We are currently performing a multilevel analysis of initial diagnosis, primary refractory and relapse acute myeloid leukemia (AML) specimens from pediatric patients, using the resources of UPPMAX (Project # sens2018102 and sens2018512) as well as various SciLifeLab core facilities.
In order to get a more complete picture of the leukemic cells, we are performing studies at the genome, epigenome, transcriptome and proteome level, followed by a systems biological approach for full integration of the data sets.
This SNIC SENS application focuses on a similar project, for which data currently are being generated. Here we are studying initial diagnostic specimens from a specific subgroup of pediatric AML, referred to as “not otherwise specified” (NOS). The AML, NOS subgroup is a large heterogeneous group of patients with none of the genetic aberrations currently included in the WHO classification system of AML.
We are currently generating a rather large data set including sensitive personal data. Included are whole genome sequencing- (WGS-), whole exome sequencing- (WES-), transcriptome sequencing- (RNA-seq-), and genome wide DNA methylation analysis, as well as proteome studies using high resolution mass spectrometry.
During the first 1-2 months after the data have been delivered and the project has been initiated, the majority of the computing intense analyses will be performed, including e.g. processing of the RNA-seq raw data and initial variant calling of various types.