Affymetrix Microarray Laboratory

The Department of Molecular Medicine and Haematology has been involved in Leukaemia and Lymphoma diagnosis and research for more than twenty years. Current services include immunophenotyping, molecular cytogenetics (FISH, M-FISH) and PCR (including QT-PCR) for the surrounding academic hospitals. The Department recently established the Affymetrix GS3000 platform for gene expression profiling (GEP) and genotyping. The Research Diagnostics Group (headed by Dr Lesley Scott) and the Cytogenetics Group (headed by Dr Pascale Willem) currently make use of the Affymetrix Platform for research purposes: (1) to investigate the pathology of leukaemias and lymphomas and to develop a single-platform diagnostic assay for leukaemia classification which is intended to complement existing diagnostic profiles and address skills shortage for current services; (2) to assess copy-number alterations in a number of cancers with high prevalence in South Africa, including oesophageal and colorectal cancers. The Cytogenetics group is also soon to begin complementing existing routine cytogenetic diagnostics with Affymetrix genotyping arrays.

This Department has engaged with members from the Wits School of Information and Electrical Engineering in an effort to apply engineering principles and artificial intelligence algorithms towards the development of a GEP classifier. Clinical information is combined with GEP to determine the accuracy of classification while also exploring microarray data to determine the functionality and mechanisms of disease pathogenesis. This group holds fortnightly focus meetings which discuss technicalities of microarray technology and also recently hosted a workshop on genome-wide association studies. The workshop brought together experts in human genetics to discuss the prospect of performing genome-wide association studies in a Southern African setting.

The Facility

The dual Laser capacity Affymetrix Research Microarray Platform is a complete work-station for Affymetrix GeneChips. It is suitable for gene expression profiling, exon array analysis, SNP discovery, tiling arrays etc. Also part of the microarray facility is an Agilent Bioanalyzer used for nucleic acid analysis.

Contact information

Lesley Scott, Tel: +27 11 489 8565