Project leader: Chris Mattocks

Comparative Sequence Analysis (CSA) is a simple method for directly comparing base-lined raw data from equivalent sequencing reactions on different samples without the need for base calling. The control sequence electropherogram is split into its four component traces (one for each base), which are overlaid with equivalent traces from a second reaction. The resulting format allows simple and rapid visualisation of any differences (mutations) between the two sets of traces. Because the assay is based on sequencing, mutations can be characterised as well as identified. Moreover, because there has been minimal software manipulation of the data, heterozygous mutations that are difficult to pick up using standard sequencing analysis techniques have been shown to be easily detectable in a single direction using CSA. Finally, and perhaps most importantly from a diagnostic point of view, CSA is a simple and rapid technique for verifying normal sequence data with a very high degree of confidence.
In its simplest form CSA is essentially sequence data analysed using fragment analysis software. Robust protocols exist for performing this analysis on data generated by the ABI 377 and ABI 3100. However we would be interested in any attempts to perform this type of analysis on other platforms.

In addition to dissemination information about manual CSA we are currently working in collaboration with the Cancer Genome Project at the Welcome Trust Sanger Institute (Hinxton, Cambridge) to develop robust and simple to use software to automate CSA.

This software will be available for trial evaluation in UKGTN laboratories in the near future.