ACGT partner institution – the University of Pretoria (UP) hosted an Illumina Sequencing and Genotyping Workshop on 20 August 2009 at UP to showcase the powerful application of next-generation DNA sequencing technology and introduce the newly installed SNP (single nucleotide polymorphism) Genotyping platform at UP.
The Workshop was hosted by the Department of Genetics at UP in collaboration with Whitehead Scientific (Pty) Ltd, with ACGT contributor – Prof Zander Myburg of UP – heading up the organisation of the event. The workshop programme featured speakers from UP, University of the Western Cape (UWC) and Whitehead Scientific and focused on the practical application of Whole Genome Sequencing on the Illumina Genome Analyser at the UWC and Multiplex Genotyping Analysis on the Illumina BeadXpress Platform at UP.
UWC took the opportunity to share its experience of using its Genome Analyser by way of a talk by Prof Jasper Rees, while Ryan Vogt of Whitehead Scientific explained the practical genotyping and sequencing applications of both the Genome Analyser and the BeadXpress, respectively. Prof Myburgh then completed proceedings with a discussion around considerations for planning genotyping projects using the BeadXpress Platform.
The Illumina BeadXpress Platform at the University of Pretoria was acquired as part of the ACGT’s participation in the Generation Challenge Programme, and has recently been installed for use, the initial application focusing on the screening of cassava varieties for SNP markers linked to drought tolerance.
The BeadXpress system from Illumina offers a cost effective platform for assaying 1 to 384 SNPs in essentially any number of individuals. Its main advantages include lower costs per SNP than on the Bead Array Reader, easier assay of variable numbers of samples, and the ability to create ASPE assays for small numbers of SNPs.