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Rebecca Olin, MD, MS


AACR 2022: A New Approach to Analyzing Copy Number Abnormalities in AML

By: Gavin Calabretta, BS
Posted: Thursday, April 28, 2022

Copy number aberrations (CNAs) are widely used for diagnostic classification and risk stratification in the context of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), but the current detection method, conventional cytogenetic analysis, is prone to shortcomings, including low resolution and subjective bias introduced from visual interpretation. Thus, Lyu et al, of the Affiliated Cancer Hospital of Zhengzhou University, China, tested the ability of a shallow whole-genome sequencing-based assay to depict genomic CNA profiles of patients with newly diagnosed AML and MDS. The results, which were presented at the American Association for Cancer Research (AACR) Annual Meeting 2022 (Abstract 5263), suggested that the assay, named LeukoPrint, may provide an accurate and cost-effective alternative to traditional cytogenetic analysis.

“With the technological advances of next-generation sequencing, the current conventional cytogenetic analysis test and the molecular tests are likely to be challenged by whole-genome sequencing, which is a more unbiased method to detect all types of genomic aberrations,” explained the analysts. They added that whole-genome sequencing can also detect aberrations that have not been previously defined by other researchers.

The study enrolled 107 total patients, of whom 63 had AML and 44 had MDS. The authors harvested genomic DNA from the patients’ bone marrow and performed a genome-wide CNA analysis through an automated pipeline. Through the same classification systems that are used for conventional cytogenetic analysis, CNAs defined by the European LeukemiaNet and Revised International Prognostic Scoring System were used to stratify patient risk groups.

At the individual patient level, LeukoPrint demonstrated 98.1% concordance between CNA profiles and cytogenetics and/or fluorescence in situ hybridization. The assay also improved overall diagnostic yield by redefining risk categories for 16 patients using new information that it automatically curated. Moreover, nearly identical CNA profiles were obtained from paired plasma and bone marrow samples, suggesting that peripheral blood may serve as a potential alternative to spare bone marrow aspiration.

Disclosure: For full disclosures of the study authors, visit

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