German scientists have announced a new technique to look at the DNA mutations within a single cell, which could detect genetic variants in cancer patients and aid diagnosis.
Dr Ashley Sanders and colleagues at the European Molecular Biology Laboratory in Heidelberg, Germany, explain that research so far has focused on measuring the RNA within a cell, but the DNA has received much less attention.
The team believe their new method could lead to faster, cheaper and more detailed cancer diagnosis, as it “outperforms existing techniques with respect to the information received."
In the journal Nature Biotechnology they write: “Structural variation, involving deletions, duplications, inversions and translocations of DNA segments, is a major source of genetic variability in somatic cells and can dysregulate cancer-related pathways. However, discovering somatic structural variations in single cells has been challenging.”
They developed ‘single-cell tri-channel processing’ (scTRIP), a computational framework that highlights structural variations in individual cells, and went on to test scTRIP on 565 single cells.
In leukaemia samples from patients, scTRIP revealed four times more structural variations than current methods . This “could improve disease classification for precision medicine,” they write.
Dr Sanders said: “Our new method to study genetic variations in individual cells could transform the field of mutation detection.”
Co-author Dr Tobias Marschall adds: “These first results show that our method is outperforming existing ones significantly. Our method is much faster and cheaper than methods currently in use to uncover genetic variants in single cells. This might be very useful for clinical applications.”
The team hopes that looking at the DNA will provide a new level of understanding in how genetic changes drive different cell behaviours, making the new method useful to both researchers and clinicians.
Sanders AD, Meiers S, Ghareghani M, Porubsky D, Jeong H, van Vliet MACC, Rausch T, Richter-Pechańska P, Kunz JB, Jenni S, Bolognini D, Longo GMC, Raeder B, Kinanen V, Zimmermann J, Benes V, Schrappe M, Mardin BR, Kulozik AE, Bornhauser B, Bourquin JP, Marschall T, Korbel JO. “Single-cell analysis of structural variations and complex rearrangements with tri-channel-processing”, Nature Biotechnology, doi: 10.1038/s41587-019-0366-x