The BioPAD Microarray Platform Project

The BioPAD funded Microarray Platform Project was started in June 2005, with the aim of increasing capacity in microarray science in the BioPAD region. Led by Professor Dave Berger, its activities are centered at the ACGT microarray facility at the University of Pretoria, with additional input coming from inqaba biotec, and the University of the Witwatersrand.

In its first two years of operation, the project has achieved many of its aims, by providing a unique and much needed resource to researchers from all over South Africa and by facilitating the training of several young scientists in all aspects of microarray techniques including experimental design, technical lab skills and data analysis.

Activities at the project are divided into three major work packages, namely standard operating procedures (SOPs), training, and support of external users:

Standard operating procedures covering all aspects of microarray experiments have been developed and tested in the labs of the project members. These SOPs are regularly updated and are freely available, along with plenty of other useful information on the facilities website.

In-house training at the project has focused on an experiment comparing the oligonucleotide and cDNA microarray platforms. Individuals within the platform have contributed their particular skills to the group, resulting in a core of well-trained scientists capable of performing all aspects of microarray experiments and using these skills to provide assistance to external users. Trainees from inqaba biotec have provided sequencing and oligonucleotide synthesis services for the project, and have also learned how to complete microarray experiments on their own.

One of the biggest achievements in the first phase of the project has been the hosting of two major microarray workshops, where scientists from several institutes and South African universities converged on Pretoria for a full week of lab work and lectures. In all, over 40 attendees have been given the experience of completing a simple microarray experiment from RNA extraction to image analysis, and enjoyed lectures on experimental design, data analysis and the lab experiences of visiting experts.

A promising outcome of the project is that several of the course participants have since gone on to successfully perform microarray experiments in their own research, many of them making use of the facilities at the ACGT lab, and producing results that have been incorporated in theses, published articles in peer-reviewed journals, and presentations at national and international conferences.

Development has not been restricted to Pretoria, as an exciting aspect of the project has been the involvement of researchers from Wits. A new node of expertise is developing in Johannesburg, and a microarray users group that meets to discuss technical and experimental issues has been formed to support users there.

With the solid foundations developed during the last two years, the BioPAD supported microarray platform project at the ACGT microarray facility is ready to maintain its track record of excellence and provide increasing in depth support to greater than ever numbers of researchers in the years ahead.

By Luke Solomon, Microarray Scientist-in-Training, University of Pretoria