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Updated: Sep 9, 2025

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Transcript isoform diversity defines molecular subtypes and prognosis in acute myeloid leukemia through long-read
Xiaoguang Shi1, Shuai Wang2, Shuting Yu2
1Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai 200025, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
None:
Acute myeloid leukemia (AML) is a genetically complex and clinically heterogeneous hematopoietic malignancy. This study employs long-read transcriptome analysis using oxford nanopore technologies sequencing on 60 primary AML bone marrow samples. This approach delivers comprehensive isoform-level resolution of splicing abnormalities and overcomes limitations of short-read sequencing. We detect extensive AML-specific splicing anomalies and identify 119,278 previously unannotated transcript isoforms. Of these, 80,294 (67.31%) contain complete open reading frames, with 9,812 (12.22%) validated using liquid chromatography-tandem mass spectrometry. Quantitative analysis in 175 RNA sequencing samples enables non-negative matrix factorization clustering, defining distinct molecular subtypes. These isoform-defined subtypes exhibit strong correlations with patient prognosis, indicating their potential as biomarkers for clinical classification. The findings highlight alternative splicing as a major contributor to AML molecular heterogeneity and provide a valuable foundation for advancing precision medicine and developing innovative therapeutic strategies targeting splicing abnormalities in AML.
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