres, Karl R. Beutner, Kristiyana Kaneva, Yan Yang, Kelly A. Potts, Andrew Frazier, Iris Braunstein, Brett M. Mahon, Michael A. Thompson, Kate Sasser, Halla Nimeiri, Lewis J. Kraft, Francisco M. De La Vega, Guillermo Garcia-Manero. Comprehensive whole genome sequencing (WGS) assay provides diagnostic insight into clinically relevant genomic alterations across myeloid malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7172.