New method reads the genetic code directly in tumour tissue

Accurate diagnostic tests are crucial when choosing the right treatment regime for cancer patients. This is why scientists from Stockholm University and Uppsala University continuously work on improving methods for analysing cancer tissues. For the first time, it is now possible to read the genetic code of individual cancer cells in their original location in the tissue. The results are published in Nature Methods.


Today 30-40% of the population in Europe will be diagnosed with cancer during their lifetime. With new advanced tools to study protein, DNA and RNA in tissue or blood samples from patients a new era of personalized medicine has been entered. Personalized medicine at its best will provide the right drug in the right dose to the right patient, thereby minimizing unnecessary suffering and increase response to therapy. This demands sophisticated diagnostic tests.

The research group headed by Mats Nilsson, professor of Biochemistry/molecular diagnostics at Stockholm University, has since the beginning of year 2000 developed new diagnostic tools based on analysis of genetic information (DNA and RNA) in cells and in body fluids. During this time, DNA sequencing technologies have seen a rapid development and this has revolutionized large-scale biology research. – We can now use sequencing chemistry directly in cancer tissue speciemens to read the genetic code and obtain information of specific RNA molecules in individual cells in their original context in the tissue. This is the first time in situ sequencing has been performed in this way and it offers obvious advantages, says Mats Nilsson.

By in situ sequencing the amount of RNA expression in both tumour cells and in the surrounding environment of stromal cells can be analysed. It is known that not only the tumour cells are of importance for cancer growth but also how they interact with the cells surrounding the cancer cells. Existing methods have not been able to resolve this complexity in tissues. – Combining the detailed information from existing single cell analysis with our in situ sequencing method can be powerful and find great use in both research and diagnostics, says Mats Nilsson.

The method developed by Mats Nilsson and the other researchers at Science for Life Laboratory (SciLifeLab) use sequencing for the study of numerous different markers and mutations at the same time. Here, 39 different RNA molecules are analysed in the same tissue and provide a more complete picture than the standard laborious method used by pathologist today.


In situ sequencing for RNA analysis in preserved tissue and cells

Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C. and Nilsson, M.

Nature Methods, online 14 July 2013

Read the scientific article


Last updated: 2013-07-14

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