Abstract 5069: Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis

Abstract

Abstract Cytogenetics forms the cornerstone of diagnostic genetic testing in leukemia, providing both prognostic and diagnostic information to help guide treatment. Currently, standard-of-care cytogenetics in acute myeloid leukemia (AML) is composed of a combination of karyotyping, FISH testing, and in some cases chromosomal microarray analysis, each test offering a unique combination of advantages and weaknesses. A particular challenge for this combination of tests is the delivery of results in a timely and comprehensive manner. To overcome these limitations, we have developed OncoTerra, a proximity-ligation-sequencing based method which can rapidly detect all classes of variants detected by cytogenetics tests in a single assay. We applied OncoTerra to a cohort of more than 100 samples from a SWOG AML trial (S0106), benchmarking sensitivity and specificity of the variants. We observed an overall >0.95 sensitivity and a specificity of 1 for the variants identified by cytogenetics and identified numerous cryptic variants. Overall, we identified variants that changed the diagnostic risk stratification of 15% of the patient involved in the trial based on the ELN 2022 criteria. This translated into better overall prediction of outcomes of patients in the trial and has identified both known and novel variants missed by standard-of-care tools. Citation Format: Stephen Eacker, Maika Malig, Mary Wood, Alexander Muratov, Olga Sala-Torra, Ivan Liachko, Cecilia Yeung, Jerald Radich. Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis [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 5069.