Genomes 2008, Paris #3

Yesterday highlights included Julian Parkhill's highly anticipated reveal of how the Wellcome Trust Sanger Institute are making use of the next-generation sequencing technology.

His talk, entitled "Variation detection in highly monomorphic bacteria using new sequencing technologies" demonstrated the use of 454 and Solexa sequencing on Salmonella enterica serovar Typhi. The use of the term "monomorphic" is well-justified, the 20 strains sequenced were virtually indistinguishable using standard typing techniques such as MLST. Fortunately, over 2000 SNPs were identified by sequencing, and much interesting information was demonstrated by a population structure diagram and whole genome tree. One interesting idea was the use of nurses with GPS machines recording the co-ordinates where each sample was taken. It is clear that these techniques will become more widespread as the next-generation sequencing machines become more available.

Interestingly, the technique used was to sequence each strain with both 454 and Solexa technologies, and only using SNPs which agreed with both techniques. Julian even admitted to finding a few small errors in the original S. typhi sequence through the use of this technique.