Centre for Comparative Genomics
The CENTRE FOR COMPARATIVE GENOMICS Sequencing/genotyping service
The Centre owes its origins to an equipment grant from NERC in 2005. The purpose of the CCG was to establish a high-throughput sequencing and genotyping facility for a North London consortium consisting of UCL Biology, The Institute of Zoology (Regent's Park), and the Queen Mary School of Biological and Chemical Sciences (Mile End). After some refurbishment problems and negotiations with Applied Biosystems, the Centre first opened for business on a somewhat memorable day here in London -- for other reasons -- 7 July 2005.
High-throughput sequencing and genotyping is transforming our understanding of the origins and maintenance of biodiversity. In typical molecular population/evolution studies, a handful of genes are sequenced, or a small panel of loci are genotyped. Far greater power is beginning to emerge from studies using thousands of genotypes or sequences from large samples across the global distributions of species.
Major projects proposed for the Centre for Comparative Genomics (CCG) include genomic analyses of natural selection, studies of "partitioning" or population admixture (both between wild species, and also among human populations), evolutionary developmental genetics, and large-scale phylogeny and phylogeography. Comparative genomics requires high-throughput "resequencing" and genotyping (particularly microsatellites and SNPs) across the biodiversity spectrum from populations within species such as humans, insects or other animals, plants or microbes, and samples from related species in studies of speciation, phylogeography and molecular evolution.
Comparative genomics is still data-limited, but appropriate data analysis is as important as the data. A major strength of the Centre for Comparative Genomics is our internationally recognized molecular phylogenetics statistical group (led by Prof. Ziheng Yang FRS), as well as the Centre for Human Genetics and associated HUGO gene nomenclature bionformatics group (led by Prof. Sue Povey). UCL Biology is a co-founding member of UCL's CoMPLEX, an interdisciplinary mathematics, physics and bioinformatics research and postgraduate centre. The Department also houses the Centre for Research on Ageing (particularly Prof. Linda Partridge FRS and Dr. David Gems). There are also many other active UCL Biology research groups working on evolutionary genomics or population genetics problems in humans, animals, microbes or plants (see the list of Personnel). This combination of world-class multidisciplinary expertise makes the CCG the optimal environment for post-genomic research.
At Queen Mary's School of Biological and Chemical Sciences, there is world-class expertise in coalescence theory and population structure, including applications in genetic demography, phylogeography, speciation, conservation, forensic, and plant science (Prof. Richard Nichols and Dr. Andrew Leitch). At the Institute of Zoology (Zoological Society of London), the Genetic Variation, Fitness and Adaptability research group (headed by Dr. Bill Jordan) are well known for their genetics-based research on molecular ecology and conservation problems. CCG members belong to the regional, multi-institution Centre of Ecology and Evolution, including The Natural History Museum, the Institute of Zoology, Queen Mary, among members from many other London area institutions.
The Centre for Comparative Genomics currently houses a sequencing/genotyping facility based on an ABI 96-capillary 3730xl DNA Analyzer. This facility is manned by technical staff who maintain and run the equipment and is overseen by an advisory team. The ABI machine uses the latest technology to provide low cost per unit run as well as flexibility for genotyping or sequencing. Several 3100 machines are also available to members of the consortium for lower-throughput work. The facility is housed in The Galton Laboratory, a branch of UCL Biology housed in Wolfson House, NW1 2HE.
SERVICES AT THE CENTRE FOR COMPARATIVE GENOMICS
CCG offers high throughput sequencing and genotyping services
DNA Analyzer facility. The idea is to provide an extremely
system with low labour costs. Therefore, we normally accept
only. Consortium members currently benefit from a service that
only the cost of consumables, due to support from NERC (these
may rise when the grant lapses in 2008). Feel free to look at
structure online. Non-members or scientists who have an
be included in the CCG consortium should feel free to discuss
options, specialized needs, and our charging structure (see below) with Mari-Wyn
Burley or Fraser
Simpson, who manage the
UCL Research Department of Genetics, Evolution and Environment Darwin Building, Gower Street, London, WC1E 6BT Tel: (+44) 020 7679 2236 Fax: (+44) 020 7679 7193
UCL Research Department of Genetics, Evolution and Environment Darwin Building, Gower Street, London, WC1E 6BT
Tel: Fax: (+44) 020 7679 7193
Kevin Fowler, UCL, GEE
David Gems, UCL, GEE
Duncan Greig, UCL, GEE
Linda Partridge DBE, FRS UCL, GEE
Andrew Pomiankowski, UCL, GEE
Max Reuter, UCL, GEE
Joanne Santini, UCL, GEE
Hazel Smith, UCL, GEE
Max Telford, UCL, GEE
Ziheng Yang, FRS UCL, GEE
Bill Jordan, Institute of Zoology
Mari-Wyn Burley, UCL GEE
Simpson, UCL GEE
CHARGES FOR GENOTYPING AND SEQUENCING
NOTE: All prices are subject to change without notice.
The idea of the CCG is to encourage higher throughput at knockdown prices. All prices are therefore per 96-well plate. If you want to do smaller jobs, you must pay the whole plate charge (which could still be advantageous for a ½ plate, say).
(For smaller jobs, you may want to investigate other services, such as UCL Pharmacology's service - contact Stuart Martin at firstname.lastname@example.org)
a) Machine-ready. i.e. sequencing reaction already done and cleaned up
Consortium members: £40 per 96 wells (approx. £0.40/sequence)
Outside consortium: £120 per 96 wells (approx. £1.20/sequence)
b) Sequencing run with sequencing reaction using BigDyev3.1
Consortium members: £80 per 96 wells (approx. £0.80/sequence)
Outside consortium: £220 per 96 wells (approx. £2.20/sequence)
NB If you want to do your own sequencing reactions (which is more economical!), but don’t know how or don’t want to buy lots of Big Dye, we can advise. Call Mari-Wyn on 07904 959771
2. Genotyping (includes microsatellites/STRs,AFLP, SNPlex,
Consortium members: £60 per 96 wells (approx. £0.60/well)
Outside consortium: £140 per 96 wells (approx. £1.40/well)
Page last modified on 19 apr 11 17:00