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A k-mer based transcriptomics analysis for NPM1-mutated AML

Silva, R.; Riedel, C.; Guibert, B.; Ruffle, F.; Boureux, A.; Commes, T.

2023-02-02 genetic and genomic medicine
10.1101/2023.01.31.23285241 medRxiv
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MotivationAcute Myeloid Leukemia is a highly heterogeneous disease. Although current classifications are well-known and widely adopted, many patients experience drug resistance and disease relapse. New biomarkers are needed to make classifications more reliable and propose personalized treatment. ResultsWe performed tests on a large scale in 3 AML cohorts, 1112 RNAseq samples. The accuracy to distinguish NPM1 mutant and non-mutant patients using machine learning models achieved more than 95% in three different scenarios. Using our approach, we found already described genes associated with NPM1 mutations and new genes to be investigated. Furthermore, we provide a new view to search for signatures/biomarkers and explore diagnosis/prognosis, at the k-mer level. AvailabilityCode available at https://github.com/railorena/npm1aml and https://osf.io/4s9tc/. The cohorts used in this article were authorized for use. Contact*therese.commes@inserm.fr

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