EU-funded scientists in Sweden have developed a novel method to study genetic variation directly in individual cells and in tissues. Their findings, published in the journal Nature Methods, provide valuable new insights into gene expression in humans that could significantly improve diagnostic tests. The new method is an outcome of two EU-funded projects: COMICS ('Comet assay and cell array for fast and efficient genotoxicity testing'), which received EUR 3.2 million under the 'Life sciences, genomics and biotechnology for health' Thematic area of the Sixth Framework Programme (FP6) to develop reliable ways to test the effects of chemicals on human genetic material without resorting to animal experiments, and READNA ('Revolutionary approaches and devices for nucleic acid analysis'), financed with EUR 12 million under the Health Theme of the Seventh Framework Programme (FP7) to revolutionise nucleic acid analysis methods. Genotoxic chemicals interfere with the normal process of DNA (deoxyribonucleic acid) repair, and can affect cancer risk in individuals. Reliable, highly sensitive tests for the effects of these compounds are avidly sought, as current methods can only analyse large groups of cells and can be time-consuming as well as error-prone. According to the new study, led by Dr Mats Nilsson of Uppsala University in Sweden, existing assays are not sensitive enough: molecules in rare cells can easily escape detection, and it is not possible to tell which of the molecules detected originate from which cells. This represents a serious stumbling block in diagnostic tests for cancer, for example, as tumours are made up of a jumble of healthy and cancerous cells. New assays with single-molecule sensitivity, the authors say, are therefore essential. Building on previous methods developed by the same team, the researchers were able to convert messenger RNA (mRNA) into a type of DNA molecule that can be detected by 'padlock probes', fluorescent probes which lock onto the DNA after hybridisation, making it possible to study DNA repair at the molecular level in individual cells. 'The method allows us to study biological processes in individual cells, as opposed to the average states of large numbers of cells,' explained Dr Nilsson. Most assays give results that represent an average result for a large number of cells; in a given sample, signals indicating the workings of a small minority of cells can be drowned out by those generated by the majority of cells. Padlock probes can amplify the minority signals making it possible to directly identify genetic variation at the mRNA (messenger ribonucleic acid) level (in molecules produced by active genes) in cells in microscopic preparations. This has major implications for the study of tumour tissue. The novel method also opens the door for scientists to study the effects of genetic variants on different types of cells and tissues, as the probes can be used to distinguish similar genetic sequences. 'Hitting the proverbial needle in the haystack should now be possible,' Dr Nilsson said. 'This should entail significantly more sensitive and precise diagnostic methods, improving the prospects that patients will receive the treatment they need.'