Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms

In this study, we aimed to comprehensively characterize in 113 myeloproliferative neoplasms (MPN) patients the mutational landscape of the granulocyte transcriptome using RNA sequencing data. We implemented workflows for fusion and variant calling, and differential splicing analysis for patients with hotspot SF3B1 mutations. Finally, we characterized the neoantigen landscape on individualized level taking each patient's HLA genotype (derived from the same RNA-seq dataset) into account.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001004788	This dataset contains whole-transcriptome sequencing data of 113 myeloproliferative neoplasms (MPN) patients and 15 controls. Patients were diagnosed with essential thrombocythemia, polycythemia vera, primary myelofibrosis, and secondary acute myeloid leukemia. The data were pooled from 5 different sequencing experiments as indicated using an Illumina HiSeq2000 machine. All samples were sequenced paired-end. Sequenced samples were processed with custom workflows for discovery of fusion genes, SNVs and Indels calling, and identification of splicing abnormalities.	Illumina HiSeq 2000	145

Publications	Citations
Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms. Schischlik F, Jäger R, Rosebrock F, Hug E, Schuster M, Holly R, Fuchs E, Milosevic Feenstra JD, Bogner E, Gisslinger B, Schalling M, Rumi E, Pietra D, Fischer G, Faé I, Vulliard L, Menche J, Haferlach T, Meggendorfer M, Stengel A, Bock C, Cazzola M, Gisslinger H, Kralovics R. Blood 134: 2019 199-210	46
PD-L1 overexpression correlates with JAK2-V617F mutational burden and is associated with 9p uniparental disomy in myeloproliferative neoplasms. Milosevic Feenstra JD, Jäger R, Schischlik F, Ivanov D, Eisenwort G, Rumi E, Schuster M, Gisslinger B, Machherndl-Spandl S, Bettelheim P, Krauth MT, Keil F, Bock C, Cazzola M, Gisslinger H, Kralovics R, Valent P. Am J Hematol 97: 2022 390-400	11
Interleukin-1 contributes to clonal expansion and progression of bone marrow fibrosis in JAK2V617F-induced myeloproliferative neoplasm. Rahman MF, Yang Y, Le BT, Dutta A, Posyniak J, Faughnan P, Sayem MA, Aguilera NS, Mohi G. Nat Commun 13: 2022 5347	20