An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

Color separation is an essential step of the data processing in the four-dy e fluorescence detection strategy used in automated DNA sequencing. In this paper, we propose a model to describe the crosstalk phenomenon, and show h ow the assumptions of the model are supported by experimental data. The cro sstalk matrix is estimated via a reparameterization based on a mapping betw een the distribution of fluorescence intensities and that of dye concentrat ions. An iterative algorithm is designed to implement the estimation. To ev aluate the color-correction quality of a crosstalk matrix, we propose a qua ntitative measure based on the distribution of the color-corrected data. We illustrate this method by applying it to a sequencing trace of slab gel el ectrophoresis obtained at the Human Genome Center at Lawrence Berkeley Nati onal Laboratory, and that of capillary electrophoresis provided by the Depa rtment of Chemistry at UC, Berkeley. The accuracy of this method is also as sessed by the bootstrap method.