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Next Generation Sequencing and Bioinformatics
at the University of Edinburgh


GenePool News                               [back to main News page]

01 July 2009:

GenePool MRC Hub Launches
New Illumina GAIIx sequencer purchased
Dr Karim Gharbi joins GenePool
GenePool data underpin paper in Genome Research


GenePool MRC Hub Launches [01 July 2009]

Today the GenePool officially launches its participation in the MRC's 'sequencing hubs' network. The MRC has funded four Hubs to provide next genertion sequencing and bioinformatics facilities to the UK's biomedical research base, and the GenePool (along with ATG in Liverpool, Addenbrookes in Cambridge and Oxford) were chosen to deliver this exciting development.

The GenePool bid was a collaborative proposal from the Universities of Edinburgh, Dundee, Glasgow and Aberdeen, and the MRC's Human Genetics Unit in Edinburgh. The proposal includes significant co-funding from all the collaborating Universities and the MRC HGU.

The GenePool's funding is for three years and includes provision for
• installation of sequence selection technologies to permit directed resequencing of target genome regions
• additional instrumentation to deliver even more sequence data to collaborators
• additional wet lab technologists to deliver high quality sample preparation
• additional bioinformaticians in the GenePool and
• additional bioinformaticians in the collaborating universities.

Together, these investments will build on the GenePool model, and deliver both state-of-the-art genomics data generation, and high-quality, biological-problem-focussed bioinformatics analyses to researchers in biomedical science throughout our 'catchment' area.

Please contact us at genepool@ed.ac.uk to discuss this exciting development, and to see how we can work with you to deliver advanced genomics analyses for your research programmes.


New Illumina GAIIx sequencer purchased [01 July 2009]

The pressure of user requests has prompted the GenePool to bring forward planned investment in next generation sequencing technology. In some ways, the GenePool is a victim of its own success: delivery of data to users has simply encouraged them and others to apply to us for next-generation sequence delivery, in particular high-volume short read data. This has resulted in a 'queue for data' which is very unsatisfying for us in the GenePool, and for collaborators waiting for data.

Therefore, the GenePool has invested in a second Illumina sequencing instrument, the GA IIx. This new version of the Illumina GA series is specified to deliver 75 base paired end reads, and can generate therefore over 10 Gbase per instrument run (about 1 week). The instrument will be delivered and installed in July 2009, and will be delivering data by August.

This installation will both reduce the 'queue' and also allow the GenePool to offer new kinds of project based on the longer reads and increased read density of the GA IIx compared to our existing II instrument.

The GenePool is also now well placed to exploit the posted likely increases in throughput and read length for the Illumina GA series (up to 100 base paired end reads, and over 20 Gbase per instrument run) promised by Illumina for this year.

Please contact us at genepool-solexa@ed.ac.uk to discuss this development, and to see how we can work with you to deliver advanced genomics analyses for your research programmes.


Dr Karim Gharbi joins GenePool [01 July 2009]

Today, as part of the opening of the GenePool's MRC Hub project, Dr Karim Gharbi joined the facility as Scientific Manager. Karim joins the team of ten people in the GenePool dedicated to delivery of high quality data and analyses to our collaborators.

Karim was previously based at the University of Glasgow, where he worked on the genetics of immunity to parasites in fish, amongst other genomics-based projects. He brings to the GenePool a wealth of experience in academic genomics research, and will be the main point of contact for collaborators enquiring about the kinds of analyses possible at the GenePool.

Karim is the first of a number of appointments to the GenePool over the next few months as we ramp up our capacity to deliver high-volume genomics data to our user community.


GenePool data underpin paper in Genome Research [01 July 2009]

Published in Genome Research today is a paper from a collaboration between Prof. Peter Keightley's lab and the GenePool, investigating one of the fundamental variables in evolution: the genomic mutation rate. Evolution by natural selection acts on variation between individuals, and the ultimate source of that variation is mutation. So the mode and tempo of evolution sensitively depends on the rate at which new mutations arise.

Peter and the team investigated Drosophila melanogaster mutation accumulation lines that had been inbred for an average of 262 generations, and generated ~12-fold resequencing data for three genomes using Illumina technology. Mapping the reads to the reference D. melanogaster genome permitted the identification of over 70 mutations (across ~70 Mbase of the genome that had rad depths of over 5 in all three genomes sequenced), most of which were confirmed by Sanger sequencing. The answer: 3.5 x 10e-9 per base per generation.

The patterns of substitution identified also suggest that ~15% of mutations are deleterious, and that the base content (GC%) of D. melanogaster is not determined by mutation pressure alone.

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
Peter D. Keightley, Urmi Trivedi, Marian Thomson, Fiona Oliver, Sujai Kumar, and Mark L. Blaxter [GenePool authors in bold]
Genome Res. 2009;19 1195-1201

http://www.genome.org/cgi/doi/10.1101/gr.091231.109

Contact Peter Keightley at Keightley.genomeres2009@gmail.com


 


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This is version 2.2 of the GenePool website (July 2009).