Most genetic studies of multi-factorial disease generate a large set of loci associated with disease phenotypes. To identify the exact molecular alteration behind the association, full sequence information from these loci is often required from a large number of affected and control subjects. Even with current development in sequencing capacity, it will remain too expensive to sequence whole genomes. We have developed a technique to efficiently extract relevant parts of genomes for sequencing. We have further developed a rapid, simple, and cost-effective assay to detect copy-number variation, which is a common cause of multi-factorial disease. Mutations often cause aberrant expression in specific cells. Ultimately, expression levels should be measured on a single-cell level, and preferably in the preserved context of tissues, not to overlook alterations in minority cell populations. We are developing an in situ genotyping technique that allows detection of individual transcript molecules with allelic resolution in tissue samples.
Key references:
Dahl, F., et al. (2007). Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc. Natl. Acad. Sci. USA 104, 9387-9392.
Jarvius, J., et al. (2006). Digital quantification using amplified single-molecule detection. Nature Methods 3, 725-727.
Larsson, C., et al. (2004). In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes. Nature Methods 1, 227-232.
Nilsson, M., et al. (2006). Analyzing genes using closing and replicating circles. Trends Biotechnol. 24, 83-88.
