Combining genomic and transcriptomic profiling allows real-time stratification of hematologic malignancies

Anna Dolnik

Anna Dolnik, Charité University Medicine Berlin


Classification of hematopoietic malignancies is based on World Health Organisation (WHO) guidelines and requires assessment of genomic aberrations. Using whole genome sequencing with Oxford Nanopore technology we routinely create high-resolution copy number variation profiles based on a 24h run using one flow cell. A complementary transcriptome sequencing allows the analysis of fusion genes in a similar timeframe. This combined genome- and transcriptome-wide Oxford Nanopore-based sequencing workflow provides the opportunity to rapidly characterize hematologic malignancies at the molecular level, which is needed for improved genotype-based treatment strategies.


Anna Dolnik is a PostDoc at the Charité - University Medicine Berlin, Campus Virchow in Germany. A trained biologist, she switched to processing Illumina shotgun sequencing in 2012, working at the edge of biology and bioinformatics. In 2016, Anna obtained her first experiences of Oxford Nanopore technology through resequencing of novel fusion genes found in acute myeloid leukemia (AML) with complex karyotype. Since the end of 2018, she routinely uses a GridION for better characterization of hematologic malignancies. The focus of her research is clonal evolution in AML, identification of cancer driving genes and characterization of complex changes in cancer genomes by whole genome sequencing.