Friday, 15:00

Seminar over. By all accounts it was a very productive and stimulating meeting. Scientists at the MRC Gambia are very keen to exploit genome-level studies through next-generation sequencing in their work, with organisms as diverse as Chlamydia (which causes blindness through the devastating disease trachoma), Mycobacterium africanum, malaria and HIV-2. The metagenome concept, presented this morning by Karen Nelson and George Weinstock is a rich potential source of new knowledge, and the MRC has an incredible resource of patient and epidemiological information, samples and isolates to exploit. These can prime many very exciting metagenome level projects. An existing project is the nasopharyngeal metagenome in babies, through using a combination of Sanger and 454 sequencing by Brenda Kwambana, in collaboration with the University of Leicester. There is excitement about extending the study further.

We had a long discussion about how genomics and next-generation sequencing could be applied to Africa. There was agreement that the MRC Gambia are well posed to ask very interesting questions, borne out of their wide-ranging and long-term surveillance projects taking place across the country and neighbouring countries. This is the area of greatest strength and confidence. The group felt that the MRC Gambia was not quite ready to get its own next-generation sequencer, but that was a clear aspiration for the future. Important right now is to build up strengths in the bioinformatics and subsequent data analysis. Some Linux servers hosted locally would help immensely because their Internet (provided by satellite link) is too slow to use services like NCBI BLAST satisfactorily. I have offered to help them with this as much as we can – perhaps donating a few older servers and sending DVD-ROMs of the latest software and databases to get under way. Karen, George and myself have offered to host Gambians interested in bioinformatics to gain more skills.

Will write more on the contents of the seminars soon and upload pictures from today. However, now it is time to relax a little bit, perhaps have a swim – it is very hot today and the skies are clear for the first time. Karen Nelson and her husband have decided to visit Dakar in Senegal, an 800km drive, in a ‘bush taxi’ which is pretty much the bravest (or stupidest) thing I’ve ever heard. They plan to visit Goree Island, the departure point of the slave ships to the USA and an important ‘roots’ tour destination.

Update 13/12/08

A few pictures of the conference:

Dinner at Ngala Lodge before the conference started
Dinner at Ngala Lodge before the conference started
George Weinstock giving a talk on the international human microbiome
George Weinstock giving a talk on the international human microbiome
Martin Antonio in full flow
Martin Antonio in full flow
The conference group photo
The conference group photo, in the centre bottom row is Hilton Whittle, virology legend and head of MRC Gambia

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