AT A GLANCE Graduated in 1987 from Cardiff University, in Cardiff, Wales, UK, with a degree in biochemistry. Became technical support manager under Martin Evans and Peter Kille for the Cardiff University RNA Expression Center in April 2000. Interests include playing rugby, hillwalking, and beer connoisseurship.
QWhat role do microarrays play in research at Cardiff?
AMicroarrays are being used in the widest possible bioscience context, including transcript profiling of connective tissue diseases, neural differentiation, eco-toxicology and microbial diversity, amongst others.
We have spotted down subtractive cDNA clones generated from rainbow trout fry in experiments to investigate the impact of cadmium on rainbow trout development. We have also arrayed oligonucleotides (~17mers) in order to profile microbial populations. However, currently our main arrays are made from the NIA (National Institute on Aging) mouse 15K clone set, and are used for neural differentiation, as well as research into breast cancer, arthritis, Alzhiemerís disease and Huntingtonís disease.
QWhat types of microarrays do you use and in what combination?
AIn Cardiff we have access to a shared Affymetrix system based at the University of Wales College of Medicine, whilst internally we exploit solid pin robotics to generate oligo and cDNA spotted arrays. We find the latter has the advantage of giving us the ability to use and adapt our large clone libraries to specific projects. Prefabricated macro- and microarrays are also widely exploited by research projects within the school.
QHave you developed any special protocols for optimization of array performance?
AUsing the GeneTAC LSIV from Genomic Solutions enables us to use an agarose gel, locally called the ìJohn gelî after the PhD student who came up with the idea, to monitor incorporation of dyes in our targets before hybridization. The four lasers that we have available for scanning allow hybridization of other dyes, enabling us to monitor the quality of spotting and the concentration of DNA spotted.
QHow many spots have you been able to put down on one array?
ACurrently we can spot 6,912 elements onto a single slide, and we are about to start trying out the RA-1 from Genomic Solutions, which will give us a capacity of just over 20,000 per slide. We have been working on the philosophy that it is more important to get clean data first, then as your techniques improve, you can move up to higher densities and achieve the same results.
QWhat kind of arrayer do you use to make your own arrays?
AWe have a Flexys workstation from Genomic Solutions, which can spot up to 7,000 elements per array. To ensure generation of reproducible hybridization we also employ the [Genomic Solutions] GeneTAC Hyb Station.
QWhat methods do you use to analyze microarray data?
APrimary data acquisition is performed using either commercially available software such as GeneTAC Integrator or public domain software such as Scanalyze. Binary analysis is performed using Integrator or Spotfire, whilst for clustering we employ J-express from the European Bioinformatics Institute (EBI).
QWhat is the biggest challenge you face in working with microarrays?
AEnsuring that a diverse spectrum of users can generate quality data that is reproducible.
QHow do you tackle these challenges?
ABy running array courses and indoctrinating good practice habits into researchers.
QWhat bits of advice would you give to a colleague who is setting up and running a core microarray facility?
ADonít try to do a 30,000-element array immediately, and donít expect everything to work at first.
QIf you could make out a wish list for microarray technology advances or improvements over the next couple of years, what do you most want or need?
AMy wish list would include dyes with distinct and sharp absorbance and emission peaks to minimize crossover talk when using four lasers, and internationally available standard calibrators to facilitate comparative data analysis throughout the community.