We have generated and published many data -omics data modalities from cell lines and patients and with leukemia.We have previously used parts of this data to design a classification of >1000 pediatric ALL patients using supervised and unsupervised methods- based on methods previously developed by our group (Nordlund et al, Genome Biology 2013; Nordlund et al, Clinical Epigenetics 2015; Duran-Furrer et al, Nature Medicine 2020, Krali et al, npj precision oncology 2023, etc).
In our continuation project we are working on combining all the different data modalities to provide a better, more holistic understanding of leukemia phenotypes.
All of the raw data from patient samples (all data types that can contain genetic variants) are analyzed on secure Bianca cluster. Only the processed and filtered data will be made available on Rackham, ie. the most variable DNA methylation sites, gene counts, and limited phenotypes. We will import numerous public datasets to be able to improve our understanding of the genes and pathways affected by differentially methylated or expressed genes, and incorporate these with functional data obtained from commercially available cell lines.
We understand Rackham will be decommissioned at the end of 2024 and will move over to the UU solution by the end of the year.