Anna Dolnik from the Charite University Medicine Berlin in Germany presented at London Calling 2022 “Combined CRISPR/Cas9 targeted enrichment and whole-genome sequencing allows real-time stratification of acute myeloid leukemia (AML).” AML patient stratification, Dolnik explained, relies on identification of copy number and fusion transcripts. Dolnik mentioned they had presented on ONT-based AML systems before at London Calling. In this project, they updated an ONT-based karyotyping approach. The system uses a tiling approach with CRISPR-Cas9 based targeted enrichment of genes. In their lab, they developed this system and can detect tandem duplications in one gene as an example. Even with samples that were degraded (RNA), they were still able to detect targets and differences. Using a combination of CRISPR-Cas9 and WGS, the team can map relevant aberrations. They also did a “pull-down” approach of partner genes using the CRISPR-Cas9 tiling approach. The pull-down allowed identification of translocations. Dolnik concluded that:
- Combined whole genome sequencing and CRISPR-Cas9 targeted sequencing are promising for quick detection of genomic aberrations.
- This approach can be adjusted using pools of oligos for different needs, offering personalized medicine.
- Newer kits and chemistries may further improve the workflow.
The approach Dolnik’s group could be applied to numerous other diseases and also prokaryotic genome changes. Dolnik did mention their approach uses 6-9 ug amounts of DNA!
