Long read sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS
Miller, C. A.; Srivatsan, S. N.; Kramer, M. H.; Ramakrishnan, S. M.; Fronick, C. C.; Fulton, R. S.; Helton, N. M.; Ley, T. J.; Walter, M. J.
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The alternative splicing landscape of cancer transcriptomes remains poorly characterized, since short read sequencing cannot resolve complete transcript structures. Using the Oxford Nanopore cDNA platform, we generated nearly 2 billion long reads (median 25.8 million per sample) from 71 human samples, including 48 acute myeloid leukemia or myelodysplastic syndrome samples, 25 of which had splicing-factor gene mutations (in SRSF2, U2AF1, or SF3B1). An additional 23 samples were from sorted hematopoietic cell populations from healthy individuals. We identified 174,162 novel isoforms absent from the reference transcriptome, and proteomic validation confirmed that many are translated. We also identified isoforms enriched in spliceosome-mutant samples, and found proteomic evidence of frequent nonsense-mediated decay regulation of novel transcripts. This dataset is a valuable community resource, enabling detection of new transcripts in short read data sets. An interactive portal to explore splicing patterns in these data is available at https://leylab.org/isoforms/.
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