Population genomic and evolutionary biology of complex systems

The analysis of complex biological systems has been revolutionised by access to the raw genotypes, respresented by sequence and DNA fragment analyses, of the organisms studied. Generation of this sequence and fragment data in a timely, efficient and cost-effective manner is central to many aspects of research carried out in the Institute of Cell, Animal and Population Biology and the Centre for Genome Research, University of Edinburgh. We would like to upgrade our very successful BBSRC-funded automated genetic analyser service from its current gel-based instruments to a state of the art capillary instrument. The increased throughput and versatility if the chosen instrument, the ABI 3730, will facilitate many research programs funded by the BBSRC including:
1 understanding the determinants of patterns of molecular evolution and the evolution of genomes, with particular reference to the effect of breeding systems and sex chromosomes on mutation patterns.
2 the population and quantitative genetics of of neutral and selected variation in wild and model populations with an emphasis on understanding the interplay between population history, current fitness and interactions between species and environments.
3 the use of sequence data to reveal the biology of parasitism, in developing robust phylogenies for parasites and other metazoans and in estimating diversity within phyla and within species.
4 supporting genomics-based programs investigating developmental mechanisms in stem cells and the evolution of pattern formation.

We have installed and successfully exploited a high-throughput DNA sequencing instrument in our inteagrted genetics service facility. The instrument, an ABI 3730 48-capillary sequencer has performed to specification, delivering up to 0.5 million bases of DNA sequence per day. The instrument is part of a service that works with University of Edinburgh School of Biological Sciences researchers to help them generate and analyse data for their diverse research projects. We have assisted over 300 different scientists in their research on early development, stemm cells, the evolution of sex, the biology of natural communities of parasites and hosts, and drug and vaccine development for human diseases. Indeed the service has been so succesful that we were able to use the BBSRC funding to persuade our university to lend us the funds to purchase a second ABI 3730 instrument, doubling our output. In the case of this investment by BBSRC, the end of the grant award period does not mark the end of the project, as we expect both instruments to be delivering DNA sequencing service for years to come.

The ease of access (including the lowered cost) to high throughput sequencing has encouraged users to design experiments where sequencing is used as acore analytical tool rather than a luxury item. We have developed in house capacity and skills to deliver a wide range of sequencing products, such as large insert clone sequencing, genotyping using microsatellites, sequencing and assembly of biodiversity markers, etc.
The ABI3730 performed at or above specification from day one, and has been a workhorse of the service ever since, for example running over 80000 samples in 2007. We use the ABI 3730 for all modes of sequence generation, from direct sequencing of PCR products to directed sequencing of large insert clones. The service routinely processes 1000 samples per day. The ABI3730 is also used for genotyping using panels of microsatellites, and this service is seeing increasing demand - so much so that we have now dedicated a technician to perform ‘service’ genotyping for major users. Downtime for servicing and maintenance has been well within the 5% estimated.
The output from the sequencing instrument (circa 50 Mb/year) has resulted in numerous data depositions in the International Nucleotide Sequence Database Consortium databases (EMBL/GenBank) as well as analysed depositions in NERC's ENVBase and the ArrayExpress microarray database.
The success of the GenePool use of the ABI3730 instruments allowed us to bid succesfully to be the firat institution in Scotland to have installed and running both of the leading 'next generation' sequencing instruments, the Illumina SOLEXA GA1, and the Roche 454 FLX, representing an additional investment of over £0.8 M.